@sjcrh/proteinpaint-client 2.170.13 → 2.170.15

package/dist/chunk-HJGGXQZ5.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/d3-regression/dist/d3-regression.js", "../plots/scatter/viewmodel/scatterLasso.ts", "../plots/scatter/model/scatterModel.ts", "../plots/scatter/viewmodel/scatterLegendInteractivity.ts", "../plots/scatter/view/scatterView.ts", "../plots/scatter/viewmodel/scatterLegend.ts", "../plots/scatter/viewmodel/scatterTooltip.ts", "../plots/scatter/viewmodel/scatterZoom.ts", "../plots/scatter/viewmodel/scatterViewModelBase.ts", "../plots/scatter/viewmodel/scatterViewModel.ts", "../plots/scatter/viewmodel/scatterViewModel2DLarge.ts", "../plots/singleCellPlot.js"],
-  "sourcesContent": ["// https://github.com/HarryStevens/d3-regression#readme Version 1.3.10. Copyright 2022 Harry Stevens.\n(function (global, factory) {\n  typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports) :\n  typeof define === 'function' && define.amd ? define(['exports'], factory) :\n  (global = global || self, factory(global.d3 = {}));\n}(this, (function (exports) { 'use strict';\n\n  function _slicedToArray(arr, i) {\n    return _arrayWithHoles(arr) || _iterableToArrayLimit(arr, i) || _nonIterableRest();\n  }\n\n  function _arrayWithHoles(arr) {\n    if (Array.isArray(arr)) return arr;\n  }\n\n  function _iterableToArrayLimit(arr, i) {\n    var _arr = [];\n    var _n = true;\n    var _d = false;\n    var _e = undefined;\n\n    try {\n      for (var _i = arr[Symbol.iterator](), _s; !(_n = (_s = _i.next()).done); _n = true) {\n        _arr.push(_s.value);\n\n        if (i && _arr.length === i) break;\n      }\n    } catch (err) {\n      _d = true;\n      _e = err;\n    } finally {\n      try {\n        if (!_n && _i[\"return\"] != null) _i[\"return\"]();\n      } finally {\n        if (_d) throw _e;\n      }\n    }\n\n    return _arr;\n  }\n\n  function _nonIterableRest() {\n    throw new TypeError(\"Invalid attempt to destructure non-iterable instance\");\n  }\n\n  // Adapted from vega-statistics by Jeffrey Heer\n  // License: https://github.com/vega/vega/blob/f058b099decad9db78301405dd0d2e9d8ba3d51a/LICENSE\n  // Source: https://github.com/vega/vega/blob/f058b099decad9db78301405dd0d2e9d8ba3d51a/packages/vega-statistics/src/regression/points.js\n  function points(data, x, y, sort) {\n    data = data.filter(function (d, i) {\n      var u = x(d, i),\n          v = y(d, i);\n      return u != null && isFinite(u) && v != null && isFinite(v);\n    });\n\n    if (sort) {\n      data.sort(function (a, b) {\n        return x(a) - x(b);\n      });\n    }\n\n    var n = data.length,\n        X = new Float64Array(n),\n        Y = new Float64Array(n); // extract values, calculate means\n\n    var ux = 0,\n        uy = 0,\n        xv,\n        yv,\n        d;\n\n    for (var i = 0; i < n;) {\n      d = data[i];\n      X[i] = xv = +x(d, i, data);\n      Y[i] = yv = +y(d, i, data);\n      ++i;\n      ux += (xv - ux) / i;\n      uy += (yv - uy) / i;\n    } // mean center the data\n\n\n    for (var _i = 0; _i < n; ++_i) {\n      X[_i] -= ux;\n      Y[_i] -= uy;\n    }\n\n    return [X, Y, ux, uy];\n  }\n  function visitPoints(data, x, y, cb) {\n    var iterations = 0;\n\n    for (var i = 0, n = data.length; i < n; i++) {\n      var d = data[i],\n          dx = +x(d, i, data),\n          dy = +y(d, i, data);\n\n      if (dx != null && isFinite(dx) && dy != null && isFinite(dy)) {\n        cb(dx, dy, iterations++);\n      }\n    }\n  }\n\n  // return the coefficient of determination, or R squared.\n\n  function determination(data, x, y, uY, predict) {\n    var SSE = 0,\n        SST = 0;\n    visitPoints(data, x, y, function (dx, dy) {\n      var sse = dy - predict(dx),\n          sst = dy - uY;\n      SSE += sse * sse;\n      SST += sst * sst;\n    });\n    return 1 - SSE / SST;\n  }\n\n  // Returns the angle of a line in degrees.\n  function angle(line) {\n    return Math.atan2(line[1][1] - line[0][1], line[1][0] - line[0][0]) * 180 / Math.PI;\n  } // Returns the midpoint of a line.\n\n  function midpoint(line) {\n    return [(line[0][0] + line[1][0]) / 2, (line[0][1] + line[1][1]) / 2];\n  }\n\n  // returns a smooth line.\n\n  function interpose(xmin, xmax, predict) {\n    var l = Math.log(xmax - xmin) * Math.LOG10E + 1 | 0;\n    var precision = 1 * Math.pow(10, -l / 2 - 1),\n        maxIter = 1e4;\n    var points = [px(xmin), px(xmax)],\n        iter = 0;\n\n    while (find(points) && iter < maxIter) {\n    }\n\n    return points;\n\n    function px(x) {\n      return [x, predict(x)];\n    }\n\n    function find(points) {\n      iter++;\n      var n = points.length;\n      var found = false;\n\n      for (var i = 0; i < n - 1; i++) {\n        var p0 = points[i],\n            p1 = points[i + 1],\n            m = midpoint([p0, p1]),\n            mp = px(m[0]),\n            a0 = angle([p0, m]),\n            a1 = angle([p0, mp]),\n            a = Math.abs(a0 - a1);\n\n        if (a > precision) {\n          points.splice(i + 1, 0, mp);\n          found = true;\n        }\n      }\n\n      return found;\n    }\n  }\n\n  // Ordinary Least Squares from vega-statistics by Jeffrey Heer\n  // License: https://github.com/vega/vega/blob/f058b099decad9db78301405dd0d2e9d8ba3d51a/LICENSE\n  // Source: https://github.com/vega/vega/blob/f058b099decad9db78301405dd0d2e9d8ba3d51a/packages/vega-statistics/src/regression/ols.js\n  function ols(uX, uY, uXY, uX2) {\n    var delta = uX2 - uX * uX,\n        slope = Math.abs(delta) < 1e-24 ? 0 : (uXY - uX * uY) / delta,\n        intercept = uY - slope * uX;\n    return [intercept, slope];\n  }\n\n  function exponential () {\n    var x = function x(d) {\n      return d[0];\n    },\n        y = function y(d) {\n      return d[1];\n    },\n        domain;\n\n    function exponential(data) {\n      var n = 0,\n          Y = 0,\n          YL = 0,\n          XY = 0,\n          XYL = 0,\n          X2Y = 0,\n          xmin = domain ? +domain[0] : Infinity,\n          xmax = domain ? +domain[1] : -Infinity;\n      visitPoints(data, x, y, function (dx, dy) {\n        var ly = Math.log(dy),\n            xy = dx * dy;\n        ++n;\n        Y += (dy - Y) / n;\n        XY += (xy - XY) / n;\n        X2Y += (dx * xy - X2Y) / n;\n        YL += (dy * ly - YL) / n;\n        XYL += (xy * ly - XYL) / n;\n\n        if (!domain) {\n          if (dx < xmin) xmin = dx;\n          if (dx > xmax) xmax = dx;\n        }\n      });\n\n      var _ols = ols(XY / Y, YL / Y, XYL / Y, X2Y / Y),\n          _ols2 = _slicedToArray(_ols, 2),\n          a = _ols2[0],\n          b = _ols2[1];\n\n      a = Math.exp(a);\n\n      var fn = function fn(x) {\n        return a * Math.exp(b * x);\n      },\n          out = interpose(xmin, xmax, fn);\n\n      out.a = a;\n      out.b = b;\n      out.predict = fn;\n      out.rSquared = determination(data, x, y, Y, fn);\n      return out;\n    }\n\n    exponential.domain = function (arr) {\n      return arguments.length ? (domain = arr, exponential) : domain;\n    };\n\n    exponential.x = function (fn) {\n      return arguments.length ? (x = fn, exponential) : x;\n    };\n\n    exponential.y = function (fn) {\n      return arguments.length ? (y = fn, exponential) : y;\n    };\n\n    return exponential;\n  }\n\n  function linear () {\n    var x = function x(d) {\n      return d[0];\n    },\n        y = function y(d) {\n      return d[1];\n    },\n        domain;\n\n    function linear(data) {\n      var n = 0,\n          X = 0,\n          // sum of x\n      Y = 0,\n          // sum of y\n      XY = 0,\n          // sum of x * y\n      X2 = 0,\n          // sum of x * x\n      xmin = domain ? +domain[0] : Infinity,\n          xmax = domain ? +domain[1] : -Infinity;\n      visitPoints(data, x, y, function (dx, dy) {\n        ++n;\n        X += (dx - X) / n;\n        Y += (dy - Y) / n;\n        XY += (dx * dy - XY) / n;\n        X2 += (dx * dx - X2) / n;\n\n        if (!domain) {\n          if (dx < xmin) xmin = dx;\n          if (dx > xmax) xmax = dx;\n        }\n      });\n\n      var _ols = ols(X, Y, XY, X2),\n          _ols2 = _slicedToArray(_ols, 2),\n          intercept = _ols2[0],\n          slope = _ols2[1],\n          fn = function fn(x) {\n        return slope * x + intercept;\n      },\n          out = [[xmin, fn(xmin)], [xmax, fn(xmax)]];\n\n      out.a = slope;\n      out.b = intercept;\n      out.predict = fn;\n      out.rSquared = determination(data, x, y, Y, fn);\n      return out;\n    }\n\n    linear.domain = function (arr) {\n      return arguments.length ? (domain = arr, linear) : domain;\n    };\n\n    linear.x = function (fn) {\n      return arguments.length ? (x = fn, linear) : x;\n    };\n\n    linear.y = function (fn) {\n      return arguments.length ? (y = fn, linear) : y;\n    };\n\n    return linear;\n  }\n\n  // Returns the medium value of an array of numbers.\n  function median(arr) {\n    arr.sort(function (a, b) {\n      return a - b;\n    });\n    var i = arr.length / 2;\n    return i % 1 === 0 ? (arr[i - 1] + arr[i]) / 2 : arr[Math.floor(i)];\n  }\n\n  var maxiters = 2,\n      epsilon = 1e-12;\n  function loess () {\n    var x = function x(d) {\n      return d[0];\n    },\n        y = function y(d) {\n      return d[1];\n    },\n        bandwidth = .3;\n\n    function loess(data) {\n      var _points = points(data, x, y, true),\n          _points2 = _slicedToArray(_points, 4),\n          xv = _points2[0],\n          yv = _points2[1],\n          ux = _points2[2],\n          uy = _points2[3],\n          n = xv.length,\n          bw = Math.max(2, ~~(bandwidth * n)),\n          yhat = new Float64Array(n),\n          residuals = new Float64Array(n),\n          robustWeights = new Float64Array(n).fill(1);\n\n      for (var iter = -1; ++iter <= maxiters;) {\n        var interval = [0, bw - 1];\n\n        for (var i = 0; i < n; ++i) {\n          var dx = xv[i],\n              i0 = interval[0],\n              i1 = interval[1],\n              edge = dx - xv[i0] > xv[i1] - dx ? i0 : i1;\n          var W = 0,\n              X = 0,\n              Y = 0,\n              XY = 0,\n              X2 = 0,\n              denom = 1 / Math.abs(xv[edge] - dx || 1); // Avoid singularity\n\n          for (var k = i0; k <= i1; ++k) {\n            var xk = xv[k],\n                yk = yv[k],\n                w = tricube(Math.abs(dx - xk) * denom) * robustWeights[k],\n                xkw = xk * w;\n            W += w;\n            X += xkw;\n            Y += yk * w;\n            XY += yk * xkw;\n            X2 += xk * xkw;\n          } // Linear regression fit\n\n\n          var _ols = ols(X / W, Y / W, XY / W, X2 / W),\n              _ols2 = _slicedToArray(_ols, 2),\n              a = _ols2[0],\n              b = _ols2[1];\n\n          yhat[i] = a + b * dx;\n          residuals[i] = Math.abs(yv[i] - yhat[i]);\n          updateInterval(xv, i + 1, interval);\n        }\n\n        if (iter === maxiters) {\n          break;\n        }\n\n        var medianResidual = median(residuals);\n        if (Math.abs(medianResidual) < epsilon) break;\n\n        for (var _i = 0, arg, _w; _i < n; ++_i) {\n          arg = residuals[_i] / (6 * medianResidual); // Default to epsilon (rather than zero) for large deviations\n          // Keeping weights tiny but non-zero prevents singularites\n\n          robustWeights[_i] = arg >= 1 ? epsilon : (_w = 1 - arg * arg) * _w;\n        }\n      }\n\n      return output(xv, yhat, ux, uy);\n    }\n\n    loess.bandwidth = function (bw) {\n      return arguments.length ? (bandwidth = bw, loess) : bandwidth;\n    };\n\n    loess.x = function (fn) {\n      return arguments.length ? (x = fn, loess) : x;\n    };\n\n    loess.y = function (fn) {\n      return arguments.length ? (y = fn, loess) : y;\n    };\n\n    return loess;\n  } // Weighting kernel for local regression\n\n  function tricube(x) {\n    return (x = 1 - x * x * x) * x * x;\n  } // Advance sliding window interval of nearest neighbors\n\n\n  function updateInterval(xv, i, interval) {\n    var val = xv[i],\n        left = interval[0],\n        right = interval[1] + 1;\n    if (right >= xv.length) return; // Step right if distance to new right edge is <= distance to old left edge\n    // Step when distance is equal to ensure movement over duplicate x values\n\n    while (i > left && xv[right] - val <= val - xv[left]) {\n      interval[0] = ++left;\n      interval[1] = right;\n      ++right;\n    }\n  } // Generate smoothed output points\n  // Average points with repeated x values\n\n\n  function output(xv, yhat, ux, uy) {\n    var n = xv.length,\n        out = [];\n    var i = 0,\n        cnt = 0,\n        prev = [],\n        v;\n\n    for (; i < n; ++i) {\n      v = xv[i] + ux;\n\n      if (prev[0] === v) {\n        // Average output values via online update\n        prev[1] += (yhat[i] - prev[1]) / ++cnt;\n      } else {\n        // Add new output point\n        cnt = 0;\n        prev[1] += uy;\n        prev = [v, yhat[i]];\n        out.push(prev);\n      }\n    }\n\n    prev[1] += uy;\n    return out;\n  }\n\n  function logarithmic () {\n    var x = function x(d) {\n      return d[0];\n    },\n        y = function y(d) {\n      return d[1];\n    },\n        base = Math.E,\n        domain;\n\n    function logarithmic(data) {\n      var n = 0,\n          X = 0,\n          Y = 0,\n          XY = 0,\n          X2 = 0,\n          xmin = domain ? +domain[0] : Infinity,\n          xmax = domain ? +domain[1] : -Infinity,\n          lb = Math.log(base);\n      visitPoints(data, x, y, function (dx, dy) {\n        var lx = Math.log(dx) / lb;\n        ++n;\n        X += (lx - X) / n;\n        Y += (dy - Y) / n;\n        XY += (lx * dy - XY) / n;\n        X2 += (lx * lx - X2) / n;\n\n        if (!domain) {\n          if (dx < xmin) xmin = dx;\n          if (dx > xmax) xmax = dx;\n        }\n      });\n\n      var _ols = ols(X, Y, XY, X2),\n          _ols2 = _slicedToArray(_ols, 2),\n          intercept = _ols2[0],\n          slope = _ols2[1],\n          fn = function fn(x) {\n        return slope * Math.log(x) / lb + intercept;\n      },\n          out = interpose(xmin, xmax, fn);\n\n      out.a = slope;\n      out.b = intercept;\n      out.predict = fn;\n      out.rSquared = determination(data, x, y, Y, fn);\n      return out;\n    }\n\n    logarithmic.domain = function (arr) {\n      return arguments.length ? (domain = arr, logarithmic) : domain;\n    };\n\n    logarithmic.x = function (fn) {\n      return arguments.length ? (x = fn, logarithmic) : x;\n    };\n\n    logarithmic.y = function (fn) {\n      return arguments.length ? (y = fn, logarithmic) : y;\n    };\n\n    logarithmic.base = function (n) {\n      return arguments.length ? (base = n, logarithmic) : base;\n    };\n\n    return logarithmic;\n  }\n\n  function quad () {\n    var x = function x(d) {\n      return d[0];\n    },\n        y = function y(d) {\n      return d[1];\n    },\n        domain;\n\n    function quadratic(data) {\n      var _points = points(data, x, y),\n          _points2 = _slicedToArray(_points, 4),\n          xv = _points2[0],\n          yv = _points2[1],\n          ux = _points2[2],\n          uy = _points2[3],\n          n = xv.length;\n\n      var X2 = 0,\n          X3 = 0,\n          X4 = 0,\n          XY = 0,\n          X2Y = 0,\n          i,\n          dx,\n          dy,\n          x2;\n\n      for (i = 0; i < n;) {\n        dx = xv[i];\n        dy = yv[i++];\n        x2 = dx * dx;\n        X2 += (x2 - X2) / i;\n        X3 += (x2 * dx - X3) / i;\n        X4 += (x2 * x2 - X4) / i;\n        XY += (dx * dy - XY) / i;\n        X2Y += (x2 * dy - X2Y) / i;\n      }\n\n      var Y = 0,\n          n0 = 0,\n          xmin = domain ? +domain[0] : Infinity,\n          xmax = domain ? +domain[1] : -Infinity;\n      visitPoints(data, x, y, function (dx, dy) {\n        n0++;\n        Y += (dy - Y) / n0;\n\n        if (!domain) {\n          if (dx < xmin) xmin = dx;\n          if (dx > xmax) xmax = dx;\n        }\n      });\n\n      var X2X2 = X4 - X2 * X2,\n          d = X2 * X2X2 - X3 * X3,\n          a = (X2Y * X2 - XY * X3) / d,\n          b = (XY * X2X2 - X2Y * X3) / d,\n          c = -a * X2,\n          fn = function fn(x) {\n        x = x - ux;\n        return a * x * x + b * x + c + uy;\n      };\n\n      var out = interpose(xmin, xmax, fn);\n      out.a = a;\n      out.b = b - 2 * a * ux;\n      out.c = c - b * ux + a * ux * ux + uy;\n      out.predict = fn;\n      out.rSquared = determination(data, x, y, Y, fn);\n      return out;\n    }\n\n    quadratic.domain = function (arr) {\n      return arguments.length ? (domain = arr, quadratic) : domain;\n    };\n\n    quadratic.x = function (fn) {\n      return arguments.length ? (x = fn, quadratic) : x;\n    };\n\n    quadratic.y = function (fn) {\n      return arguments.length ? (y = fn, quadratic) : y;\n    };\n\n    return quadratic;\n  }\n\n  // Source: https://github.com/Tom-Alexander/regression-js/blob/master/src/regression.js#L246\n  // License: https://github.com/Tom-Alexander/regression-js/blob/master/LICENSE\n  // ...with ideas from vega-statistics by Jeffrey Heer\n  // Source: https://github.com/vega/vega/blob/f21cb8792b4e0cbe2b1a3fd44b0f5db370dbaadb/packages/vega-statistics/src/regression/poly.js\n  // License: https://github.com/vega/vega/blob/f058b099decad9db78301405dd0d2e9d8ba3d51a/LICENSE\n\n  function polynomial () {\n    var x = function x(d) {\n      return d[0];\n    },\n        y = function y(d) {\n      return d[1];\n    },\n        order = 3,\n        domain;\n\n    function polynomial(data) {\n      // Use more efficient methods for lower orders\n      if (order === 1) {\n        var o = linear().x(x).y(y).domain(domain)(data);\n        o.coefficients = [o.b, o.a];\n        delete o.a;\n        delete o.b;\n        return o;\n      }\n\n      if (order === 2) {\n        var _o = quad().x(x).y(y).domain(domain)(data);\n\n        _o.coefficients = [_o.c, _o.b, _o.a];\n        delete _o.a;\n        delete _o.b;\n        delete _o.c;\n        return _o;\n      }\n\n      var _points = points(data, x, y),\n          _points2 = _slicedToArray(_points, 4),\n          xv = _points2[0],\n          yv = _points2[1],\n          ux = _points2[2],\n          uy = _points2[3],\n          n = xv.length,\n          lhs = [],\n          rhs = [],\n          k = order + 1;\n\n      var Y = 0,\n          n0 = 0,\n          xmin = domain ? +domain[0] : Infinity,\n          xmax = domain ? +domain[1] : -Infinity;\n      visitPoints(data, x, y, function (dx, dy) {\n        ++n0;\n        Y += (dy - Y) / n0;\n\n        if (!domain) {\n          if (dx < xmin) xmin = dx;\n          if (dx > xmax) xmax = dx;\n        }\n      });\n      var i, j, l, v, c;\n\n      for (i = 0; i < k; ++i) {\n        for (l = 0, v = 0; l < n; ++l) {\n          v += Math.pow(xv[l], i) * yv[l];\n        }\n\n        lhs.push(v);\n        c = new Float64Array(k);\n\n        for (j = 0; j < k; ++j) {\n          for (l = 0, v = 0; l < n; ++l) {\n            v += Math.pow(xv[l], i + j);\n          }\n\n          c[j] = v;\n        }\n\n        rhs.push(c);\n      }\n\n      rhs.push(lhs);\n\n      var coef = gaussianElimination(rhs),\n          fn = function fn(x) {\n        x -= ux;\n        var y = uy + coef[0] + coef[1] * x + coef[2] * x * x;\n\n        for (i = 3; i < k; ++i) {\n          y += coef[i] * Math.pow(x, i);\n        }\n\n        return y;\n      },\n          out = interpose(xmin, xmax, fn);\n\n      out.coefficients = uncenter(k, coef, -ux, uy);\n      out.predict = fn;\n      out.rSquared = determination(data, x, y, Y, fn);\n      return out;\n    }\n\n    polynomial.domain = function (arr) {\n      return arguments.length ? (domain = arr, polynomial) : domain;\n    };\n\n    polynomial.x = function (fn) {\n      return arguments.length ? (x = fn, polynomial) : x;\n    };\n\n    polynomial.y = function (fn) {\n      return arguments.length ? (y = fn, polynomial) : y;\n    };\n\n    polynomial.order = function (n) {\n      return arguments.length ? (order = n, polynomial) : order;\n    };\n\n    return polynomial;\n  }\n\n  function uncenter(k, a, x, y) {\n    var z = Array(k);\n    var i, j, v, c; // initialize to zero\n\n    for (i = 0; i < k; ++i) {\n      z[i] = 0;\n    } // polynomial expansion\n\n\n    for (i = k - 1; i >= 0; --i) {\n      v = a[i];\n      c = 1;\n      z[i] += v;\n\n      for (j = 1; j <= i; ++j) {\n        c *= (i + 1 - j) / j; // binomial coefficent\n\n        z[i - j] += v * Math.pow(x, j) * c;\n      }\n    } // bias term\n\n\n    z[0] += y;\n    return z;\n  } // Given an array for a two-dimensional matrix and the polynomial order,\n  // solve A * x = b using Gaussian elimination.\n\n\n  function gaussianElimination(matrix) {\n    var n = matrix.length - 1,\n        coef = [];\n    var i, j, k, r, t;\n\n    for (i = 0; i < n; ++i) {\n      r = i; // max row\n\n      for (j = i + 1; j < n; ++j) {\n        if (Math.abs(matrix[i][j]) > Math.abs(matrix[i][r])) {\n          r = j;\n        }\n      }\n\n      for (k = i; k < n + 1; ++k) {\n        t = matrix[k][i];\n        matrix[k][i] = matrix[k][r];\n        matrix[k][r] = t;\n      }\n\n      for (j = i + 1; j < n; ++j) {\n        for (k = n; k >= i; k--) {\n          matrix[k][j] -= matrix[k][i] * matrix[i][j] / matrix[i][i];\n        }\n      }\n    }\n\n    for (j = n - 1; j >= 0; --j) {\n      t = 0;\n\n      for (k = j + 1; k < n; ++k) {\n        t += matrix[k][j] * coef[k];\n      }\n\n      coef[j] = (matrix[n][j] - t) / matrix[j][j];\n    }\n\n    return coef;\n  }\n\n  function power () {\n    var x = function x(d) {\n      return d[0];\n    },\n        y = function y(d) {\n      return d[1];\n    },\n        domain;\n\n    function power(data) {\n      var n = 0,\n          X = 0,\n          Y = 0,\n          XY = 0,\n          X2 = 0,\n          YS = 0,\n          xmin = domain ? +domain[0] : Infinity,\n          xmax = domain ? +domain[1] : -Infinity;\n      visitPoints(data, x, y, function (dx, dy) {\n        var lx = Math.log(dx),\n            ly = Math.log(dy);\n        ++n;\n        X += (lx - X) / n;\n        Y += (ly - Y) / n;\n        XY += (lx * ly - XY) / n;\n        X2 += (lx * lx - X2) / n;\n        YS += (dy - YS) / n;\n\n        if (!domain) {\n          if (dx < xmin) xmin = dx;\n          if (dx > xmax) xmax = dx;\n        }\n      });\n\n      var _ols = ols(X, Y, XY, X2),\n          _ols2 = _slicedToArray(_ols, 2),\n          a = _ols2[0],\n          b = _ols2[1];\n\n      a = Math.exp(a);\n\n      var fn = function fn(x) {\n        return a * Math.pow(x, b);\n      },\n          out = interpose(xmin, xmax, fn);\n\n      out.a = a;\n      out.b = b;\n      out.predict = fn;\n      out.rSquared = determination(data, x, y, YS, fn);\n      return out;\n    }\n\n    power.domain = function (arr) {\n      return arguments.length ? (domain = arr, power) : domain;\n    };\n\n    power.x = function (fn) {\n      return arguments.length ? (x = fn, power) : x;\n    };\n\n    power.y = function (fn) {\n      return arguments.length ? (y = fn, power) : y;\n    };\n\n    return power;\n  }\n\n  exports.regressionExp = exponential;\n  exports.regressionLinear = linear;\n  exports.regressionLoess = loess;\n  exports.regressionLog = logarithmic;\n  exports.regressionPoly = polynomial;\n  exports.regressionPow = power;\n  exports.regressionQuad = quad;\n\n  Object.defineProperty(exports, '__esModule', { value: true });\n\n})));\n", "import { getSamplelstTW, getFilter, addNewGroup } from '../../../mass/groups.js'\nimport { getId } from '#mass/nav'\nimport { renderTable } from '../../../dom/table.ts'\nimport type { Scatter } from '../scatter.js'\nimport type { TableCell, TableColumn, TableRow } from '#dom'\nexport class ScatterLasso {\n\tscatter: Scatter\n\tmodel: any\n\tview: any\n\tinteractivity: any\n\tselectedItems!: any[]\n\n\tconstructor(scatter: Scatter) {\n\t\tthis.scatter = scatter\n\t\tthis.model = scatter.model\n\t\tthis.view = scatter.view\n\t\tthis.interactivity = scatter.interactivity\n\t}\n\n\tstart(chart) {\n\t\tif (this.scatter.config.lassoOn) {\n\t\t\tchart.lasso\n\t\t\t\t.items()\n\t\t\t\t.attr('transform', c => this.model.transform(chart, c, 1 / 2))\n\t\t\t\t.style('fill-opacity', c => (this.model.getOpacity(c) != 0 ? 0.5 : 0))\n\t\t\t\t.classed('not_possible', true)\n\t\t\t\t.classed('selected', false)\n\t\t}\n\t}\n\n\tdraw(chart) {\n\t\tif (this.scatter.config.lassoOn) {\n\t\t\t// Style the possible dots\n\n\t\t\tchart.lasso\n\t\t\t\t.possibleItems()\n\t\t\t\t.attr('transform', c => this.model.transform(chart, c, 1.2))\n\t\t\t\t.style('fill-opacity', c => this.model.getOpacity(c))\n\t\t\t\t.classed('not_possible', false)\n\t\t\t\t.classed('possible', true)\n\n\t\t\t//Style the not possible dot\n\t\t\tchart.lasso\n\t\t\t\t.notPossibleItems()\n\t\t\t\t.attr('transform', c => this.model.transform(chart, c, 1 / 2))\n\t\t\t\t.style('fill-opacity', c => (this.model.getOpacity(c) != 0 ? 0.5 : 0))\n\t\t\t\t.classed('not_possible', true)\n\t\t\t\t.classed('possible', false)\n\t\t}\n\t}\n\n\tend(dragEnd, chart) {\n\t\tif (this.scatter.config.lassoOn) {\n\t\t\t// Reset classes of all items (.possible and .not_possible are useful\n\t\t\t// only while drawing lasso. At end of drawing, only selectedItems()\n\t\t\t// should be used)\n\t\t\tchart.lasso.items().classed('not_possible', false).classed('possible', false)\n\t\t\t// Style the selected dots\n\t\t\tchart.lasso.selectedItems().attr('transform', c => this.model.transform(chart, c, 1.3))\n\t\t\tchart.lasso.items().style('fill-opacity', c => this.model.getOpacity(c))\n\t\t\tthis.selectedItems = []\n\t\t\tfor (const item of chart.lasso.selectedItems()) {\n\t\t\t\tconst data = item.__data__\n\t\t\t\tif ('sampleId' in data && !(data.hidden['category'] || data.hidden['shape'])) this.selectedItems.push(item)\n\t\t\t}\n\t\t\tchart.lasso.notSelectedItems().attr('transform', c => this.model.transform(chart, c))\n\t\t\tconst samples = this.selectedItems.map(item => item.__data__)\n\t\t\tthis.showLassoMenu(dragEnd.sourceEvent, samples)\n\t\t}\n\t}\n\n\tshowLassoMenu(event, samples) {\n\t\tthis.view.dom.tip.clear().hide()\n\t\tif (samples.length == 0) return\n\t\tthis.view.dom.tip.show(event.clientX, event.clientY)\n\n\t\tconst menuDiv = this.view.dom.tip.d.append('div')\n\t\tmenuDiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text(`List ${samples.length} samples`)\n\t\t\t.on('click', event => {\n\t\t\t\tthis.view.dom.tip.hide()\n\t\t\t\tthis.showTable(\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'Group ' + (this.scatter.config.groups.length + 1),\n\t\t\t\t\t\titems: samples\n\t\t\t\t\t},\n\t\t\t\t\tevent.clientX,\n\t\t\t\t\tevent.clientY,\n\t\t\t\t\ttrue\n\t\t\t\t)\n\t\t\t})\n\n\t\tif (this.scatter.app.getState().nav.header_mode === 'with_tabs')\n\t\t\tmenuDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text('Add to a group')\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tthis.createGroup(samples)\n\t\t\t\t\tthis.view.dom.tip.hide()\n\t\t\t\t})\n\n\t\tif (this.scatter.app.getState().nav.header_mode === 'with_tabs')\n\t\t\tmenuDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text('Add to a group and filter')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tconst tw = this.createGroup(samples)\n\t\t\t\t\tthis.interactivity.addToFilter(tw)\n\t\t\t\t\tthis.view.dom.tip.hide()\n\t\t\t\t})\n\n\t\tif ('sample' in samples[0])\n\t\t\tmenuDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text('Open sample view')\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tconst groupSamples: any[] = []\n\t\t\t\t\tfor (const sample of samples) groupSamples.push({ sampleId: sample.sampleId, sampleName: sample.sample })\n\t\t\t\t\tthis.scatter.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tid: getId(),\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tchartType: 'sampleView',\n\t\t\t\t\t\t\tsamples: groupSamples\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\tthis.view.dom.tip.hide()\n\t\t\t\t})\n\t}\n\n\tcreateGroup(samples) {\n\t\tconst group = {\n\t\t\tname: 'Group',\n\t\t\titems: samples\n\t\t}\n\t\tconst tw = getSamplelstTW([group])\n\t\tconst filter = getFilter(tw)\n\t\taddNewGroup(this.scatter.app, filter, this.scatter.state.groups)\n\t\treturn tw\n\t}\n\n\tlassoReset(chart) {\n\t\tconst mainG = chart.mainG\n\n\t\tif (this.scatter.config.lassoOn) {\n\t\t\tchart.lasso\n\t\t\t\t.items(mainG.select('.sjpcb-scatter-series').selectAll('path[name=\"serie\"]'))\n\t\t\t\t.targetArea(mainG)\n\t\t\t\t.on('start', () => this.start(chart))\n\t\t\t\t.on('draw', () => this.draw(chart))\n\t\t\t\t.on('end', event => this.end(event, chart))\n\t\t\t// this seems to clear stale lasso data as sometimes seen\n\t\t\t// when the global filter is changed between lassoing\n\t\t\t// uncertain explanation: the svg and mainG is potentially different between rerenders,\n\t\t\t// so the previous mainG.call(chart.lasso) inside toggle_lasso is on a removed mainG????\n\t\t\tmainG.on('.zoom', null)\n\t\t\tmainG.on('mousedown.drag', null)\n\t\t\tmainG.call(chart.lasso)\n\t\t} else {\n\t\t\tchart.mainG.on('.dragstart', null)\n\t\t\tchart.mainG.on('.drag', null)\n\t\t\tchart.mainG.on('.dragend', null)\n\t\t}\n\t}\n\n\tgetCategoryInfo(d, category) {\n\t\tif (!(category in d)) return ''\n\t\treturn d[category]\n\t}\n\n\tshowTable(group, x, y, addGroup) {\n\t\tconst rows: TableRow[] = []\n\t\tconst columns: TableColumn[] = []\n\t\tconst first = group.items[0]\n\t\tif ('sample' in first) columns.push(formatCell('Sample', 'label'))\n\t\tif (this.scatter.config.term) columns.push(formatCell(this.scatter.config.term.term.name, 'label'))\n\t\tif (this.scatter.config.term2) columns.push(formatCell(this.scatter.config.term2.term.name, 'label'))\n\t\tif (this.scatter.config.colorTW) columns.push(formatCell(this.scatter.config.colorTW.term.name, 'label'))\n\t\tif (this.scatter.config.shapeTW) columns.push(formatCell(this.scatter.config.shapeTW.term.name, 'label'))\n\t\tlet info = false\n\t\tconst hasSampleName = 'sample' in group.items[0]\n\n\t\tfor (const item of group.items) {\n\t\t\tconst row: TableCell[] = []\n\t\t\tif (hasSampleName) row.push(formatCell(item.sample))\n\t\t\tif (this.scatter.config.term) row.push(formatCell(this.getCategoryInfo(item, 'x')))\n\t\t\tif (this.scatter.config.term2) row.push(formatCell(this.getCategoryInfo(item, 'y')))\n\t\t\tif (this.scatter.config.colorTW) row.push(formatCell(this.getCategoryInfo(item, 'category')))\n\t\t\tif (this.scatter.config.shapeTW) row.push(formatCell(this.getCategoryInfo(item, 'shape')))\n\t\t\tif ('info' in item) {\n\t\t\t\tinfo = true\n\t\t\t\tconst values: any = []\n\t\t\t\tfor (const [k, v] of Object.entries(item.info)) values.push(`${k}: ${v}`)\n\t\t\t\trow.push(formatCell(values.join(', ')))\n\t\t\t}\n\t\t\trows.push(row)\n\t\t}\n\t\tif (info) columns.push(formatCell('Info', 'label'))\n\n\t\tthis.view.dom.tip.clear()\n\t\tconst div = this.view.dom.tip.d.append('div').style('padding', '5px')\n\t\tconst headerDiv = div.append('div').style('margin-top', '5px')\n\n\t\tconst groupDiv = headerDiv\n\t\t\t.append('div')\n\t\t\t.html('&nbsp;' + group.name)\n\t\t\t.style('font-size', '0.9rem')\n\t\t\t.on('click', () => {\n\t\t\t\tconst isEdit = groupDiv.select('input').empty()\n\t\t\t\tif (!isEdit) return\n\t\t\t\tgroupDiv.html('')\n\t\t\t\tconst input = groupDiv\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('value', group.name)\n\t\t\t\t\t.on('change', async () => {\n\t\t\t\t\t\tconst name = input.node().value\n\t\t\t\t\t\tif (name) group.name = name\n\t\t\t\t\t\telse input.node().value = group.name\n\t\t\t\t\t\tgroupDiv.html('&nbsp;' + group.name)\n\t\t\t\t\t})\n\t\t\t\tinput.node().focus()\n\t\t\t\tinput.node().select()\n\t\t\t})\n\t\tconst tableDiv = div.append('div')\n\t\tconst buttons: any[] = []\n\t\tif (addGroup) {\n\t\t\tconst addGroupCallback = {\n\t\t\t\ttext: 'Add to a group',\n\t\t\t\tcallback: indexes => {\n\t\t\t\t\tconst items: any[] = []\n\t\t\t\t\tfor (const i of indexes) items.push(this.selectedItems[i].__data__)\n\t\t\t\t\tconst group = {\n\t\t\t\t\t\tname: `Group ${this.scatter.config.groups.length + 1}`,\n\t\t\t\t\t\titems,\n\t\t\t\t\t\tindex: this.scatter.config.groups.length\n\t\t\t\t\t}\n\t\t\t\t\tconst filter = getFilter(getSamplelstTW([group]))\n\t\t\t\t\taddNewGroup(this.scatter.app, filter, this.scatter.state.groups)\n\t\t\t\t}\n\t\t\t}\n\t\t\tbuttons.push(addGroupCallback)\n\t\t}\n\n\t\tconst columnButton = {\n\t\t\ttext: 'View',\n\t\t\tcallback: async (event, i) => {\n\t\t\t\tconst sample = group.items[i]\n\t\t\t\tthis.interactivity.openSampleView(sample)\n\t\t\t}\n\t\t}\n\t\tconst columnButtons: any[] = hasSampleName ? [columnButton] : []\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tdiv: tableDiv,\n\t\t\tshowLines: true,\n\t\t\t//maxWidth: columns.length * '15' + 'vw',\n\t\t\tmaxHeight: '35vh',\n\t\t\tbuttons,\n\t\t\tselectAll: true,\n\t\t\tcolumnButtons\n\t\t})\n\n\t\tthis.view.dom.tip.show(x, y, false, false)\n\n\t\tfunction formatCell(column: string, name = 'value'): any {\n\t\t\tconst dict = {}\n\t\t\tdict[name] = column\n\t\t\treturn dict\n\t\t}\n\t}\n}\n", "import { shapesArray } from '#dom'\nimport { rgb } from 'd3-color'\nimport { scaleLinear as d3Linear, scaleTime } from 'd3-scale'\nimport { axisLeft, axisBottom } from 'd3-axis'\nimport { regressionPoly } from 'd3-regression'\nimport type { Scatter } from '../scatter'\nimport { getDateFromNumber } from '../../../../shared/utils/src/terms.js'\nimport type {\n\tScatterResponse,\n\tScatterChart,\n\tColorLegendItem,\n\tShapeLegendItem,\n\tScatterDataResult\n} from '../scatterTypes.js'\n//icons have size 16x16\nexport const shapes = shapesArray\n\nconst numberOfSamplesCutoff = 20000 // if map is greater than cutoff, switch from svg to canvas rendering\n\nexport class ScatterModel {\n\tstartGradient: any\n\tstopGradient: any\n\trange: any\n\tcharts!: ScatterChart[]\n\tis2DLarge: boolean\n\tis3D: boolean\n\taxisOffset: any\n\tfilterSampleStr: string | null = null\n\tscatter: Scatter\n\n\tconstructor(scatter: Scatter) {\n\t\tthis.startGradient = {}\n\t\tthis.stopGradient = {}\n\t\tthis.scatter = scatter\n\t\tthis.axisOffset = { x: 80, y: 30 }\n\t\tthis.is2DLarge = false\n\t\tthis.is3D = false\n\t}\n\n\t// creates an opts object for the vocabApi.someMethod(),\n\t// may need to add a new method to client/termdb/vocabulary.js\n\t// for now, just add methods to TermdbVocab,\n\t// later on, add methods with same name to FrontendVocab\n\tgetDataRequestOpts() {\n\t\tconst c: any = this.scatter.config\n\n\t\tif (c.singleCellPlot) return c\n\t\tconst coordTWs: any = []\n\t\tif (c.term) coordTWs.push(c.term)\n\t\tif (c.term2) coordTWs.push(c.term2)\n\t\t//If filter is provided in the config use it. The config filter includes the term filter, used by the report plot\n\t\tconst filter = this.scatter.parentId ? this.scatter.state.termfilter.filter : this.scatter.getFilter()\n\t\tconst opts: any = {\n\t\t\tname: c.name, // the actual identifier of the plot, for retrieving data from server\n\t\t\tcolorTW: c.colorTW,\n\t\t\tfilter,\n\t\t\tcoordTWs,\n\t\t\tchartType: this.scatter.type\n\t\t}\n\t\tif (this.scatter.state.termfilter.filter0) opts.filter0 = this.scatter.state.termfilter.filter0\n\t\tif (c.colorColumn) opts.colorColumn = c.colorColumn\n\t\tif (c.shapeTW) opts.shapeTW = c.shapeTW\n\t\tif (c.scaleDotTW) {\n\t\t\tif (!c.scaleDotTW.q) c.scaleDotTW.q = {}\n\t\t\tc.scaleDotTW.q.mode = 'continuous'\n\t\t\topts.scaleDotTW = c.scaleDotTW\n\t\t}\n\t\tif (c.term0) opts.divideByTW = c.term0\n\t\topts.excludeOutliers = this.scatter.settings.excludeOutliers\n\n\t\treturn opts\n\t}\n\n\tasync initData() {\n\t\ttry {\n\t\t\tconst reqOpts = this.getDataRequestOpts()\n\t\t\tif (reqOpts.coordTWs?.length == 1 && this.scatter.type == 'sampleScatter') return //To allow removing a term in the controls, though nothing is rendered (summary tab with violin active)\n\n\t\t\tconst data: ScatterResponse = await this.scatter.app.vocabApi.getScatterData(\n\t\t\t\treqOpts,\n\t\t\t\tthis.scatter.api?.getAbortSignal()\n\t\t\t)\n\t\t\tthis.is3D = this.scatter.config.term0?.q.mode == 'continuous'\n\t\t\tif ('error' in data) throw data.error\n\t\t\tthis.range = data.range\n\t\t\tthis.charts = []\n\t\t\tfor (const [key, chartData] of Object.entries(data.result)) {\n\t\t\t\tif (!Array.isArray(chartData.samples)) throw 'data.samples[] not array'\n\t\t\t\tthis.createChart(key, chartData)\n\t\t\t}\n\t\t\tthis.initRanges()\n\t\t} catch (e: any) {\n\t\t\tif (this.scatter.app.isAbortError(e)) return\n\t\t\tconsole.error(e)\n\t\t\tthrow e.message || e\n\t\t}\n\t}\n\n\tcreateChart(id: string, data: ScatterDataResult) {\n\t\tconst cohortSamples: any[] = data.samples.filter(sample => 'sampleId' in sample)\n\t\tif (cohortSamples.length > numberOfSamplesCutoff) this.is2DLarge = true\n\t\tconst colorLegend: Map<string, ColorLegendItem> = new Map(data.colorLegend)\n\t\tconst shapeLegend: Map<string, ShapeLegendItem> = new Map(data.shapeLegend)\n\t\tthis.charts.push({ id, data, cohortSamples, colorLegend, shapeLegend })\n\t}\n\n\tasync initRanges() {\n\t\tlet samples: any[] = []\n\t\tfor (const chart of this.charts) samples = samples.concat(chart.data.samples)\n\t\tif (samples.length > numberOfSamplesCutoff) this.is2DLarge = true\n\t\tif (samples.length == 0) return\n\t\tconst s0 = samples[0] //First sample to start reduce comparisons\n\t\tconst [xMin, xMax, yMin, yMax, zMin, zMax, scaleMin, scaleMax] = samples.reduce(\n\t\t\t(s, d) => [\n\t\t\t\td.x < s[0] ? d.x : s[0],\n\t\t\t\td.x > s[1] ? d.x : s[1],\n\t\t\t\td.y < s[2] ? d.y : s[2],\n\t\t\t\td.y > s[3] ? d.y : s[3],\n\t\t\t\td.z < s[4] ? d.z : s[4],\n\t\t\t\td.z > s[5] ? d.z : s[5],\n\t\t\t\t'scale' in d ? (d.scale < s[6] ? d.scale : s[6]) : Number.POSITIVE_INFINITY,\n\t\t\t\t'scale' in d ? (d.scale > s[7] ? d.scale : s[7]) : Number.NEGATIVE_INFINITY\n\t\t\t],\n\t\t\t[s0.x, s0.x, s0.y, s0.y, s0.z, s0.z, s0.scale, s0.scale]\n\t\t)\n\t\tconst settings = this.scatter.settings\n\t\tfor (const chart of this.charts) {\n\t\t\tchart.ranges = {\n\t\t\t\txMin: settings.minXScale != null ? settings.minXScale : settings.useGlobalMinMax ? this.range.xMin : xMin,\n\t\t\t\txMax: settings.maxXScale != null ? settings.maxXScale : settings.useGlobalMinMax ? this.range.xMax : xMax,\n\t\t\t\tyMin: settings.minYScale != null ? settings.minYScale : settings.useGlobalMinMax ? this.range.yMin : yMin,\n\t\t\t\tyMax: settings.maxYScale != null ? settings.maxYScale : settings.useGlobalMinMax ? this.range.yMax : yMax,\n\t\t\t\tzMin,\n\t\t\t\tzMax,\n\t\t\t\tscaleMin,\n\t\t\t\tscaleMax\n\t\t\t}\n\t\t}\n\t}\n\n\tgetOpacity(c) {\n\t\tif ('sampleId' in c) {\n\t\t\tconst hidden = c.hidden?.['category'] || c.hidden?.['shape']\n\t\t\tif (this.filterSampleStr) {\n\t\t\t\tif (!c.sample?.toLowerCase().includes(this.filterSampleStr.toLowerCase())) {\n\t\t\t\t\tif (hidden) return 0\n\t\t\t\t\telse return 0.1\n\t\t\t\t} else return 1.2\n\t\t\t}\n\t\t\tconst opacity = hidden ? 0 : this.scatter.settings.opacity\n\t\t\treturn opacity\n\t\t}\n\t\tconst refOpacity = this.scatter.settings.showRef ? this.scatter.settings.opacity : 0\n\t\treturn refOpacity\n\t}\n\n\tgetShape(chart, c) {\n\t\tconst index = chart.shapeLegend.get(c.shape).shape % shapes.length\n\t\treturn shapes[index]\n\t}\n\n\t/** Returns the calculated coordinate or the min/max axis\n\t * cap set by the user. */\n\tgetCoordinates(chart, c) {\n\t\tconst cx = () => {\n\t\t\treturn getCoordinate(c.x, this.scatter.settings.minXScale, this.scatter.settings.maxXScale)\n\t\t}\n\t\tconst cy = () => {\n\t\t\treturn getCoordinate(c.y, this.scatter.settings.minYScale, this.scatter.settings.maxYScale)\n\t\t}\n\t\tconst x = chart.xAxisScale(cx())\n\t\tconst y = chart.yAxisScale(cy())\n\t\treturn { x, y }\n\t}\n\n\tgetScale(chart, c, factor = 1) {\n\t\tconst isRef = !('sampleId' in c)\n\t\tlet scale\n\t\tif (!this.scatter.config.scaleDotTW || isRef) {\n\t\t\tscale = 'sampleId' in c ? this.scatter.settings.size : this.scatter.settings.refSize\n\t\t} else {\n\t\t\tconst range = this.scatter.settings.maxShapeSize - this.scatter.settings.minShapeSize\n\t\t\tif (this.scatter.settings.scaleDotOrder == 'Ascending')\n\t\t\t\tscale =\n\t\t\t\t\tthis.scatter.settings.minShapeSize +\n\t\t\t\t\t((c.scale - chart.ranges.scaleMin) / (chart.ranges.scaleMax - chart.ranges.scaleMin)) * range\n\t\t\telse\n\t\t\t\tscale =\n\t\t\t\t\tthis.scatter.settings.maxShapeSize -\n\t\t\t\t\t((c.scale - chart.ranges.scaleMin) / (chart.ranges.scaleMax - chart.ranges.scaleMin)) * range\n\t\t}\n\t\tconst zoom = this.is2DLarge ? this.scatter.zoom : 1 //if not 2d large the whole chart is zoomed\n\t\tscale = (zoom * scale * factor) / 3\n\t\tif (this.filterSampleStr) {\n\t\t\tif (c.sample?.toLowerCase().includes(this.filterSampleStr.toLowerCase())) scale = scale * 2\n\t\t\telse scale = scale * 0.8\n\t\t}\n\t\treturn scale\n\t}\n\n\ttransform(chart, c, factor = 1) {\n\t\tconst scale = this.getScale(chart, c, factor)\n\t\tconst particleSize = 16 * scale\n\t\tconst { x, y } = this.getCoordinates(chart, c)\n\t\tconst offSetX = x - particleSize / 2\n\t\tconst offSetY = y - particleSize / 2\n\t\tconst transform = `translate(${offSetX},${offSetY}) scale(${scale})` // original icons are scaled to 0.3\n\t\treturn transform\n\t}\n\n\tgetColor(c, chart) {\n\t\tif (this.scatter.config.colorTW?.q.mode == 'continuous' && 'sampleId' in c) {\n\t\t\tconst [min, max] = chart.colorGenerator.domain()\n\t\t\tif (c.category < min) return chart.colorGenerator(min)\n\t\t\tif (c.category > max) return chart.colorGenerator(max)\n\t\t\tconst color = chart.colorGenerator(c.category)\n\t\t\treturn color\n\t\t}\n\t\tif (c.category == 'Default') return this.scatter.settings.defaultColor\n\t\tconst category = chart.colorLegend.get(c.category)\n\t\treturn category.color\n\t}\n\n\tasync addGroup(group) {\n\t\tgroup.plotId = this.scatter.id\n\t\tawait this.scatter.app.vocabApi.addGroup(group)\n\t}\n\n\tgetStrokeWidth(c) {\n\t\tconst opacity = this.getOpacity(c)\n\t\tif (opacity <= 0.2)\n\t\t\t//hidden by filter or search\n\t\t\treturn 0\n\t\tif (opacity == 1.2)\n\t\t\t//samples searched\n\t\t\treturn 2\n\t\treturn 1\n\t}\n\n\tasync processData() {\n\t\tconst term0Values = this.scatter.config.term0?.term.values\n\t\tif (term0Values) {\n\t\t\t// sort the divideBy subCharts based on pre-defined term0 order in db\n\t\t\tconst orderedLabels: any = Object.values(term0Values).sort((a: any, b: any) =>\n\t\t\t\t'order' in a && 'order' in b ? a.order - b.order : 0\n\t\t\t)\n\t\t\tthis.charts.sort(\n\t\t\t\t(a, b) => orderedLabels.findIndex(v => v.label == a.id) - orderedLabels.findIndex(v => v.label == b.id)\n\t\t\t)\n\t\t}\n\t\tfor (const chart of this.charts) {\n\t\t\tthis.initAxes(chart)\n\t\t\tconst regressionType = this.scatter.settings.regression\n\n\t\t\tif (!regressionType || regressionType == 'None') continue\n\t\t\tlet regression\n\t\t\tconst data: any = []\n\t\t\tawait chart.cohortSamples.forEach(c => {\n\t\t\t\tdata.push(this.getCoordinates(chart, c))\n\t\t\t})\n\t\t\tlet regressionCurve\n\t\t\t// if (regressionType == 'Loess') {\n\t\t\t// \tregression = regressionLoess()\n\t\t\t// \t\t.x(c => c.x)\n\t\t\t// \t\t.y(c => c.y)\n\t\t\t// \t\t.bandwidth(0.25)\n\t\t\t// \tregressionCurve = regression(data)\n\t\t\t// } else\n\t\t\tif (regressionType == 'Polynomial') {\n\t\t\t\tregression = regressionPoly()\n\t\t\t\t\t.x(c => c.x)\n\t\t\t\t\t.y(c => c.y)\n\t\t\t\t\t.order(3)\n\t\t\t\tregressionCurve = regression(data)\n\t\t\t} else if (regressionType == 'Lowess') {\n\t\t\t\tconst X: any = [],\n\t\t\t\t\tY: any = []\n\t\t\t\tfor (const sample of data) {\n\t\t\t\t\tX.push(sample.x)\n\t\t\t\t\tY.push(sample.y)\n\t\t\t\t}\n\t\t\t\tregressionCurve = await this.scatter.app.vocabApi.getLowessCurve({ coords: { X, Y } })\n\t\t\t} else {\n\t\t\t\tthrow `unsupported regression type='${regressionType}'`\n\t\t\t}\n\t\t\tchart.regressionCurve = regressionCurve\n\t\t}\n\t}\n\n\tinitAxes(chart) {\n\t\tif (chart.data.samples.length == 0) return\n\t\tconst offsetX = this.axisOffset.x\n\t\tconst offsetY = this.axisOffset.y\n\t\tconst xMin = chart.ranges.xMin\n\t\tconst xMax = chart.ranges.xMax\n\t\tconst yMin = chart.ranges.yMin\n\t\tconst yMax = chart.ranges.yMax\n\t\t//unless there is a capping in the min/max values add a minimal extra space in the plot\n\t\tconst extraSpaceX =\n\t\t\tthis.scatter.settings.minXScale != null || this.scatter.settings.maxXScale != null ? 0 : (xMax - xMin) * 0.01 //extra space added to avoid clipping the particles on the X axis\n\t\tconst extraSpaceY =\n\t\t\tthis.scatter.settings.minYScale != null || this.scatter.settings.maxYScale != null ? 0 : (yMax - yMin) * 0.01 //extra space added to avoid clipping the particles on the Y axis\n\t\tchart.xAxisScale = d3Linear()\n\t\t\t.domain([xMin - extraSpaceX, xMax + extraSpaceX])\n\t\t\t.range([offsetX, this.scatter.settings.svgw + offsetX])\n\t\tif (this.scatter.config.term && this.scatter.config.term.term.type == 'date') {\n\t\t\tconst xMinDate = getDateFromNumber(xMin - extraSpaceX)\n\t\t\tconst xMaxDate = getDateFromNumber(xMax + extraSpaceX)\n\n\t\t\tchart.xAxisScaleTime = scaleTime()\n\t\t\t\t.domain([xMinDate, xMaxDate])\n\t\t\t\t.range([offsetX, this.scatter.settings.svgw + offsetX])\n\n\t\t\tchart.axisBottom = axisBottom(chart.xAxisScaleTime)\n\t\t} else chart.axisBottom = axisBottom(chart.xAxisScale)\n\t\tconst svgh = this.scatter.settings.svgh\n\t\tchart.yAxisScale = d3Linear()\n\t\t\t.domain([yMax + extraSpaceY, yMin - extraSpaceY])\n\t\t\t.range([offsetY, svgh + offsetY])\n\t\tif (this.scatter.config.term2 && this.scatter.config.term2.term.type == 'date') {\n\t\t\tconst yMinDate = getDateFromNumber(yMin - extraSpaceY)\n\t\t\tconst yMaxDate = getDateFromNumber(yMax + extraSpaceY)\n\n\t\t\tchart.yAxisScaleTime = scaleTime()\n\t\t\t\t.domain([yMinDate, yMaxDate])\n\t\t\t\t.range([offsetY, this.scatter.settings.svgh + offsetY])\n\n\t\t\tchart.axisLeft = axisLeft(chart.yAxisScaleTime)\n\t\t} else chart.axisLeft = axisLeft(chart.yAxisScale)\n\n\t\tchart.zAxisScale = d3Linear().domain([chart.ranges.zMin, chart.ranges.zMax]).range([0, this.scatter.settings.svgd])\n\n\t\tconst gradientColor = rgb(this.scatter.settings.defaultColor)\n\t\tif (!this.scatter.config.startColor) {\n\t\t\tthis.scatter.config.startColor = {}\n\t\t\tthis.scatter.config.stopColor = {}\n\t\t}\n\t\t// supply start and stop color, if term has hardcoded colors, use; otherwise use default\n\t\tif (!this.scatter.config.startColor[chart.id]) {\n\t\t\tthis.scatter.config.startColor[chart.id] =\n\t\t\t\tthis.scatter.config.colorTW?.term.continuousColorScale?.minColor ||\n\t\t\t\tgradientColor.brighter().brighter().toString()\n\t\t}\n\n\t\tif (!this.scatter.config.stopColor[chart.id]) {\n\t\t\tthis.scatter.config.stopColor[chart.id] =\n\t\t\t\tthis.scatter.config.colorTW?.term.continuousColorScale?.maxColor || gradientColor.darker().toString()\n\t\t}\n\n\t\t// Handle continuous color scaling when color term wrapper is in continuous mode\n\t\tif (this.scatter.config.colorTW?.q.mode === 'continuous') {\n\t\t\t// Extract and sort all sample values for our calculations\n\t\t\t// We filter out any values that are explicitly defined in the term values\n\t\t\t// This gives us the raw numerical data we need for scaling\n\t\t\tconst colorValues = chart.cohortSamples\n\t\t\t\t.filter(\n\t\t\t\t\ts => !this.scatter.config.colorTW.term.values || !(s.category in this.scatter.config.colorTW.term.values)\n\t\t\t\t)\n\t\t\t\t.map(s => s.category)\n\t\t\t\t.sort((a, b) => a - b)\n\t\t\tchart.colorValues = colorValues // to use it in renderLegend\n\t\t\t// Determine min/max based on current mode\n\t\t\tlet min, max, index\n\t\t\tconst settings = this.scatter.config.settings.sampleScatter\n\n\t\t\tswitch (settings.colorScaleMode) {\n\t\t\t\t// Fixed mode: Use user-defined min/max values\n\t\t\t\t// This is useful when you want consistent scaling across different views\n\t\t\t\tcase 'fixed':\n\t\t\t\t\tmin = settings.colorScaleMinFixed\n\t\t\t\t\tmax = settings.colorScaleMaxFixed\n\t\t\t\t\tbreak\n\n\t\t\t\tcase 'percentile':\n\t\t\t\t\t// Percentile mode: Scale based on data distribution\n\t\t\t\t\tmin = colorValues[0] // Start at the first value of the array for percentile mode\n\t\t\t\t\t// Calculate the value at the specified percentile\n\t\t\t\t\t// This helps handle outliers by focusing on the main distribution\n\t\t\t\t\tindex = Math.floor((colorValues.length * settings.colorScalePercentile) / 100)\n\t\t\t\t\tmax = colorValues[index]\n\t\t\t\t\tbreak\n\n\t\t\t\tcase 'auto':\n\t\t\t\tdefault:\n\t\t\t\t\t// Auto mode (default): Use the full range of the data\n\t\t\t\t\t// This gives the most accurate representation of the actual data distribution\n\t\t\t\t\tmin = colorValues[0]\n\t\t\t\t\tmax = colorValues[colorValues.length - 1] // Since the values are already sorted in ascending\n\t\t\t\t\t// order just get the first and last values\n\t\t\t\t\tbreak\n\t\t\t}\n\n\t\t\t// Create the color generator using d3's linear scale\n\t\t\t// This maps our numerical range to a color gradient\n\n\t\t\tchart.colorGenerator = d3Linear()\n\t\t\t\t.domain([min, max])\n\t\t\t\t.range([this.scatter.config.startColor[chart.id], this.scatter.config.stopColor[chart.id]])\n\n\t\t\t// Store the current range for reference\n\t\t\t// This is useful when we need to recreate the color generator\n\t\t\t// or check the current scaling values\n\t\t\tchart.currentColorRange = { min, max }\n\t\t}\n\t}\n}\n\nexport function getCoordinate(val: number, min: number | null, max: number | null) {\n\tif (min != null && val < min) return min\n\tif (max != null && val > max) return max\n\treturn val\n}\n", "import { Menu } from '#dom/menu'\nimport { rgb } from 'd3-color'\nimport { shapeSelector } from '../../../dom/shapes.js'\nimport type { Scatter } from '../scatter.js'\nimport { scaleLinear as d3Linear } from 'd3-scale'\nexport class ScatterLegendInteractivity {\n\tscatter: Scatter\n\tshapeTW: any\n\tcolorTW: any\n\n\tconstructor(scatter: Scatter) {\n\t\tthis.scatter = scatter\n\t}\n\n\tonLegendClick(chart, name, key, e, category) {\n\t\tconst tw = this.scatter.config[name]\n\t\tconst isColorTW = name == 'colorTW'\n\t\tconst hidden = tw.q.hiddenValues ? key in tw.q.hiddenValues : false\n\t\tconst hiddenCount = tw.q.hiddenValues ? Object.keys(tw.q.hiddenValues).length : 0\n\n\t\tif (hidden && hiddenCount == 1) {\n\t\t\t//show hidden category and skip menu\n\t\t\tthis.hideCategory(tw, key, false)\n\t\t\tthis.dispatchConfig(name, tw)\n\t\t\treturn\n\t\t}\n\t\tconst menu = new Menu({ padding: '0px' })\n\t\tconst div = menu.d.append('div')\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text(hidden ? 'Show' : 'Hide')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.hideCategory(tw, key, !hidden)\n\t\t\t\tmenu.hide()\n\t\t\t\tthis.dispatchConfig(name, tw)\n\t\t\t})\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text('Show only')\n\t\t\t.on('click', () => {\n\t\t\t\tconst map = name == 'colorTW' ? chart.colorLegend : chart.shapeLegend\n\t\t\t\tfor (const mapKey of map.keys())\n\t\t\t\t\tthis.hideCategory(\n\t\t\t\t\t\ttw,\n\t\t\t\t\t\tmapKey,\n\t\t\t\t\t\ttw.term.type == 'geneVariant' && tw.q.type == 'values' ? !mapKey.startsWith(key) : mapKey != key\n\t\t\t\t\t)\n\n\t\t\t\tmenu.hide()\n\t\t\t\tthis.dispatchConfig(name, tw)\n\t\t\t})\n\t\tif (hiddenCount > 1)\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text('Show all')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tmenu.hide()\n\t\t\t\t\tconst map = isColorTW ? chart.colorLegend : chart.shapeLegend\n\t\t\t\t\tfor (const mapKey of map.keys()) this.hideCategory(tw, mapKey, false)\n\t\t\t\t\tthis.dispatchConfig(name, tw)\n\t\t\t\t})\n\t\tif (isColorTW) {\n\t\t\tconst color = rgb(category.color).formatHex()\n\t\t\tconst input: any = div\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '0px 10px')\n\t\t\t\t.text('Color:')\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'color')\n\t\t\t\t.attr('value', color)\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tthis.changeColor(category.key, input.node().value)\n\t\t\t\t\tmenu.hide()\n\t\t\t\t})\n\t\t}\n\t\tif (!isColorTW) {\n\t\t\t//is shape\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text('Change shape')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tdiv.selectAll('*').remove()\n\t\t\t\t\tconst callback = index => {\n\t\t\t\t\t\tthis.changeShape(category.key, index)\n\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t}\n\t\t\t\t\tshapeSelector(div, callback)\n\t\t\t\t})\n\t\t}\n\n\t\tmenu.showunder(e.target)\n\t}\n\n\tasync changeShape(key, shape) {\n\t\tconst tw = this.scatter.config.shapeTW\n\t\tif (!tw.term.values) tw.term.values = {}\n\t\tif (!tw.term.values[key]) tw.term.values[key] = {}\n\t\ttw.term.values[key].shape = shape\n\t\tawait this.scatter.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.scatter.id,\n\t\t\tconfig: { shapeTW: tw }\n\t\t})\n\t}\n\n\tdispatchConfig(name, tw) {\n\t\tthis.scatter.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.scatter.id,\n\t\t\tconfig: { [name]: tw }\n\t\t})\n\t}\n\n\thideCategory(tw, key, hide) {\n\t\tif (!tw.q) tw.q = {}\n\t\tif (!tw.q.hiddenValues) tw.q.hiddenValues = {}\n\t\tconst value =\n\t\t\t!(tw.term.type == 'geneVariant' && tw.q.type == 'values') && tw.term.values[key]\n\t\t\t\t? tw.term.values[key]\n\t\t\t\t: { key: key, label: key }\n\n\t\tif (!hide) delete tw.q.hiddenValues[key]\n\t\telse tw.q.hiddenValues[key] = value\n\t\tif (key == 'Ref') {\n\t\t\tthis.scatter.settings.showRef = !hide\n\t\t\tthis.scatter.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.scatter.id,\n\t\t\t\tconfig: {\n\t\t\t\t\tsettings: { sampleScatter: this.scatter.settings }\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tchangeGradientColor(chart, color, idx) {\n\t\tconst hexColor = rgb(color).formatHex()\n\t\tconst colorKey = idx == 0 ? 'startColor' : 'stopColor'\n\t\tthis.scatter.config[colorKey][chart.id] = hexColor\n\n\t\t// Recreate color generator with current settings\n\t\tconst range = chart.currentColorRange || chart.colorGenerator.domain()\n\t\tchart.colorGenerator = d3Linear()\n\t\t\t.domain(range)\n\t\t\t.range([this.scatter.config.startColor[chart.id], this.scatter.config.stopColor[chart.id]])\n\n\t\t// Update the configuration\n\t\tthis.scatter.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.scatter.id,\n\t\t\tconfig: this.scatter.config\n\t\t})\n\t}\n\n\tasync changeColor(key, color) {\n\t\tconst tw = this.scatter.config.colorTW\n\t\tif (!tw.term.values) tw.term.values = {}\n\t\tif (!tw.term.values[key]) tw.term.values[key] = {}\n\t\ttw.term.values[key].color = color\n\t\tawait this.scatter.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.scatter.id,\n\t\t\tconfig: { colorTW: tw }\n\t\t})\n\t}\n}\n", "import { fillTermWrapper } from '#termsetting'\nimport { Menu } from '#dom'\nimport type { Scatter } from '../scatter.js'\nimport { isNumericTerm } from '#shared/terms.js'\nimport { roundValueAuto } from '#shared/roundValue.js'\n\nexport const minShapeSize = 0.2\nexport const maxShapeSize = 6\n\nexport class ScatterView {\n\topts: any\n\tdom: any\n\tscatter: Scatter\n\tloading: any\n\tloadingDiv: any\n\ttooltip: any\n\ttooltipDiv: any\n\tchart: any\n\tchartDiv: any\n\n\tconstructor(scatter: Scatter) {\n\t\tthis.opts = scatter.opts\n\t\tthis.scatter = scatter\n\n\t\tconst leftDiv = this.opts.holder.insert('div').style('display', 'inline-block')\n\t\tconst controlsHolder = leftDiv.insert('div').style('display', 'inline-block')\n\n\t\tconst rightDiv = this.opts.holder.insert('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\tconst loadingDiv = rightDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', '24px')\n\t\t\t.text('Loading ...')\n\t\tconst bannerDiv = rightDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('padding', '24px')\n\t\t\t.style('font-size', '16px')\n\t\tconst headerDiv = rightDiv.append('div')\n\t\tconst mainDiv = rightDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('flex-direction', 'row')\n\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t.style('max-width', '100vw')\n\n\t\tthis.dom = {\n\t\t\tloadingDiv,\n\t\t\tbannerDiv,\n\t\t\theaderDiv,\n\t\t\tmainDiv,\n\t\t\theader: this.opts.header,\n\t\t\t//holder,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\ttooltip: new Menu({ padding: '2px', offsetX: 10, offsetY: 0 }),\n\t\t\tcontrolsHolder,\n\t\t\ttoolsDiv: leftDiv.insert('div')\n\t\t}\n\n\t\tif (this.dom.header) {\n\t\t\tconst chartName = splitCamelCase(this.scatter.type).toUpperCase()\n\t\t\tthis.dom.header.html(\n\t\t\t\t`${\n\t\t\t\t\tthis.scatter.config.name || ''\n\t\t\t\t} <span style=\"opacity:.6;font-size:.7em;margin-left:10px;\">${chartName}</span>`\n\t\t\t)\n\t\t}\n\t}\n\n\tgetControlInputs() {\n\t\tconst hasRef = this.scatter.model.charts[0]?.data.samples.find(s => !('sampleId' in s)) || false\n\t\tconst scaleDotOption = {\n\t\t\ttype: 'term',\n\t\t\tconfigKey: 'scaleDotTW',\n\t\t\tchartType: 'sampleScatter',\n\t\t\tusecase: { target: 'sampleScatter', detail: 'numeric' },\n\t\t\ttitle: 'Scale sample by term value',\n\t\t\tlabel: 'Scale by',\n\t\t\tvocabApi: this.scatter.app.vocabApi,\n\t\t\tnumericEditMenuVersion: ['continuous'],\n\t\t\t//Eventually this will be corrected with usecase.detail\n\t\t\t//When single cell, only relevant terms will be displayed\n\t\t\t//in the tree\n\t\t\tgetDisplayStyle: () => {\n\t\t\t\treturn this.scatter.config?.singleCellPlot ? 'none' : ''\n\t\t\t}\n\t\t}\n\t\tconst shapeOption = {\n\t\t\ttype: 'term',\n\t\t\tconfigKey: 'shapeTW',\n\t\t\tchartType: 'sampleScatter',\n\t\t\tusecase: { target: 'sampleScatter', detail: 'shapeTW' },\n\t\t\ttitle: 'Categories to assign a shape',\n\t\t\tlabel: 'Shape',\n\t\t\tvocabApi: this.scatter.app.vocabApi,\n\t\t\tnumericEditMenuVersion: ['discrete'],\n\t\t\t//Eventually this will be corrected with usecase.detail\n\t\t\t//When single cell, only relevant terms will be displayed\n\t\t\t//in the tree\n\t\t\tgetDisplayStyle: () => {\n\t\t\t\treturn this.scatter.config?.singleCellPlot ? 'none' : ''\n\t\t\t},\n\t\t\tprocessInput: async tw => {\n\t\t\t\t//only discrete mode allowed so set discrete mode and fill term wrapper to add the bins\n\t\t\t\tif (isNumericTerm(tw?.term)) {\n\t\t\t\t\ttw.q = { mode: 'discrete' } //use discrete mode by default\n\t\t\t\t\tawait fillTermWrapper(tw, this.scatter.app.vocabApi)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tconst shapeSizeOption = {\n\t\t\tlabel: 'Sample size',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'sampleScatter',\n\t\t\tsettingsKey: 'size',\n\t\t\ttitle: 'Sample size, represents the factor used to scale the sample',\n\t\t\tmin: 0,\n\t\t\tstep: 0.1\n\t\t}\n\t\tconst step = (maxShapeSize - minShapeSize) / 10\n\t\tconst minShapeSizeOption = {\n\t\t\tlabel: 'Min size',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'sampleScatter',\n\t\t\tsettingsKey: 'minShapeSize',\n\t\t\ttitle: 'Minimum sample size',\n\t\t\tmin: minShapeSize,\n\t\t\tmax: maxShapeSize,\n\t\t\tstep\n\t\t}\n\t\tconst maxShapeSizeOption = {\n\t\t\tlabel: 'Max size',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'sampleScatter',\n\t\t\tsettingsKey: 'maxShapeSize',\n\t\t\ttitle: 'Maximum sample size',\n\t\t\tmin: minShapeSize,\n\t\t\tmax: maxShapeSize,\n\t\t\tstep\n\t\t}\n\t\tconst orientation = {\n\t\t\tlabel: 'Scale order',\n\t\t\ttype: 'radio',\n\t\t\tchartType: 'sampleScatter',\n\t\t\tsettingsKey: 'scaleDotOrder',\n\t\t\toptions: [\n\t\t\t\t{ label: 'Ascending', value: 'Ascending' },\n\t\t\t\t{ label: 'Descending', value: 'Descending' }\n\t\t\t]\n\t\t}\n\t\tconst refSizeOption = {\n\t\t\tlabel: 'Reference size',\n\t\t\ttype: 'number',\n\t\t\tchartType: 'sampleScatter',\n\t\t\tsettingsKey: 'refSize',\n\t\t\ttitle: 'It represents the area of the reference symbol in square pixels',\n\t\t\tmin: 0,\n\t\t\tstep: 0.1\n\t\t}\n\t\tconst showAxes = {\n\t\t\tboxLabel: '',\n\t\t\tlabel: 'Show axes',\n\t\t\ttype: 'checkbox',\n\t\t\tchartType: 'sampleScatter',\n\t\t\tsettingsKey: 'showAxes',\n\t\t\ttitle: `Option to show/hide plot axes`,\n\t\t\ttestid: 'showAxes'\n\t\t}\n\n\t\tconst inputs: any = [\n\t\t\t{\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'colorTW',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tusecase: { target: 'sampleScatter', detail: 'colorTW' },\n\t\t\t\ttitle: 'Categories to color the samples',\n\t\t\t\tlabel: 'Color',\n\t\t\t\tvocabApi: this.scatter.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['continuous', 'discrete'],\n\t\t\t\t//Eventually this will be corrected with usecase.detail\n\t\t\t\t//When single cell, only relevant terms will be displayed\n\t\t\t\t//in the tree\n\t\t\t\tgetDisplayStyle: () => {\n\t\t\t\t\treturn this.scatter.config?.singleCellPlot ? 'none' : ''\n\t\t\t\t}\n\t\t\t},\n\n\t\t\t{\n\t\t\t\tlabel: 'Opacity',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tsettingsKey: 'opacity',\n\t\t\t\ttitle: 'It represents the opacity of the elements',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 1,\n\t\t\t\tstep: 0.1\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Chart width',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tsettingsKey: 'svgw'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Chart height',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tsettingsKey: 'svgh'\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show contour map',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tsettingsKey: 'showContour',\n\t\t\t\ttitle:\n\t\t\t\t\t\"Shows the density of point clouds. If 'Color' is used in continous mode, it uses it to weight the points when calculating the density contours. If 'Z/Divide by' is added in continous mode, it used it instead.\"\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Save zoom transform',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tsettingsKey: 'saveZoomTransform',\n\t\t\t\ttitle: `Option to save the zoom transformation in the state. Needed if you want to save a session with the actual zoom and pan applied`,\n\t\t\t\tprocessInput: value => this.saveZoomTransform(value)\n\t\t\t}\n\t\t]\n\t\tif (this.scatter.settings.showContour)\n\t\t\tinputs.push(\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Color contours',\n\t\t\t\t\tboxLabel: '',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tsettingsKey: 'colorContours'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Contour bandwidth',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tsettingsKey: 'contourBandwidth',\n\t\t\t\t\ttitle: 'Reduce to increase resolution.',\n\t\t\t\t\tmin: 5,\n\t\t\t\t\tmax: 50,\n\t\t\t\t\tstep: 5\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Contour thresholds',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tsettingsKey: 'contourThresholds',\n\t\t\t\t\ttitle: 'Increase to enhance contour detail.',\n\t\t\t\t\tmin: 5,\n\t\t\t\t\tmax: 30,\n\t\t\t\t\tstep: 5\n\t\t\t\t}\n\t\t\t)\n\t\tif (this.scatter.config.sampleCategory) {\n\t\t\tconst options: any = Object.values(this.scatter.config.sampleCategory.tw.term.values).map((v: any) => ({\n\t\t\t\tlabel: v.label || v.key,\n\t\t\t\tvalue: v.key\n\t\t\t}))\n\t\t\tif (this.scatter.config.sampleCategory.order)\n\t\t\t\toptions.sort((elem1, elem2) => {\n\t\t\t\t\tconst i1 = this.scatter.config.sampleCategory.order.indexOf(elem1.value)\n\t\t\t\t\tconst i2 = this.scatter.config.sampleCategory.order.indexOf(elem2.value)\n\t\t\t\t\tif (i1 < i2) return -1\n\t\t\t\t\treturn 1\n\t\t\t\t})\n\t\t\tif (!this.scatter.settings.sampleCategory)\n\t\t\t\tthis.scatter.settings.sampleCategory = this.scatter.config.sampleCategory.defaultValue || ''\n\t\t\toptions.push({ label: 'All', value: '' })\n\t\t\tconst sampleCategory = {\n\t\t\t\tlabel: 'Sample type',\n\t\t\t\ttype: 'dropdown',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tsettingsKey: 'sampleCategory',\n\t\t\t\toptions\n\t\t\t}\n\t\t\tinputs.push(sampleCategory)\n\t\t}\n\n\t\tif (!this.scatter.model.is2DLarge && !this.scatter.config.singleCellPlot) {\n\t\t\tconst isPremade = this.scatter.config.name !== undefined && !this.scatter.config.term\n\t\t\tinputs.unshift({\n\t\t\t\ttype: 'term',\n\t\t\t\tconfigKey: 'term0',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tusecase: { target: 'sampleScatter', detail: 'term0' },\n\t\t\t\ttitle: 'Term to to divide by categories or to use as Z coordinate',\n\t\t\t\tlabel: 'Z / Divide by',\n\t\t\t\tvocabApi: this.scatter.app.vocabApi,\n\t\t\t\tnumericEditMenuVersion: ['discrete', 'continuous'],\n\t\t\t\tprocessInput: tw => {\n\t\t\t\t\tif (!isPremade && isNumericTerm(tw?.term)) tw.q = { mode: 'continuous' } //use continuous mode by default if not premade plot\n\t\t\t\t}\n\t\t\t})\n\t\t} else if (!this.scatter.config.singleCellPlot) {\n\t\t\tinputs.push(\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Sample size',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tsettingsKey: 'threeSize',\n\t\t\t\t\ttitle: 'Sample size',\n\t\t\t\t\tmin: 0,\n\t\t\t\t\tmax: 1,\n\t\t\t\t\tstep: 0.001\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Field of Vision',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tsettingsKey: 'threeFOV',\n\t\t\t\t\ttitle: 'Field of Vision',\n\t\t\t\t\tmin: 50,\n\t\t\t\t\tmax: 90,\n\t\t\t\t\tstep: 1\n\t\t\t\t}\n\t\t\t)\n\t\t}\n\t\tif (this.scatter.config.term) {\n\t\t\tinputs.unshift(\n\t\t\t\t...[\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\tconfigKey: 'term',\n\t\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\t\tusecase: { target: 'sampleScatter', detail: 'numeric' },\n\t\t\t\t\t\ttitle: 'X coordinate to plot the samples',\n\t\t\t\t\t\tlabel: 'X',\n\t\t\t\t\t\tvocabApi: this.scatter.app.vocabApi,\n\t\t\t\t\t\tmenuOptions: '!remove',\n\t\t\t\t\t\tnumericEditMenuVersion: ['continuous']\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\tconfigKey: 'term2',\n\t\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\t\tusecase: { target: 'sampleScatter', detail: 'numeric' },\n\t\t\t\t\t\ttitle: 'Y coordinate to plot the samples',\n\t\t\t\t\t\tlabel: 'Y',\n\t\t\t\t\t\tvocabApi: this.scatter.app.vocabApi,\n\t\t\t\t\t\tmenuOptions: '!remove',\n\t\t\t\t\t\tnumericEditMenuVersion: ['continuous']\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t)\n\t\t\tif (!this.scatter.model.is3D) {\n\t\t\t\tinputs.splice(4, 0, shapeOption)\n\t\t\t\tinputs.splice(5, 0, scaleDotOption)\n\t\t\t\tif (this.scatter.config.scaleDotTW) {\n\t\t\t\t\tinputs.splice(6, 0, minShapeSizeOption)\n\t\t\t\t\tinputs.splice(7, 0, maxShapeSizeOption)\n\t\t\t\t\tinputs.splice(8, 0, orientation)\n\t\t\t\t\tif (hasRef) inputs.splice(9, 0, refSizeOption)\n\t\t\t\t} else {\n\t\t\t\t\tinputs.splice(6, 0, shapeSizeOption)\n\t\t\t\t\tif (hasRef) inputs.splice(7, 0, refSizeOption)\n\t\t\t\t}\n\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Show regression',\n\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tsettingsKey: 'regression',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'None', value: 'None' },\n\t\t\t\t\t\t//{ label: 'Loess', value: 'Loess' },\n\t\t\t\t\t\t{ label: 'Lowess', value: 'Lowess' },\n\t\t\t\t\t\t{ label: 'Polynomial', value: 'Polynomial' }\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t} else {\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Chart depth',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tsettingsKey: 'svgd'\n\t\t\t\t})\n\t\t\t\tinputs.push({\n\t\t\t\t\tlabel: 'Field of vision',\n\t\t\t\t\ttitle: 'Camera field of view, in degrees',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tsettingsKey: 'fov'\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tinputs.push(showAxes, ...this.getMinMaxInputs())\n\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Default color',\n\t\t\t\ttype: 'color',\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tsettingsKey: 'defaultColor'\n\t\t\t})\n\t\t} else if (!this.scatter.model.is2DLarge) {\n\t\t\tinputs.splice(2, 0, shapeOption)\n\t\t\tinputs.splice(3, 0, scaleDotOption)\n\t\t\tif (this.scatter.config.scaleDotTW) {\n\t\t\t\tinputs.splice(4, 0, minShapeSizeOption)\n\t\t\t\tinputs.splice(5, 0, maxShapeSizeOption)\n\t\t\t\tinputs.splice(6, 0, orientation)\n\t\t\t\tif (hasRef) inputs.splice(7, 0, refSizeOption)\n\t\t\t} else {\n\t\t\t\tinputs.splice(4, 0, shapeSizeOption)\n\t\t\t\tif (hasRef) inputs.splice(5, 0, refSizeOption)\n\t\t\t}\n\t\t\tinputs.push(showAxes)\n\t\t}\n\n\t\tthis.mayAddControlLabels(inputs)\n\n\t\treturn inputs\n\t}\n\n\tgetMinMaxInputs() {\n\t\tconst xMin = roundValueAuto(this.scatter.model.range.xMin)\n\t\tconst xMax = roundValueAuto(this.scatter.model.range.xMax)\n\t\tconst xStep = (xMax - xMin) / 10\n\t\tconst yMin = roundValueAuto(this.scatter.model.range.yMin)\n\t\tconst yMax = roundValueAuto(this.scatter.model.range.yMax)\n\t\tconst yStep = (yMax - yMin) / 10\n\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\tlabel: 'X axis minimum',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: this.scatter.type,\n\t\t\t\tsettingsKey: 'minXScale',\n\t\t\t\ttitle: `Set the minimum X axis value between ${xMin} and ${xMax}`,\n\t\t\t\tplaceholder: `${xMin}`,\n\t\t\t\tmin: xMin,\n\t\t\t\tmax: xMax,\n\t\t\t\tstep: xStep\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'X axis maximum',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: this.scatter.type,\n\t\t\t\tsettingsKey: 'maxXScale',\n\t\t\t\ttitle: `Set the maximum X axis value between ${xMin} and ${xMax}`,\n\t\t\t\tplaceholder: `${xMax}`,\n\t\t\t\tmin: xMin,\n\t\t\t\tmax: xMax,\n\t\t\t\tstep: xStep,\n\t\t\t\tprocessInput: value => {\n\t\t\t\t\t/** When the user deletes a value, setNumberInput()\n\t\t\t\t\t * in controls.config.js sets it to input.min. Instead,\n\t\t\t\t\t * reset to default value to allow the user to delete\n\t\t\t\t\t * the value. */\n\t\t\t\t\tconst n = this.dom.controlsHolder.selectAll('input').filter(function (this: any) {\n\t\t\t\t\t\treturn this.placeholder == `${xMax}`\n\t\t\t\t\t})\n\t\t\t\t\tif (!n.node().value) return xMax\n\t\t\t\t\telse return value\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Y axis minimum',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: this.scatter.type,\n\t\t\t\tsettingsKey: 'minYScale',\n\t\t\t\ttitle: `Set the minimum Y axis value between ${yMin} and ${yMax}`,\n\t\t\t\tplaceholder: `${yMin}`,\n\t\t\t\tmin: yMin,\n\t\t\t\tmax: yMax,\n\t\t\t\tstep: yStep\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Y axis maximum',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: this.scatter.type,\n\t\t\t\tsettingsKey: 'maxYScale',\n\t\t\t\ttitle: `Set the maximum Y axis value between ${yMin} and ${yMax}`,\n\t\t\t\tplaceholder: `${yMax}`,\n\t\t\t\tmin: yMin,\n\t\t\t\tmax: yMax,\n\t\t\t\tstep: yStep,\n\t\t\t\tprocessInput: value => {\n\t\t\t\t\t/** When the user deletes a value, setNumberInput()\n\t\t\t\t\t * in controls.config.js sets it to input.min. Instead,\n\t\t\t\t\t * reset to default value to allow the user to delete\n\t\t\t\t\t * the value. */\n\t\t\t\t\tconst n = this.dom.controlsHolder.selectAll('input').filter(function (this: any) {\n\t\t\t\t\t\treturn this.placeholder == `${yMax}`\n\t\t\t\t\t})\n\t\t\t\t\tif (!n.node().value) return yMax\n\t\t\t\t\telse return value\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\t\treturn inputs\n\t}\n\n\tmayAddControlLabels(inputs) {\n\t\tconst controlLabels = structuredClone(this.scatter.config.controlLabels)\n\t\tif (!controlLabels) return\n\t\tlet term1input, term2input, term0input\n\t\tfor (const i of inputs) {\n\t\t\tif (i.configKey == 'term') term1input = i\n\t\t\telse if (i.configKey == 'term2') term2input = i\n\t\t\telse if (i.configKey == 'term0') term0input = i\n\t\t}\n\t\tif (term1input && term2input) {\n\t\t\t// term1 and term2 inputs\n\t\t\t// append X/Y/Z labels to controlLabels\n\t\t\t// note: should not append when term1 and term2 inputs\n\t\t\t// are absent (e.g. tSNE), because having only a Z coordinate\n\t\t\t// does not make sense\n\t\t\tif (controlLabels.term1) term1input.label = controlLabels.term1.label + ' (X)'\n\t\t\tif (controlLabels.term2) term2input.label = controlLabels.term2.label + ' (Y)'\n\t\t\tif (term0input && controlLabels.term0) term0input.label = controlLabels.term0.label + ' (Z)'\n\t\t}\n\t}\n\n\tsaveZoomTransform(value: any) {\n\t\tif (value) this.scatter.vm.scatterZoom.saveZoomTransform()\n\t\treturn value\n\t}\n}\n\n/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n\t\ttermdbConfig is accessible at chartsInstance.state.termdbConfig{}\n\t\tmass option is accessible at chartsInstance.app.opts{}\n\t*/\nfunction splitCamelCase(text) {\n\treturn text.split(/(?=[A-Z])/).join(' ')\n}\n", "import { ColorScale, getMaxLabelWidth, Menu } from '#dom'\nimport { select } from 'd3-selection'\nimport { rgb } from 'd3-color'\nimport { morigin, dt2label } from '#shared/common.js'\nimport { shapes } from '../model/scatterModel.js'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { ScatterLegendInteractivity } from './scatterLegendInteractivity.js'\nimport { minShapeSize, maxShapeSize } from '../view/scatterView.js'\nimport type { Scatter } from '../scatter.js'\nimport type { ScatterLegendItem } from '../scatterTypes.js'\n\nexport class ScatterLegend {\n\tscatter: Scatter\n\tvm: any\n\tmodel: any\n\tinteractivity: any\n\tlegendInteractivity: ScatterLegendInteractivity\n\tchangeGradientColor: any\n\n\tconstructor(scatter: Scatter) {\n\t\tthis.scatter = scatter\n\t\tthis.vm = scatter.vm\n\t\tthis.model = scatter.model\n\t\tthis.interactivity = scatter.interactivity\n\t\tthis.legendInteractivity = new ScatterLegendInteractivity(scatter)\n\t}\n\t//Dynamically calculate the length of the legend labels\n\tgetLegendLabelWidth(chart, key, svg, size) {\n\t\tconst legend: Map<string, ScatterLegendItem> = chart[`${key}Legend`]\n\t\tif (!legend) return 0\n\t\tconst labels: any = []\n\t\tfor (const [k, v] of legend.entries()) {\n\t\t\tif (k != 'Ref') labels.push(`${k}, n=(${v.sampleCount})`)\n\t\t}\n\t\tlabels.push(this.scatter.config[`${key}TW`]?.term?.name ?? '')\n\n\t\t// Add 70 for icons, paddings, etc.\n\t\tconst width = getMaxLabelWidth(svg, labels, size) + 70\n\t\treturn width\n\t}\n\n\tgetFontSize(chart, legend) {\n\t\tlet fontSize = 0.9\n\t\tif (chart.colorLegend.size < 10 && chart.shapeLegend.size < 10) return fontSize\n\t\tconst top = 20\n\t\t//legend is a Map<string, ScatterLegendItem>\n\t\tif (legend.size > top) {\n\t\t\tfontSize = Math.min(0.9, top / legend.size)\n\t\t\tif (fontSize < 0.7) fontSize = 0.7\n\t\t}\n\t\treturn fontSize\n\t}\n\n\trenderLegend(chart, step) {\n\t\tconst legendG = chart.legendG\n\t\tlegendG.selectAll('*').remove()\n\t\tlet offsetX = 0\n\t\tlet offsetY = 15\n\t\tlet legendHeight = 0\n\t\tif (!this.scatter.config.colorTW && !this.scatter.config.shapeTW && !this.scatter.config.colorColumn) {\n\t\t\tif (this.scatter.config.scaleDotTW) {\n\t\t\t\tchart.scaleG = legendG\n\t\t\t\t\t.append('g')\n\t\t\t\t\t.attr('transform', `translate(${offsetX + 45},${this.scatter.vm.legendHeight - 150})`)\n\t\t\t\tthis.drawScaleDotLegend(chart)\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\tlet title\n\t\tlet title0 = this.scatter.config.term0\n\t\t\t? `${this.scatter.config.term0.term.name + ' ' + chart.id}, n=${chart.cohortSamples.length}`\n\t\t\t: `${chart.cohortSamples.length} ${\n\t\t\t\t\tthis.scatter.config.sampleType ? this.scatter.config.sampleType + 's' : 'samples'\n\t\t\t  }`\n\t\tif (this.model.filterSampleStr) title0 += `, search = ${this.model.filterSampleStr}`\n\t\tlegendG.append('text').attr('x', 0).attr('y', offsetY).text(title0).style('font-weight', 'bold')\n\t\tconst fontSize = this.getFontSize(chart, chart.colorLegend)\n\t\tconst scale = chart.colorLegend.size > 20 || chart.shapeLegend.size > 20 ? 0.6 : 0.7 //if many categories, reduce size\n\n\t\tconst colorG = legendG.append('g').style('font-size', `${fontSize}em`)\n\t\toffsetY += step + 20\n\t\tif (this.scatter.config.colorTW || this.scatter.config.colorColumn) {\n\t\t\ttitle = `${getTitle(\n\t\t\t\tthis.scatter.config.colorTW?.term?.name || this.scatter.config.colorColumn.name,\n\t\t\t\t40,\n\t\t\t\tthis.scatter.config.shapeTW == undefined\n\t\t\t)}`\n\t\t\tconst colorRefCategory = chart.colorLegend.get('Ref')\n\n\t\t\tif (this.scatter.config.colorTW?.term?.type == 'geneVariant' && this.scatter.config.colorTW?.q.type == 'values') {\n\t\t\t\toffsetY = this.renderGeneVariantLegend(\n\t\t\t\t\tchart,\n\t\t\t\t\toffsetX,\n\t\t\t\t\toffsetY,\n\t\t\t\t\tlegendG,\n\t\t\t\t\tthis.scatter.config.colorTW,\n\t\t\t\t\t'category',\n\t\t\t\t\tchart.colorLegend,\n\t\t\t\t\tscale\n\t\t\t\t)\n\t\t\t} else {\n\t\t\t\tthis.addLegendTitle(legendG, title, offsetX, offsetY, this.scatter.config.colorTW, 'COLOR')\n\t\t\t\toffsetY += step\n\n\t\t\t\tif (this.scatter.config.colorTW?.q?.mode === 'continuous') {\n\t\t\t\t\t// Get the current domain values from our color generator\n\t\t\t\t\t// These values represent the minimum and maximum values in our dataset\n\t\t\t\t\tlet [min, max] = chart.colorGenerator.domain()\n\n\t\t\t\t\t// Extract and sort all sample values for our calculations\n\t\t\t\t\t// We filter out any values that are explicitly defined in the term values\n\t\t\t\t\t// This gives us the raw numerical data we need for scaling\n\t\t\t\t\tconst colorValues = chart.colorValues\n\t\t\t\t\tconst scaleG = colorG.append('g')\n\t\t\t\t\t// Create a ColorScale component with enhanced mode functionality\n\t\t\t\t\tconst colorScale = new ColorScale({\n\t\t\t\t\t\t// Basic visual configuration\n\t\t\t\t\t\tholder: scaleG, // SVG group to contain our color scale\n\t\t\t\t\t\tbarheight: 20, // Height of the color gradient bar\n\t\t\t\t\t\tbarwidth: 150, // Width of the color gradient bar\n\t\t\t\t\t\tcolors: [\n\t\t\t\t\t\t\t// Start and end colors for our gradient\n\t\t\t\t\t\t\tthis.scatter.config.startColor[chart.id],\n\t\t\t\t\t\t\tthis.scatter.config.stopColor[chart.id]\n\t\t\t\t\t\t],\n\t\t\t\t\t\tdomain: [min, max], // Current numerical range of our data\n\t\t\t\t\t\tposition: `0, 100`, // Position within the legend\n\t\t\t\t\t\tticks: 4, // Number of tick marks to show\n\t\t\t\t\t\ttickSize: 5, // Size of tick marks\n\t\t\t\t\t\ttopTicks: true, // Display ticks above the gradient bar\n\n\t\t\t\t\t\t// Callback for when gradient colors are changed via color picker\n\t\t\t\t\t\tsetColorsCallback: (val, idx) => {\n\t\t\t\t\t\t\tthis.legendInteractivity.changeGradientColor(chart, val, idx)\n\t\t\t\t\t\t},\n\n\t\t\t\t\t\t// Configuration for our enhanced scaling modes\n\t\t\t\t\t\tnumericInputs: {\n\t\t\t\t\t\t\t// Start with either the chart's current mode or default to 'auto'\n\t\t\t\t\t\t\tcutoffMode: this.scatter.settings.colorScaleMode,\n\t\t\t\t\t\t\t// Default percentile value for percentile mode\n\t\t\t\t\t\t\tdefaultPercentile: this.scatter.settings.colorScalePercentile,\n\n\t\t\t\t\t\t\t// This callback handles all mode changes and updates\n\t\t\t\t\t\t\tcallback: (obj: any) => {\n\t\t\t\t\t\t\t\t// Handle different modes for color scaling\n\t\t\t\t\t\t\t\tif (obj.cutoffMode === 'auto') {\n\t\t\t\t\t\t\t\t\tmin = colorValues[0]\n\t\t\t\t\t\t\t\t\tmax = colorValues[colorValues.length - 1]\n\t\t\t\t\t\t\t\t} else if (obj.cutoffMode === 'fixed') {\n\t\t\t\t\t\t\t\t\tmin = obj.min\n\t\t\t\t\t\t\t\t\tmax = obj.max\n\t\t\t\t\t\t\t\t} else if (obj.cutoffMode === 'percentile') {\n\t\t\t\t\t\t\t\t\tmin = colorValues[0]\n\t\t\t\t\t\t\t\t\tconst index = Math.floor((colorValues.length * obj.percentile) / 100)\n\t\t\t\t\t\t\t\t\tmax = colorValues[index]\n\t\t\t\t\t\t\t\t}\n\n\t\t\t\t\t\t\t\t// Dispatch the updated config\n\t\t\t\t\t\t\t\tthis.scatter.app.dispatch({\n\t\t\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\t\t\tid: this.scatter.id,\n\t\t\t\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\t\t\t\tsampleScatter: {\n\t\t\t\t\t\t\t\t\t\t\t\tcolorScaleMode: obj.cutoffMode,\n\t\t\t\t\t\t\t\t\t\t\t\tcolorScaleMinFixed: obj.cutoffMode === 'fixed' ? min : null,\n\t\t\t\t\t\t\t\t\t\t\t\tcolorScaleMaxFixed: obj.cutoffMode === 'fixed' ? max : null,\n\t\t\t\t\t\t\t\t\t\t\t\tcolorScalePercentile:\n\t\t\t\t\t\t\t\t\t\t\t\t\tobj.cutoffMode === 'percentile' ? obj.percentile : this.scatter.settings.colorScalePercentile\n\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\n\t\t\t\t\t// Initialize the color scale with current settings\n\t\t\t\t\tcolorScale.updateScale()\n\t\t\t\t\toffsetY += step * 2\n\t\t\t\t} else {\n\t\t\t\t\tfor (const [key, category] of chart.colorLegend) {\n\t\t\t\t\t\tif (key == 'Ref') continue\n\t\t\t\t\t\tconst name = key\n\t\t\t\t\t\tconst hidden = this.scatter.config.colorTW?.q.hiddenValues\n\t\t\t\t\t\t\t? key in this.scatter.config.colorTW.q.hiddenValues\n\t\t\t\t\t\t\t: false\n\t\t\t\t\t\tconst [circleG, itemG] = this.addLegendItem(\n\t\t\t\t\t\t\tchart,\n\t\t\t\t\t\t\tcolorG,\n\t\t\t\t\t\t\tcategory,\n\t\t\t\t\t\t\tname,\n\t\t\t\t\t\t\tkey,\n\t\t\t\t\t\t\toffsetX,\n\t\t\t\t\t\t\toffsetY,\n\t\t\t\t\t\t\tscale,\n\t\t\t\t\t\t\thidden\n\t\t\t\t\t\t)\n\t\t\t\t\t\tif (!this.scatter.config.colorColumn) {\n\t\t\t\t\t\t\tcircleG.on('click', e => this.legendInteractivity.onLegendClick(chart, 'colorTW', key, e, category))\n\t\t\t\t\t\t\titemG.on('click', event => this.legendInteractivity.onLegendClick(chart, 'colorTW', key, event, category))\n\t\t\t\t\t\t}\n\t\t\t\t\t\toffsetY += step\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (colorRefCategory?.sampleCount > 0) {\n\t\t\t\toffsetY = offsetY + step\n\t\t\t\tconst titleG = legendG.append('g')\n\t\t\t\ttitleG.append('text').attr('x', offsetX).attr('y', offsetY).text('Reference').style('font-weight', 'bold')\n\n\t\t\t\toffsetY = offsetY + step\n\n\t\t\t\tconst refColorG = legendG.append('g')\n\t\t\t\trefColorG\n\t\t\t\t\t.append('path')\n\t\t\t\t\t.attr('transform', () => `translate(${offsetX - 2}, ${offsetY - 4}) scale(${scale})`)\n\t\t\t\t\t.style('fill', colorRefCategory.color)\n\t\t\t\t\t.attr('d', shapes[0])\n\t\t\t\t\t.style('stroke', rgb(colorRefCategory.color).darker())\n\n\t\t\t\trefColorG.on('click', e => this.legendInteractivity.onLegendClick(chart, 'colorTW', 'Ref', e, colorRefCategory))\n\t\t\t\tconst refText = legendG\n\t\t\t\t\t.append('g')\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr('x', offsetX + 20)\n\t\t\t\t\t.attr('y', offsetY + 4)\n\t\t\t\t\t.text(`n=${colorRefCategory.sampleCount}`)\n\t\t\t\t\t.style('text-decoration', !this.scatter.settings.showRef ? 'line-through' : 'none')\n\t\t\t\t\t.attr('alignment-baseline', 'middle')\n\n\t\t\t\trefText.on('click', e => this.legendInteractivity.onLegendClick(chart, 'colorTW', 'Ref', e, colorRefCategory))\n\t\t\t}\n\t\t\tlegendHeight = offsetY\n\t\t}\n\n\t\tif (this.scatter.config.shapeTW) {\n\t\t\toffsetX = chart.colorLegendWidth\n\t\t\toffsetY = 60\n\t\t\ttitle = `${getTitle(this.scatter.config.shapeTW.term.name, 40)}`\n\t\t\tif (this.scatter.config.shapeTW.term.type == 'geneVariant' && this.scatter.config.shapeTW.q.type == 'values') {\n\t\t\t\tthis.renderGeneVariantLegend(\n\t\t\t\t\tchart,\n\t\t\t\t\toffsetX,\n\t\t\t\t\toffsetY,\n\t\t\t\t\tlegendG,\n\t\t\t\t\tthis.scatter.config.shapeTW,\n\t\t\t\t\t'shape',\n\t\t\t\t\tchart.shapeLegend,\n\t\t\t\t\tscale\n\t\t\t\t)\n\t\t\t} else {\n\t\t\t\tconst shapeG = legendG.append('g').style('font-size', `${this.getFontSize(chart, chart.shapeLegend)}em`)\n\n\t\t\t\tthis.addLegendTitle(legendG, title, offsetX, offsetY, this.scatter.config.shapeTW, 'SHAPE')\n\n\t\t\t\toffsetY += step\n\t\t\t\tconst color = 'gray'\n\t\t\t\tfor (const [key, shape] of chart.shapeLegend) {\n\t\t\t\t\tif (key == 'Ref') continue\n\t\t\t\t\tconst index = shape.shape % shapes.length\n\t\t\t\t\tconst symbol = shapes[index]\n\t\t\t\t\tconst name = key\n\t\t\t\t\tconst count = shape.sampleCount\n\t\t\t\t\tconst hidden = this.scatter.config.shapeTW.q.hiddenValues\n\t\t\t\t\t\t? key in this.scatter.config.shapeTW.q.hiddenValues\n\t\t\t\t\t\t: false\n\t\t\t\t\tconst itemG = shapeG.append('g')\n\n\t\t\t\t\titemG\n\t\t\t\t\t\t.append('path')\n\t\t\t\t\t\t.attr('transform', () => `translate(${offsetX}, ${offsetY - 4}) scale(${scale + 0.1})`) //shapes are a bit smaller than the circle shape\n\t\t\t\t\t\t.style('pointer-events', 'bounding-box')\n\t\t\t\t\t\t.style('fill', color)\n\t\t\t\t\t\t.attr('d', symbol)\n\t\t\t\t\t\t.style('stroke', rgb(color).darker())\n\n\t\t\t\t\titemG\n\t\t\t\t\t\t.append('text')\n\t\t\t\t\t\t.attr('x', offsetX + 25)\n\t\t\t\t\t\t.attr('y', offsetY + 4)\n\t\t\t\t\t\t.text(`${name}, n=${count}`)\n\t\t\t\t\t\t.style('text-decoration', hidden ? 'line-through' : 'none')\n\t\t\t\t\t\t.attr('alignment-baseline', 'middle')\n\t\t\t\t\toffsetY += step\n\t\t\t\t\titemG.on('click', event => this.legendInteractivity.onLegendClick(chart, 'shapeTW', key, event, shape))\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (offsetY > legendHeight) legendHeight = offsetY\n\t\t}\n\n\t\tif (this.scatter.config.scaleDotTW) {\n\t\t\tchart.scaleG = legendG.append('g').attr('transform', `translate(${0},${legendHeight + 50})`)\n\t\t\tthis.drawScaleDotLegend(chart)\n\t\t}\n\t}\n\n\taddLegendItem(chart, g, category, name, key, x, y, scale, hidden = false) {\n\t\tconst circleG = g.append('g')\n\t\tcircleG\n\t\t\t.append('path')\n\t\t\t.attr('d', shapes[0])\n\t\t\t.attr('transform', `translate(${x - 2}, ${y - 4}) scale(${scale})`)\n\t\t\t.style('fill', category.color)\n\t\t\t.style('stroke', rgb(category.color).darker())\n\t\tif (!this.scatter.config.colorColumn)\n\t\t\tcircleG.on('click', e => this.legendInteractivity.onLegendClick(chart, 'colorTW', key, e, category))\n\t\tconst itemG = g.append('g')\n\t\titemG\n\t\t\t.append('text')\n\t\t\t.attr('name', 'sjpp-scatter-legend-label')\n\t\t\t.attr('x', x + 20)\n\t\t\t.attr('y', y + 4)\n\t\t\t.text(`${name}, n=${category.sampleCount}`)\n\t\t\t.style('text-decoration', hidden ? 'line-through' : 'none')\n\t\t\t.attr('alignment-baseline', 'middle')\n\n\t\treturn [circleG, itemG]\n\t}\n\n\taddLegendTitle(G, title, x, y, tw, extraText) {\n\t\tconst _t = G.append('text')\n\t\t\t.attr('data-testid', 'legendTitle') // may replace id with data-testid to avoid conflict with portal\n\t\t\t.attr('x', x)\n\t\t\t.attr('y', y)\n\t\t\t.text(title)\n\t\t\t.style('font-weight', 'bold')\n\t\t//.on('click',()=>{}) TODO allow click on text to get edit/replace options for tw\n\n\t\tif (extraText) {\n\t\t\t_t.append('tspan').text(extraText).attr('dx', 7).style('font-weight', 'normal').attr('font-size', '.7em')\n\t\t}\n\t}\n\n\trenderGeneVariantLegend(chart, offsetX, offsetY, legendG, tw, cname, map, scale) {\n\t\tconst step = 125\n\t\tconst name = tw.term.name.length > 25 ? tw.term.name.slice(0, 25) + '...' : tw.term.name\n\t\tconst title = name\n\t\tconst G = legendG.append('g').style('font-size', '0.9em')\n\n\t\tthis.addLegendTitle(G, title, offsetX, offsetY, tw, cname == 'category' ? 'COLOR' : 'SHAPE')\n\n\t\toffsetX += step\n\t\tconst mutations: any = []\n\t\tfor (const value of map.values())\n\t\t\tif (value.mutation)\n\t\t\t\t//if no mutation is Ref\n\t\t\t\tmutations.push(value.mutation)\n\n\t\tconst mutationsLabels = new Set()\n\t\toffsetY += 10\n\t\tfor (const mutation of mutations) {\n\t\t\tconst dt = mutation.dt\n\t\t\tconst origin = morigin[mutation.origin]?.label\n\t\t\tconst dtlabel = origin ? `${origin[0]} ${dt2label[dt]}` : dt2label[dt]\n\t\t\tif (!mutationsLabels.has(dtlabel)) mutationsLabels.add(dtlabel)\n\t\t\telse continue\n\t\t\toffsetY += 15\n\n\t\t\tG.append('text')\n\t\t\t\t.attr('x', offsetX - step)\n\t\t\t\t.attr('y', offsetY)\n\t\t\t\t.text(origin ? `${origin} ${dt2label[dt]}` : dt2label[dt])\n\t\t\t\t.style('font-weight', 'bold')\n\t\t\toffsetY += 25\n\t\t\tfor (const [key, category] of map) {\n\t\t\t\tif (key == 'Ref') continue\n\t\t\t\tif (!key.includes(dtlabel)) continue\n\t\t\t\tconst [mkey, cat_dtlabel] = key.split(', ')\n\n\t\t\t\tif (!cat_dtlabel.includes(dtlabel)) continue\n\t\t\t\tconst itemG = G.append('g')\n\t\t\t\tif (cname == 'shape') {\n\t\t\t\t\tconst index = category.shape % shapes.length\n\t\t\t\t\titemG\n\t\t\t\t\t\t.append('path')\n\t\t\t\t\t\t.attr('transform', () => `translate(${offsetX - step - 2}, ${offsetY - 8}) scale(${scale})`)\n\t\t\t\t\t\t.style('fill', 'gray')\n\t\t\t\t\t\t.style('pointer-events', 'bounding-box')\n\t\t\t\t\t\t.attr('d', shapes[index])\n\t\t\t\t\t\t.style('stroke', rgb('gray').darker())\n\t\t\t\t\titemG.on('click', e => this.legendInteractivity.onLegendClick(chart, 'shapeTW', key, e, category))\n\t\t\t\t} else {\n\t\t\t\t\titemG\n\t\t\t\t\t\t.append('path')\n\t\t\t\t\t\t.attr('d', shapes[0])\n\t\t\t\t\t\t.attr('transform', `translate(${-2}, ${offsetY - 8}) scale(${scale})`)\n\t\t\t\t\t\t.style('fill', category.color)\n\t\t\t\t\t\t.style('stroke', rgb(category.color).darker())\n\t\t\t\t\titemG.on('click', e => this.legendInteractivity.onLegendClick(chart, 'colorTW', key, e, category))\n\t\t\t\t}\n\t\t\t\tconst hidden = tw.q.hiddenValues ? key in tw.q.hiddenValues : false\n\n\t\t\t\tconst text = mkey.toUpperCase() + (key.includes(dtlabel) ? `, n=${category.sampleCount}` : '')\n\t\t\t\tG.append('g')\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr('x', offsetX - step + 24)\n\t\t\t\t\t.attr('y', offsetY + 4)\n\t\t\t\t\t.attr('name', 'sjpp-scatter-legend-label')\n\t\t\t\t\t.style('text-decoration', hidden ? 'line-through' : 'none')\n\t\t\t\t\t.text(text)\n\t\t\t\t\t.on('click', event =>\n\t\t\t\t\t\tthis.legendInteractivity.onLegendClick(\n\t\t\t\t\t\t\tchart,\n\t\t\t\t\t\t\tcname == 'shape' ? 'shapeTW' : 'colorTW',\n\t\t\t\t\t\t\tkey,\n\t\t\t\t\t\t\tevent,\n\t\t\t\t\t\t\tcategory\n\t\t\t\t\t\t)\n\t\t\t\t\t)\n\n\t\t\t\toffsetY += 25\n\t\t\t}\n\t\t}\n\n\t\treturn offsetY\n\t}\n\n\tdrawScaleDotLegend(chart) {\n\t\tconst scaleG = chart.scaleG\n\t\tscaleG.selectAll('*').remove()\n\t\tconst width = 70\n\n\t\tconst minScale = this.scatter.settings.minShapeSize / 3\n\t\tconst maxScale = this.scatter.settings.maxShapeSize / 3\n\t\tconst order = this.scatter.settings.scaleDotOrder\n\t\tconst isAscending = order == 'Ascending'\n\n\t\tconst titleG = scaleG.append('g')\n\n\t\ttitleG.append('text').text(this.scatter.config.scaleDotTW.term.name).style('font-weight', 'bold')\n\t\tconst start = roundValueAuto(chart.ranges.scaleMin).toString()\n\t\tconst end = roundValueAuto(chart.ranges.scaleMax).toString()\n\t\tconst x = 30\n\t\tconst y = 40\n\t\tconst defaultSize = 16 //icons default size\n\n\t\tconst minSize = defaultSize * minScale\n\t\tconst maxSize = defaultSize * maxScale\n\t\tconst minRadius = minSize / 2\n\t\tconst maxRadius = maxSize / 2\n\t\tconst minG = scaleG.append('g').attr('transform', `translate(${x},${y})`)\n\t\tconst shift = 30\n\t\tminG\n\t\t\t.append('path')\n\t\t\t.attr('d', shapes[0])\n\t\t\t.style('fill', '#aaa')\n\t\t\t.style('stroke', '#aaa')\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t`translate(${isAscending ? -minRadius : -maxRadius}, ${isAscending ? -minRadius : -maxRadius}) scale(${\n\t\t\t\t\tisAscending ? minScale : maxScale\n\t\t\t\t})`\n\t\t\t)\n\n\t\tconst maxG = scaleG.append('g').attr('transform', `translate(${width + x},${y})`)\n\n\t\tmaxG\n\t\t\t.append('path')\n\t\t\t.attr('d', shapes[0])\n\t\t\t.style('fill', '#aaa')\n\t\t\t.style('stroke', '#aaa')\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t`translate(${isAscending ? -maxRadius : -minRadius}, ${isAscending ? -maxRadius : -minRadius}) scale(${\n\t\t\t\t\tisAscending ? maxScale : minScale\n\t\t\t\t})`\n\t\t\t)\n\n\t\tminG\n\t\t\t.append('text')\n\t\t\t.attr('x', isAscending ? -minRadius - shift : -maxRadius - shift)\n\t\t\t.attr('y', 5)\n\t\t\t.style('font-size', '.8em')\n\t\t\t.attr('text-anchor', 'start')\n\t\t\t.text(start)\n\n\t\tmaxG\n\t\t\t.append('text')\n\t\t\t.attr('x', isAscending ? maxSize + 5 : minSize + 5)\n\t\t\t.attr('y', 5)\n\t\t\t.style('font-size', '.8em')\n\t\t\t.text(end)\n\n\t\tminG\n\t\t\t.append('line')\n\t\t\t.attr('x1', 0)\n\t\t\t.attr('y1', isAscending ? minRadius : maxRadius)\n\t\t\t.attr('x2', width)\n\t\t\t.attr('y2', isAscending ? maxRadius : minRadius)\n\t\t\t.style('stroke', '#aaa')\n\t\tminG\n\t\t\t.append('line')\n\t\t\t.attr('x1', 0)\n\t\t\t.attr('y1', isAscending ? -minRadius : -maxRadius)\n\t\t\t.attr('x2', width)\n\t\t\t.attr('y2', isAscending ? -maxRadius : -minRadius)\n\t\t\t.style('stroke', '#aaa')\n\n\t\tscaleG\n\t\t\t.append('rect')\n\t\t\t.attr('width', 110 * this.scatter.zoom)\n\t\t\t.attr('height', 50)\n\t\t\t.attr('fill', 'transparent')\n\t\t\t.on('click', e => {\n\t\t\t\tconst menu = new Menu({ padding: '3px' })\n\t\t\t\tconst div = menu.d\n\t\t\t\tdiv.append('label').text('Min:')\n\t\t\t\tconst minInput: any = div\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'number')\n\t\t\t\t\t.attr('min', minShapeSize)\n\t\t\t\t\t.attr('step', '0.5')\n\t\t\t\t\t.attr('max', maxShapeSize)\n\t\t\t\t\t.style('width', '50px')\n\t\t\t\t\t.attr('value', this.scatter.settings.minShapeSize)\n\t\t\t\t\t.on('change', () => {\n\t\t\t\t\t\tconst value = parseFloat(minInput.node().value)\n\t\t\t\t\t\tthis.scatter.config.settings.sampleScatter.minShapeSize = value\n\t\t\t\t\t\tthis.scatter.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.scatter.id,\n\t\t\t\t\t\t\tconfig: this.scatter.config\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\tdiv.append('label').text('Max:')\n\t\t\t\tconst maxInput: any = div\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.attr('type', 'number')\n\t\t\t\t\t.attr('step', '0.5')\n\t\t\t\t\t.attr('min', minShapeSize)\n\t\t\t\t\t.attr('max', maxShapeSize)\n\t\t\t\t\t.style('width', '50px')\n\t\t\t\t\t.attr('value', this.scatter.settings.maxShapeSize)\n\t\t\t\t\t.on('change', () => {\n\t\t\t\t\t\tconst value: any = parseFloat(maxInput.node().value)\n\t\t\t\t\t\tthis.scatter.config.settings.sampleScatter.maxShapeSize = value\n\t\t\t\t\t\tthis.scatter.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.scatter.id,\n\t\t\t\t\t\t\tconfig: this.scatter.config\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\tconst divRadios = menu.d.append('div')\n\t\t\t\tdivRadios.append('label').text('Order: ')\n\t\t\t\tconst data = ['Ascending', 'Descending']\n\t\t\t\tdivRadios\n\t\t\t\t\t.selectAll('input')\n\t\t\t\t\t.data(data)\n\t\t\t\t\t.enter()\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.each((text, i, divs) => {\n\t\t\t\t\t\tconst div = select(divs[i])\n\t\t\t\t\t\tconst input = div\n\t\t\t\t\t\t\t.append('input')\n\t\t\t\t\t\t\t.attr('type', 'radio')\n\t\t\t\t\t\t\t.attr('name', 'order')\n\t\t\t\t\t\t\t.attr('id', text)\n\t\t\t\t\t\t\t.attr('value', text)\n\t\t\t\t\t\t\t.property('checked', text => text == order)\n\n\t\t\t\t\t\tdiv.append('label').text(text).attr('for', text)\n\t\t\t\t\t\tinput.on('change', e => {\n\t\t\t\t\t\t\tthis.changeScaleDotOrder(e.target.value)\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\tmenu.showunder(e.target)\n\t\t\t})\n\t}\n\n\tchangeScaleDotOrder(order) {\n\t\tthis.scatter.config.settings.sampleScatter.scaleDotOrder = order\n\t\tthis.scatter.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.scatter.id,\n\t\t\tconfig: this.scatter.config\n\t\t})\n\t}\n}\n\nexport function getTitle(name, size = 30, complete = false) {\n\tif (name.length > size && !complete) name = name.slice(0, size) + '...'\n\treturn name\n}\n", "import { mclass } from '#shared/common.js'\nimport { shapesArray } from '../../../dom/shapes.js'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { getDateStrFromNumber } from '#shared/terms.js'\nimport { rgb } from 'd3-color'\nimport type { Scatter } from '../scatter.js'\nimport { table2col } from '#dom'\nimport { getCoordinate } from '../model/scatterModel.ts'\n\nexport class ScatterTooltip {\n\tscatter: Scatter\n\tview: any\n\tchart: any\n\tsamples!: any[]\n\ttree!: any[]\n\ttableDiv: any\n\tonClick: boolean\n\tdisplaySample!: boolean\n\tparentCategories!: string[]\n\tsearchMenu: any\n\tsamplesData: any\n\tchartDiv: any\n\tlevel: any\n\tparentTW: any\n\n\tconstructor(scatter: Scatter) {\n\t\tthis.scatter = scatter\n\t\tthis.view = scatter.view\n\t\tthis.onClick = false\n\t}\n\n\tshowTooltip(event, chart) {\n\t\tif (this.scatter.config.lassoOn) return\n\t\tthis.chart = chart\n\t\tconst onClick = event.type == 'click'\n\t\tthis.onClick = onClick\n\t\tif (onClick) this.scatter.interactivity.searchMenu?.hide()\n\t\tif (!(event.target.tagName == 'path' && event.target.getAttribute('name') == 'serie')) {\n\t\t\tif (this.onClick && onClick) {\n\t\t\t\tthis.onClick = false\n\t\t\t\tthis.view.dom.tooltip.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (!onClick) {\n\t\t\t\tthis.view.dom.tooltip.hide()\n\t\t\t} //dont hide current tooltip if mouse moved away, may want to scroll\n\t\t\treturn\n\t\t}\n\t\tthis.showSampleTooltip(event.target.__data__, event.clientX, event.clientY, chart)\n\t}\n\n\tshowSampleTooltip(s2, x, y, chart) {\n\t\tthis.chart = chart\n\t\tthis.displaySample = 'sample' in s2\n\t\tconst threshold = 5 / this.scatter.zoom //Threshold should consider the zoom\n\t\t/** Avoid calculating the min and max for x and y\n\t\t * multiple times in the distance function.\n\t\t * Supply them as parameters.*/\n\t\tconst xMin = chart.xAxisScale.invert(0)\n\t\tconst xMax = chart.xAxisScale.invert(chart.width)\n\t\tconst yMin = chart.yAxisScale.invert(chart.height)\n\t\tconst yMax = chart.yAxisScale.invert(0)\n\t\tconst samples = chart.data.samples.filter(s => {\n\t\t\tconst dist = distance(s.x, s.y, s2.x, s2.y, chart, xMin, xMax, yMin, yMax)\n\t\t\tif (!('sampleId' in s) && (!this.scatter.settings.showRef || this.scatter.settings.refSize == 0)) return false\n\t\t\treturn this.scatter.model.getOpacity(s) > 0 && dist < threshold\n\t\t})\n\t\tthis.samples = samples\n\t\tsamples.sort((s1, s2) => {\n\t\t\tif (!('sampleId' in s1)) return 1\n\t\t\tif (this.scatter.config.term) {\n\t\t\t\t//coordinates from terms\n\t\t\t\tif (s1.x < s2.x) return -1\n\t\t\t\tif (s1.x > s2.x) return 1\n\t\t\t\tif (s1.y < s2.y) return -1\n\t\t\t\treturn 1\n\t\t\t}\n\n\t\t\tif (this.scatter.config.colorTW) {\n\t\t\t\tif (this.scatter.config.colorTW.term.type == 'categorical') {\n\t\t\t\t\tif (s1.category.includes(mclass.WT.label) || s1.category.includes(mclass.Blank.label)) return 1\n\t\t\t\t} // numeric\n\t\t\t\telse {\n\t\t\t\t\tif (s1.category < s2.category) return -1\n\t\t\t\t\telse if (s1.category > s2.category) return 1\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (s1.shape.includes(mclass.WT.label) || s1.shape.includes(mclass.Blank.label)) return 1\n\n\t\t\treturn -1\n\t\t})\n\t\tif (samples.length == 0) return\n\t\tthis.tree = []\n\t\tconst showCoords = this.scatter.config.term ? true : false\n\n\t\t//Building tree\n\t\tfor (const sample of samples) {\n\t\t\tconst id = `${roundValueAuto(sample.x)},${roundValueAuto(sample.y)}`\n\t\t\tlet node = this.tree.find(item => item.id == id)\n\t\t\tif (!node) {\n\t\t\t\tnode = { id, parentId: null, samples: [sample], level: 1, category: null, children: [] }\n\t\t\t\tthis.tree.push(node)\n\t\t\t\tif (showCoords) {\n\t\t\t\t\tconst xvalue = this.getCategoryValue('x', sample, this.scatter.config.term)\n\t\t\t\t\tconst xnode: any = {\n\t\t\t\t\t\tid: xvalue,\n\t\t\t\t\t\tparentId: id,\n\t\t\t\t\t\tsamples: [sample],\n\t\t\t\t\t\tlevel: 2,\n\t\t\t\t\t\tcategory: this.scatter.config.term.term.name,\n\t\t\t\t\t\tchildren: [],\n\t\t\t\t\t\tvalue: xvalue\n\t\t\t\t\t}\n\t\t\t\t\tthis.tree.push(xnode)\n\t\t\t\t\tnode.children.push(xnode)\n\t\t\t\t\tconst yvalue = this.getCategoryValue('y', sample, this.scatter.config.term2)\n\t\t\t\t\tconst ynode = {\n\t\t\t\t\t\tid: `${yvalue}${xvalue}`,\n\t\t\t\t\t\tparent: xnode,\n\t\t\t\t\t\tparentId: xvalue,\n\t\t\t\t\t\tsamples: [sample],\n\t\t\t\t\t\tlevel: 3,\n\t\t\t\t\t\tcategory: this.scatter.config.term2.term.name,\n\t\t\t\t\t\tchildren: [],\n\t\t\t\t\t\tvalue: yvalue\n\t\t\t\t\t}\n\t\t\t\t\txnode.children.push(ynode)\n\t\t\t\t\tthis.tree.push(ynode)\n\t\t\t\t\tnode.xnode = xnode\n\t\t\t\t\tnode.ynode = ynode\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tnode.samples.push(sample)\n\t\t\t\tif (showCoords) {\n\t\t\t\t\tnode.xnode.samples.push(sample)\n\t\t\t\t\tnode.ynode.samples.push(sample)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.level = showCoords ? 4 : 2 //current level after adding the parent categories\n\t\tthis.parentCategories = showCoords ? ['y', 'x', ''] : ['']\n\t\tif (showCoords) this.parentTW = this.scatter.config.term\n\t\telse this.parentTW = null\n\t\tif (this.scatter.config.colorTW) this.addNodes('category', this.scatter.config.colorTW)\n\t\tif (this.scatter.config.shapeTW) this.addNodes('shape', this.scatter.config.shapeTW)\n\t\tif (this.scatter.config.scaleDotTW) this.addNodes('scale', this.scatter.config.scaleDotTW)\n\t\tthis.view.dom.tooltip.clear()\n\t\t//Rendering tooltip\n\t\tconst div = this.view.dom.tooltip.d\n\t\tif (samples.length > 1)\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('color', '#aaa')\n\t\t\t\t.style('font-weight', 'bold')\n\t\t\t\t.html(`&nbsp;&nbsp;&nbsp;${samples.length} Samples`)\n\t\tconst tableDiv = div.append('div').style('max-height', '500px').style('overflow-y', 'scroll')\n\t\tif (samples.length > 4) tableDiv.attr('class', 'sjpp_show_scrollbar')\n\t\tthis.tableDiv = tableDiv\n\t\tconst nodes = this.tree.filter(node => (showCoords ? node.level == 1 : node.level == 2))\n\t\tif (showCoords)\n\t\t\tfor (const node of nodes) {\n\t\t\t\tif (samples.length > 1) tableDiv.append('div').style('padding', '2px')\n\t\t\t\tfor (const child of node.children) {\n\t\t\t\t\tthis.addCategory(child, null)\n\t\t\t\t}\n\t\t\t}\n\t\telse\n\t\t\tfor (const node of nodes) {\n\t\t\t\tif (samples.length > 1) tableDiv.append('div').style('padding', '2px')\n\t\t\t\tthis.addCategory(node, null)\n\t\t\t}\n\n\t\tthis.view.dom.tooltip.show(x, y, true, false)\n\t}\n\n\tgetTW(category) {\n\t\tswitch (category) {\n\t\t\tcase 'category':\n\t\t\t\treturn this.scatter.config.colorTW\n\t\t\tcase 'shape':\n\t\t\t\treturn this.scatter.config.shapeTW\n\t\t\tcase 'scale':\n\t\t\t\treturn this.scatter.config.scaleDotTW\n\t\t\tcase 'x':\n\t\t\t\treturn this.scatter.config.term\n\t\t\tcase 'y':\n\t\t\t\treturn this.scatter.config.term2\n\t\t\tdefault:\n\t\t\t\treturn null\n\t\t}\n\t}\n\n\taddCategory(node, table) {\n\t\tconst samples = this.samples\n\t\tconst chart = this.chart\n\t\tconst tw = this.getTW(node.category)\n\t\tnode.added = true\n\t\tconst hasDiscoPlot = this.scatter.state.termdbConfig.queries?.singleSampleMutation\n\t\tconst hasMetArrayPlot = this.scatter.state.termdbConfig.queries?.singleSampleGenomeQuantification\n\t\tconst div = this.tableDiv.append('div')\n\t\tif (!table) table = table2col({ holder: div, disableScroll: true, cellPadding: '5px' })\n\t\tconst sample = node.samples[0]\n\t\tif (sample.category != 'Ref') {\n\t\t\tconst [tdlabel, td] = table.addRow()\n\t\t\tconst showIcon = tw != null && (tw == this.scatter.config.colorTW || tw == this.scatter.config.shapeTW)\n\t\t\tlet label = tw ? tw.term.name : node.category\n\t\t\tif (samples.length > 1 && !this.displaySample) label = label + ` (${node.samples.length})`\n\t\t\ttdlabel.text(label)\n\n\t\t\tif (showIcon) {\n\t\t\t\tconst color =\n\t\t\t\t\ttw == this.scatter.config.colorTW\n\t\t\t\t\t\t? this.scatter.model.getColor(sample, chart)\n\t\t\t\t\t\t: this.scatter.config.colorTW\n\t\t\t\t\t\t? 'gray'\n\t\t\t\t\t\t: this.scatter.settings.defaultColor\n\t\t\t\tconst index =\n\t\t\t\t\ttw == this.scatter.config.colorTW\n\t\t\t\t\t\t? chart.shapeLegend.get('Ref').shape % shapesArray.length\n\t\t\t\t\t\t: chart.shapeLegend.get(sample.shape).shape % shapesArray.length\n\t\t\t\tconst shape = shapesArray[index]\n\t\t\t\tlet fontColor = 'black'\n\t\t\t\tconst whiteColor = rgb('white').toString()\n\n\t\t\t\tif (tw?.term.type == 'geneVariant' && tw.q.type == 'values') {\n\t\t\t\t\tfor (const id in mclass) {\n\t\t\t\t\t\tconst class_info = mclass[id]\n\t\t\t\t\t\tif (node.value.includes(class_info.label)) {\n\t\t\t\t\t\t\tif (rgb(class_info.color).toString() != whiteColor) fontColor = class_info.color\n\t\t\t\t\t\t\tnode.value = this.getCategoryValue(node.category, sample, tw, true)\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tif (this.onClick) {\n\t\t\t\t\t\ttd.append('button')\n\t\t\t\t\t\t\t.style('float', 'right')\n\t\t\t\t\t\t\t.text('Lollipop')\n\t\t\t\t\t\t\t.on('click', async () => {\n\t\t\t\t\t\t\t\tawait this.scatter.interactivity.openLollipop(label)\n\t\t\t\t\t\t\t\tthis.scatter.dom.tip.hide()\n\t\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tconst chars = node.value.toString().length\n\t\t\t\tconst width = chars * 9 + 60\n\t\t\t\tconst svg = td.append('svg').attr('width', width).attr('height', '25px')\n\t\t\t\tconst g = svg.append('g').attr('transform', 'translate(0, 14)')\n\t\t\t\tg.append('path')\n\t\t\t\t\t.attr('d', shape)\n\t\t\t\t\t.attr('fill', color)\n\t\t\t\t\t.attr('stroke', '#aaa')\n\t\t\t\t\t.attr('transform', 'translate(0, -4) scale(0.6)')\n\t\t\t\tconst text = g.append('text').attr('x', 15).attr('y', 6).attr('font-size', '0.9em')\n\t\t\t\ttext.append('tspan').text(node.value).attr('fill', fontColor)\n\t\t\t} else td.text(`${node.value}`)\n\t\t}\n\n\t\tfor (const child of node.children) if (!child.added) this.addCategory(child, table)\n\t\tif (node.children.length == 0 && this.displaySample) {\n\t\t\tfor (const sample of node.samples) {\n\t\t\t\tif ('info' in sample)\n\t\t\t\t\tfor (const [k, v] of Object.entries(sample.info)) {\n\t\t\t\t\t\tconst [tdlabel, td] = table.addRow()\n\t\t\t\t\t\ttdlabel.text(k)\n\t\t\t\t\t\ttd.text(v)\n\t\t\t\t\t}\n\n\t\t\t\tconst [tdlabel, td] = table.addRow()\n\t\t\t\ttdlabel.text('Sample')\n\t\t\t\ttd.text(sample.sample)\n\t\t\t\tif ('sampleId' in sample && this.onClick) {\n\t\t\t\t\tif (this.scatter.state.currentCohortChartTypes.includes('sampleView')) {\n\t\t\t\t\t\ttd.append('button')\n\t\t\t\t\t\t\t.style('float', 'right')\n\t\t\t\t\t\t\t.text('Sample view')\n\t\t\t\t\t\t\t.on('click', () => this.scatter.interactivity.openSampleView(sample))\n\t\t\t\t\t}\n\t\t\t\t\tif (hasDiscoPlot)\n\t\t\t\t\t\ttd.append('button')\n\t\t\t\t\t\t\t.style('float', 'right')\n\t\t\t\t\t\t\t.text('Disco')\n\t\t\t\t\t\t\t.on('click', async () => this.scatter.interactivity.openDiscoPlot(sample))\n\n\t\t\t\t\tif (hasMetArrayPlot)\n\t\t\t\t\t\ttd.append('button')\n\t\t\t\t\t\t\t.style('float', 'right')\n\t\t\t\t\t\t\t.text('Met Array')\n\t\t\t\t\t\t\t.on('click', async () => this.scatter.interactivity.openMetArray(sample))\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\taddNodes(category, tw) {\n\t\tfor (const sample of this.samples) {\n\t\t\tconst value = this.getCategoryValue(category, sample, tw)\n\t\t\tlet parentId = ''\n\t\t\tfor (const pc of this.parentCategories) parentId += this.getCategoryValue(pc, sample, this.parentTW)\n\t\t\tconst id = value + parentId\n\t\t\tlet node = this.tree.find(item => item.id == id && item.parentId == parentId)\n\t\t\tconst parent = this.tree.find(item => item.id == parentId)\n\t\t\tif (!node) {\n\t\t\t\tnode = { id, parentId, samples: [], level: this.level, category, children: [], value }\n\t\t\t\tthis.tree.push(node)\n\t\t\t}\n\t\t\tnode.samples.push(sample)\n\t\t\tif (parent) parent.children.push(node)\n\t\t}\n\t\tthis.parentCategories.unshift(category)\n\t\tthis.parentTW = tw\n\t\tthis.level++\n\t}\n\n\tgetCategoryValue(category, d, tw, includeMutation = false) {\n\t\tif (category == '') return ''\n\t\tlet value = d[category]\n\t\tif (tw?.term.type == 'geneVariant' && tw.q?.type == 'values') {\n\t\t\tconst mutation = value.split(', ')[0]\n\t\t\tfor (const id in mclass) {\n\t\t\t\tconst class_info = mclass[id]\n\t\t\t\tif (mutation == class_info.label) {\n\t\t\t\t\tconst mname = d.cat_info[category].find(m => m.class == class_info.key).mname\n\t\t\t\t\tif (mname && includeMutation) value = `${mname} ${value}`\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (tw?.term.type == 'date') value = getDateStrFromNumber(value)\n\t\telse if (typeof value == 'number' && value % 1 != 0) value = roundValueAuto(value)\n\t\treturn value\n\t}\n}\n\nexport function distance(x1: number, y1: number, x2: number, y2: number, chart: any, xMin, xMax, yMin, yMax): number {\n\tconst convertedX1 = getCoordinate(x1, xMin, xMax)\n\tconst convertedX2 = getCoordinate(x2, xMin, xMax)\n\tconst convertedY1 = getCoordinate(y1, yMin, yMax)\n\tconst convertedY2 = getCoordinate(y2, yMin, yMax)\n\tconst x = chart.xAxisScale(convertedX2) - chart.xAxisScale(convertedX1)\n\tconst y = chart.yAxisScale(convertedY2) - chart.yAxisScale(convertedY1)\n\tconst distance = Math.sqrt(Math.pow(x, 2) + Math.pow(y, 2))\n\treturn distance\n}\n", "import { zoom as d3zoom } from 'd3-zoom'\nimport { icons as icon_functions } from '#dom'\nimport type { Scatter } from '../scatter.js'\nimport { zoomIdentity } from 'd3-zoom'\n\nexport class ScatterZoom {\n\tscatter: Scatter\n\tzoomD3: any\n\tdragD3: any\n\tzoom: any\n\n\tconstructor(scatter: Scatter) {\n\t\tthis.zoom = 1\n\t\tthis.scatter = scatter\n\t\tthis.zoomD3 = d3zoom()\n\t\t\t.scaleExtent([0.1, 10])\n\t\t\t.on('zoom', event => this.handleZoom(event.transform))\n\t\t\t.filter(event => {\n\t\t\t\tif (event.type === 'wheel') return event.ctrlKey\n\t\t\t\treturn true\n\t\t\t})\n\t\t\t.on('end', async event => {\n\t\t\t\tthis.scatter.transform = event.transform\n\t\t\t\tthis.scatter.zoom = event.transform.k\n\t\t\t\tif (this.scatter.settings.saveZoomTransform) this.saveZoomTransform()\n\t\t\t})\n\t}\n\n\tasync saveZoomTransform() {\n\t\tconst transform = this.scatter.transform?.toString() || null\n\t\tthis.scatter.app.dispatch({ type: 'plot_edit', id: this.scatter.id, config: { transform } })\n\t}\n\n\tinitZoom(toolsDiv) {\n\t\tthis.zoomD3.scaleExtent([0.1, this.scatter.config.scaleDotTW ? 4 : 10])\n\n\t\ttoolsDiv.selectAll('*').remove()\n\t\tconst display = 'block'\n\t\tconst resetDiv = toolsDiv\n\t\t\t.insert('div')\n\t\t\t.style('display', display)\n\t\t\t.style('margin', '15px 10px')\n\t\t\t.attr('name', 'sjpp-reset-btn') //For unit tests\n\t\ticon_functions['restart'](resetDiv, { handler: () => this.resetToIdentity(), title: 'Reset plot to defaults' })\n\n\t\tconst zoomInDiv = toolsDiv\n\t\t\t.insert('div')\n\t\t\t.style('display', display)\n\t\t\t.style('margin', '15px 10px')\n\t\t\t.attr('name', 'sjpp-zoom-in-btn') //For unit tests\n\t\ticon_functions['zoomIn'](zoomInDiv, {\n\t\t\thandler: () => this.zoomIn(),\n\t\t\ttitle: 'Zoom in. You can also zoom in pressing the Ctrl key and using the mouse wheel'\n\t\t})\n\t\tconst zoomOutDiv = toolsDiv\n\t\t\t.insert('div')\n\t\t\t.style('display', display)\n\t\t\t.style('margin', '15px 10px')\n\t\t\t.attr('name', 'sjpp-zoom-out-btn') //For unit tests\n\t\ticon_functions['zoomOut'](zoomOutDiv, {\n\t\t\thandler: () => this.zoomOut(),\n\t\t\ttitle: 'Zoom out. You can also zoom out pressing the Ctrl key and using the mouse wheel'\n\t\t})\n\n\t\tfor (const chart of this.scatter.model.charts) {\n\t\t\tchart.mainG.call(this.zoomD3)\n\t\t}\n\n\t\tif (this.scatter.config.scaleDotTW && this.zoom > 4) this.resetToIdentity()\n\t}\n\n\thandleZoom(transform) {\n\t\tthis.zoom = transform.scale(1).k\n\t\tfor (const chart of this.scatter.model.charts) {\n\t\t\t// create new scale ojects based on event\n\t\t\tconst new_xScale = transform.rescaleX(chart.xAxisScale)\n\t\t\tconst new_yScale = transform.rescaleY(chart.yAxisScale)\n\t\t\tchart.serie.attr('transform', transform)\n\t\t\tchart.xAxis.call(chart.axisBottom.scale(new_xScale))\n\t\t\tchart.yAxis.call(chart.axisLeft.scale(new_yScale))\n\t\t\tif (this.scatter.config.lassoOn)\n\t\t\t\tchart.lasso.selectedItems().attr('transform', c => this.scatter.model.transform(chart, c, 1.2))\n\t\t\tif (this.scatter.config.scaleDotTW) this.scatter.vm.legendvm.drawScaleDotLegend(chart)\n\t\t}\n\t}\n\n\tzoomIn() {\n\t\tthis.zoom = this.zoom * 1.2\n\t\tif (!this.scatter.model.is2DLarge)\n\t\t\tfor (const chart of this.scatter.model.charts) this.zoomD3.scaleBy(chart.mainG.transition().duration(500), 1.2)\n\t}\n\n\tzoomOut() {\n\t\tthis.zoom = this.zoom * 0.8\n\t\tif (!this.scatter.model.is2DLarge)\n\t\t\tfor (const chart of this.scatter.model.charts) this.zoomD3.scaleBy(chart.mainG.transition().duration(500), 0.8)\n\t}\n\n\tresetToIdentity() {\n\t\tthis.zoom = 1\n\t\tif (!this.scatter.model.is2DLarge)\n\t\t\tfor (const chart of this.scatter.model.charts)\n\t\t\t\tchart.mainG.transition().duration(500).call(this.zoomD3.transform, zoomIdentity)\n\t}\n}\n", "import { getMaxLabelWidth } from '#dom'\nimport { select } from 'd3-selection'\nimport { line } from 'd3'\nimport { ScatterLegend } from './scatterLegend.js'\nimport { ScatterTooltip } from './scatterTooltip.js'\nimport { getTitle } from './scatterLegend.js'\nimport { ScatterZoom } from './scatterZoom.js'\nimport type { Scatter } from '../scatter.js'\n\nexport class ScatterViewModelBase {\n\tscatter: Scatter\n\tview: any\n\tmodel: any\n\tinteractivity: any\n\tlegendvm: ScatterLegend\n\tscatterTooltip: ScatterTooltip\n\tscatterZoom: ScatterZoom\n\tcanvas: any\n\tstep: any\n\tlegendHeight: any\n\n\tconstructor(scatter: Scatter) {\n\t\tthis.scatter = scatter\n\t\tthis.view = scatter.view\n\t\tthis.model = scatter.model\n\t\tthis.interactivity = scatter.interactivity\n\t\tthis.legendvm = new ScatterLegend(scatter)\n\t\tthis.scatterTooltip = new ScatterTooltip(scatter)\n\t\tthis.scatterZoom = new ScatterZoom(scatter)\n\t}\n\n\trender() {\n\t\tconst chartDivs = this.view.dom.mainDiv.selectAll(':scope > div').data(this.model.charts, chart => chart?.id)\n\t\tchartDivs.exit().remove()\n\t\tchartDivs.each((chart, i, divs) => {\n\t\t\tconst div = select(divs[i])\n\t\t\tthis.renderChart(chart, div)\n\t\t})\n\t\tchartDivs\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.each((chart, i, divs) => {\n\t\t\t\tconst div = select(divs[i])\n\t\t\t\tthis.renderChart(chart, div)\n\t\t\t})\n\t\tif (!this.model.charts?.length) {\n\t\t\t// no data\n\t\t\tthis.view.dom.bannerDiv.html(`<span>No visible scatter plot data to render</span>`).style('display', 'block')\n\t\t\treturn\n\t\t} else {\n\t\t\tthis.view.dom.bannerDiv.style('display', 'none')\n\t\t}\n\t}\n\n\trenderChart(chart, div, removePrevious = true) {\n\t\tconst s = this.scatter.settings\n\t\tdiv.style('opacity', 0).style('display', 'inline-block')\n\t\tdiv.on('mouseover', event => {\n\t\t\tif (!this.scatterTooltip.onClick) this.scatterTooltip.showTooltip(event, chart)\n\t\t})\n\t\tdiv.on('click', event => this.scatterTooltip.showTooltip(event, chart))\n\n\t\tchart.svg = div.select('svg').empty() ? div.append('svg') : div.select('svg')\n\t\tthis.renderSVG(chart, s, removePrevious)\n\t\tdiv.transition().duration(s.duration).style('opacity', 1)\n\t\tchart.chartDiv = div\n\t}\n\n\tasync renderSVG(chart, s, removePrevious) {\n\t\tconst svg = chart.svg\n\t\tlet step = Math.min((20 * 40) / chart.colorLegend.size, 25)\n\t\tif (step < 18) step = 18\n\t\tthis.step = step\n\t\tlet colorLegendSize = chart.colorLegend.size * step\n\t\tif (chart.colorLegend.get('Ref')?.sampleCount > 0) colorLegendSize += 60\n\t\tconst scaleHeight = this.scatter.config.scaleDotTW ? 200 : 100\n\t\tthis.legendHeight = Math.max(colorLegendSize, chart.shapeLegend.size * 25) + scaleHeight //legend step and header\n\n\t\tlet fontSize = this.legendvm.getFontSize(chart, chart.colorLegend)\n\n\t\t/** Becomes the x offset for the shape legend.\n\t\t * When in continuous mode, color scale renders with a\n\t\t * default width of 150. */\n\t\tconst labels: any = []\n\n\t\tif (this.scatter.config.colorTW) labels.push(getTitle(this.scatter.config.colorTW.term.name, 40) + ' COLOR')\n\t\tif (this.scatter.config.scaleDotTW) labels.push(getTitle(this.scatter.config.scaleDotTW.term.name, 40) + ' SHAPE')\n\t\tif (labels.length > 0) {\n\t\t\tconst labelsWidth = getMaxLabelWidth(svg, labels) + 40\n\t\t\tchart.colorLegendWidth =\n\t\t\t\tthis.scatter.config?.colorTW?.q.mode == 'continuous'\n\t\t\t\t\t? Math.max(175, labelsWidth)\n\t\t\t\t\t: Math.max(this.legendvm.getLegendLabelWidth(chart, 'color', svg, `${fontSize}em`), labelsWidth)\n\t\t} else chart.colorLegendWidth = 0\n\n\t\tfontSize = this.legendvm.getFontSize(chart, chart.shapeLegend)\n\t\tconst shapeWidth = this.legendvm.getLegendLabelWidth(chart, 'shape', svg, `${fontSize}em`)\n\t\tconst width = s.svgw + chart.colorLegendWidth + shapeWidth + 125\n\t\tsvg\n\n\t\t\t.attr('width', width)\n\t\t\t.attr('height', Math.max(s.svgh + 200, this.legendHeight)) //leaving some space for axis/ref/ scale legend/padding\n\t\t\t.transition()\n\t\t\t.duration(s.duration)\n\t\tthis.fillSvgSubElems(chart)\n\n\t\tawait this.renderSerie(chart, removePrevious) //wait for legendG to be defined if on 2D large or 3D\n\t\tthis.legendvm.renderLegend(chart, step)\n\t}\n\n\tfillSvgSubElems(chart) {\n\t\tconst svg = chart.svg\n\t\tlet axisG, labelsG\n\t\tif (svg.select('.sjpcb-scatter-mainG').size() == 0) {\n\t\t\tchart.G = svg.append('g').attr('class', 'sjpcb-scatter-G')\n\t\t\tchart.mainG = chart.G.append('g').attr('class', 'sjpcb-scatter-mainG')\n\t\t\taxisG = svg.append('g').attr('class', 'sjpcb-scatter-axis')\n\t\t\tlabelsG = svg.append('g').attr('class', 'sjpcb-scatter-labelsG')\n\t\t\tchart.xAxis = axisG.append('g').attr('class', 'sjpcb-scatter-x-axis')\n\t\t\tchart.yAxis = axisG\n\t\t\t\t.append('g')\n\t\t\t\t.attr('class', 'sjpcb-scatter-y-axis')\n\t\t\t\t.attr('transform', `translate(${this.model.axisOffset.x}, 0)`)\n\t\t\tchart.mainG\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('class', 'zoom')\n\t\t\t\t.attr('x', this.model.axisOffset.x)\n\t\t\t\t.attr('y', this.model.axisOffset.y)\n\t\t\t\t.attr('width', this.scatter.settings.svgw)\n\t\t\t\t.attr('height', this.scatter.settings.svgh)\n\t\t\t\t.attr('fill', 'white')\n\t\t\tconst id = 'clip' + this.scatter.id\n\t\t\tchart.clipRect = chart.svg\n\t\t\t\t.append('defs')\n\t\t\t\t.append('clipPath')\n\t\t\t\t.attr('id', id)\n\t\t\t\t.append('rect')\n\t\t\t\t.attr('x', this.model.axisOffset.x)\n\t\t\t\t.attr('y', this.model.axisOffset.y)\n\t\t\t\t.attr('width', this.scatter.settings.svgw + 10)\n\t\t\t\t.attr('height', this.scatter.settings.svgh)\n\n\t\t\tchart.serie = chart.mainG.append('g').attr('class', 'sjpcb-scatter-series')\n\n\t\t\tchart.regressionG = chart.mainG.append('g').attr('class', 'sjpcb-scatter-lowess')\n\t\t\tchart.legendG = svg.append('g').attr('class', 'sjpcb-scatter-legend')\n\t\t\tif (this.scatter.state.config.transform && chart.mainG.attr('transform') != this.scatter.state.config.transform) {\n\t\t\t\tchart.mainG.attr('transform', this.scatter.state.config.transform)\n\t\t\t}\n\t\t\tchart.G.attr('clip-path', `url(#${id})`)\n\t\t} else {\n\t\t\tchart.G = svg.select('.sjpcb-scatter-G')\n\t\t\tchart.mainG = svg.select('.sjpcb-scatter-mainG')\n\t\t\tchart.serie = chart.mainG.select('.sjpcb-scatter-series')\n\t\t\tchart.regressionG = chart.mainG.select('.sjpcb-scatter-lowess')\n\t\t\taxisG = svg.select('.sjpcb-scatter-axis')\n\t\t\tlabelsG = svg.select('.sjpcb-scatter-labelsG')\n\t\t\tchart.xAxis = axisG.select('.sjpcb-scatter-x-axis')\n\t\t\tchart.yAxis = axisG.select('.sjpcb-scatter-y-axis')\n\t\t\tchart.legendG = svg.select('.sjpcb-scatter-legend')\n\t\t\tchart.clipRect = svg.select('defs').select('clipPath').select('rect')\n\t\t}\n\n\t\tchart.axisG = axisG\n\t\tchart.labelsG = labelsG\n\t\tchart.xAxis.attr('transform', `translate(0, ${this.scatter.settings.svgh + this.model.axisOffset.y})`)\n\n\t\tchart.legendG.attr('transform', `translate(${this.scatter.settings.svgw + this.model.axisOffset.x + 50}, 20)`)\n\t\tif (chart.axisBottom) {\n\t\t\tchart.xAxis.call(chart.axisBottom)\n\t\t\tchart.yAxis.call(chart.axisLeft)\n\t\t}\n\t\tif (this.scatter.config.term) {\n\t\t\tlet termName = getTitle(this.scatter.config.term.term.name, 60)\n\t\t\tif (!this.scatter.config.colorTW && !this.scatter.config.shapeTW && !this.scatter.config.term0)\n\t\t\t\ttermName = `${termName}, n=${chart.cohortSamples.length}`\n\n\t\t\tlabelsG.selectAll('*').remove()\n\t\t\tlet text = labelsG\n\t\t\t\t.append('text')\n\t\t\t\t.attr(\n\t\t\t\t\t'transform',\n\t\t\t\t\t`translate(${this.model.axisOffset.x + this.scatter.settings.svgw / 2}, ${\n\t\t\t\t\t\tthis.scatter.settings.svgh + this.model.axisOffset.y + 40\n\t\t\t\t\t})`\n\t\t\t\t)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.text(termName)\n\t\t\t\t.style('font-size', '0.9em')\n\n\t\t\tif (termName.length > 65) {\n\t\t\t\ttext\n\t\t\t\t\t.on('mouseenter', event => {\n\t\t\t\t\t\tthis.scatter.interactivity.showText(event, this.scatter.config.term.term.name)\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseleave', () => this.view.dom.tooltip.hide())\n\t\t\t}\n\t\t\tif (this.scatter.config.term0 && !this.scatter.config.colorTW && !this.scatter.config.shapeTW) {\n\t\t\t\tconst term0Name = `${chart.id}, n=${chart.cohortSamples.length}`\n\n\t\t\t\tlabelsG\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.attr(\n\t\t\t\t\t\t'transform',\n\t\t\t\t\t\t`translate(${this.model.axisOffset.x + this.scatter.settings.svgw / 2}, ${\n\t\t\t\t\t\t\tthis.scatter.settings.svgh + this.model.axisOffset.y + 65\n\t\t\t\t\t\t})`\n\t\t\t\t\t)\n\t\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t\t.text(term0Name)\n\t\t\t}\n\t\t\tconst isEvents = this.scatter.config.term2 ? false : true\n\t\t\tconst t2name = this.scatter.config.term2?.term?.name\n\t\t\tconst term2Name = isEvents ? 'Frequency' : getTitle(t2name, 60)\n\t\t\ttext = labelsG\n\t\t\t\t.append('text')\n\t\t\t\t.attr(\n\t\t\t\t\t'transform',\n\t\t\t\t\t`translate(${this.model.axisOffset.x - 50}, ${\n\t\t\t\t\t\tthis.scatter.settings.svgh / 2 + this.model.axisOffset.y\n\t\t\t\t\t}) rotate(-90)`\n\t\t\t\t)\n\t\t\t\t.attr('text-anchor', 'middle')\n\t\t\t\t.text(term2Name)\n\t\t\t\t.style('font-size', '0.9em')\n\t\t\tif (term2Name.length > 60) {\n\t\t\t\ttext\n\t\t\t\t\t.on('mouseenter', event => {\n\t\t\t\t\t\tthis.scatter.interactivity.showText(event, this.scatter.config.term2.term.name)\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseleave', () => this.view.dom.tooltip.hide())\n\t\t\t}\n\t\t}\n\t}\n\n\trenderSerie(chart, removePrevious) {\n\t\tconst duration = this.scatter.settings.duration\n\t\tif (this.canvas) this.canvas.remove()\n\n\t\tconst g = chart.serie\n\n\t\tconst data = chart.data\n\t\tif (removePrevious) chart.serie.selectAll('*').remove()\n\n\t\t// remove all symbols as there is no data id for privacy\n\t\t//g.selectAll('path').remove()\n\n\t\tconst symbols = g.selectAll('path[name=\"serie\"]').data(data.samples)\n\t\tsymbols\n\t\t\t.transition()\n\t\t\t.duration(duration)\n\t\t\t.attr('name', 'serie')\n\t\t\t.attr('transform', c => this.model.transform(chart, c))\n\t\t\t.attr('d', c => this.model.getShape(chart, c))\n\t\t\t.attr('fill', c => this.model.getColor(c, chart))\n\t\t\t.attr('stroke', c => this.model.getColor(c, chart))\n\t\t\t.attr('stroke-width', c => this.model.getStrokeWidth(c))\n\t\t\t.style('fill-opacity', c => this.model.getOpacity(c))\n\t\tsymbols\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('name', 'serie')\n\t\t\t/*** you'd need to set the symbol position using translate, instead of previously with cx, cy for a circle ***/\n\t\t\t.attr('transform', c => this.model.transform(chart, c))\n\t\t\t.attr('d', c => this.model.getShape(chart, c))\n\t\t\t.attr('fill', c => this.model.getColor(c, chart))\n\t\t\t.attr('stroke', c => this.model.getColor(c, chart))\n\t\t\t.attr('stroke-width', c => this.model.getStrokeWidth(c))\n\t\t\t.style('fill-opacity', c => this.model.getOpacity(c))\n\t\t\t.transition()\n\t\t\t.duration(duration)\n\n\t\tthis.mayRenderRegression()\n\t}\n\n\tasync mayRenderRegression() {\n\t\tfor (const chart of this.model.charts) {\n\t\t\tchart.regressionG?.selectAll('*').remove()\n\t\t\tif (chart.regressionCurve) {\n\t\t\t\tconst l = line()\n\t\t\t\t\t.x(d => d[0])\n\t\t\t\t\t.y(d => d[1])\n\t\t\t\tconst regressionPath = chart.regressionG.append('path')\n\t\t\t\tregressionPath\n\t\t\t\t\t.attr('d', l(chart.regressionCurve))\n\t\t\t\t\t.attr('stroke', 'blue')\n\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t.style('stroke-width', '2')\n\t\t\t}\n\t\t}\n\t}\n\n\tasync addGroup(group) {\n\t\tthis.model.addGroup(group)\n\t\tthis.view.dom.tip.hide()\n\t}\n\n\tsetTools() {\n\t\tif (!this.model.charts[0]) return\n\t\tconst toolsDiv = this.view.dom.toolsDiv.style('background-color', 'white')\n\t\ttoolsDiv.selectAll('*').remove()\n\n\t\tthis.scatterZoom.initZoom(toolsDiv)\n\t}\n\n\t//2D large and 3D add an svg for the legend\n\taddLegendSVG(chart) {\n\t\tchart.chartDiv.style('margin', '20px 20px')\n\t\tchart.legendDiv = this.view.dom.mainDiv\n\t\t\t.insert('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\tchart.legendG = chart.legendDiv\n\t\t\t.append('svg')\n\t\t\t.attr('width', this.scatter.settings.svgw / 2)\n\t\t\t.attr('height', this.scatter.settings.svgh)\n\t\t\t.append('g')\n\t\t\t.attr('transform', 'translate(20, 20)')\n\t}\n}\n", "import { icons as icon_functions } from '#dom'\nimport { d3lasso } from '#common/lasso'\nimport { scaleLinear as d3Linear } from 'd3-scale'\nimport { line, extent, contourDensity, geoPath, scaleSequential, max, interpolateGreys } from 'd3'\nimport { ScatterLasso } from './scatterLasso.js'\nimport type { Scatter } from '../scatter.js'\nimport { ScatterViewModelBase } from './scatterViewModelBase.js'\n\nexport class ScatterViewModel extends ScatterViewModelBase {\n\tscatterLasso: ScatterLasso\n\n\tconstructor(scatter: Scatter) {\n\t\tsuper(scatter)\n\t\tthis.scatterLasso = new ScatterLasso(scatter)\n\t}\n\n\tfillSvgSubElems(chart) {\n\t\tsuper.fillSvgSubElems(chart)\n\t\tchart.axisG.style('opacity', this.scatter.settings.showAxes ? 1 : 0)\n\t\tchart.labelsG.style('opacity', this.scatter.settings.showAxes ? 1 : 0)\n\t}\n\n\trenderSerie(chart, removePrevious) {\n\t\tsuper.renderSerie(chart, removePrevious)\n\t\tif (this.scatter.settings.showContour) this.renderContours(chart)\n\t}\n\n\trenderContours(chart) {\n\t\tconst contourG = chart.serie\n\t\tlet zAxisScale\n\t\tif (this.scatter.config.colorTW?.q.mode == 'continuous') {\n\t\t\tconst [zMin, zMax] = extent(chart.data.samples, (d: any) => d.category) as [any, any]\n\t\t\tzAxisScale = d3Linear().domain([zMin, zMax]).range([0, 1])\n\t\t}\n\n\t\tconst data = chart.data.samples\n\t\t\t.filter(s => this.model.getOpacity(s) > 0)\n\t\t\t.map(s => {\n\t\t\t\treturn { x: chart.xAxisScale(s.x), y: chart.yAxisScale(s.y), z: zAxisScale ? zAxisScale(s.category) : 1 }\n\t\t\t})\n\t\trenderContours(\n\t\t\tcontourG,\n\t\t\tdata,\n\t\t\tthis.scatter.settings.svgw,\n\t\t\tthis.scatter.settings.svgh,\n\t\t\tthis.scatter.settings.colorContours,\n\t\t\tthis.scatter.settings.contourBandwidth,\n\t\t\tthis.scatter.settings.contourThresholds\n\t\t)\n\t}\n\n\tasync mayRenderRegression() {\n\t\tfor (const chart of this.model.charts) {\n\t\t\tchart.regressionG?.selectAll('*').remove()\n\t\t\tif (chart.regressionCurve) {\n\t\t\t\tconst l = line()\n\t\t\t\t\t.x(d => d[0])\n\t\t\t\t\t.y(d => d[1])\n\t\t\t\tconst regressionPath = chart.regressionG.append('path')\n\t\t\t\tregressionPath\n\t\t\t\t\t.attr('d', l(chart.regressionCurve))\n\t\t\t\t\t.attr('stroke', 'blue')\n\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t.style('stroke-width', '2')\n\t\t\t}\n\t\t}\n\t}\n\n\tasync toggleLasso() {\n\t\tthis.scatter.config.lassoOn = !this.scatter.config.lassoOn\n\t\tthis.scatter.app.dispatch({ type: 'plot_edit', id: this.scatter.id, config: this.scatter.config })\n\t}\n\n\tasync addGroup(group) {\n\t\tthis.model.addGroup(group)\n\t\tthis.view.dom.tip.hide()\n\t}\n\n\tsetTools() {\n\t\tsuper.setTools()\n\t\tif (this.scatter.config.singleCellPlot) return\n\t\tconst toolsDiv = this.view.dom.toolsDiv\n\t\tconst display = 'block'\n\t\tconst searchDiv = toolsDiv.insert('div').style('display', display).style('margin', '15px 10px')\n\t\tthis.view.dom.lassoDiv = toolsDiv.insert('div').style('display', display).style('margin', '15px 10px')\n\t\ticon_functions['search'](searchDiv, { handler: e => this.interactivity.searchSample(e), title: 'Search samples' })\n\t\ticon_functions['lasso'](this.view.dom.lassoDiv, {\n\t\t\thandler: () => this.toggleLasso(),\n\t\t\tenabled: this.scatter.config.lassoOn,\n\t\t\ttitle: 'Select a group of samples'\n\t\t})\n\t\tthis.view.dom.groupDiv = toolsDiv.insert('div').style('display', display).style('margin', '15px 10px')\n\n\t\tfor (const chart of this.model.charts) {\n\t\t\tif (!chart.lasso) chart.lasso = d3lasso()\n\t\t\tthis.scatterLasso.lassoReset(chart)\n\t\t}\n\t}\n\n\t//2D large and 3D add an svg for the legend\n\taddLegendSVG(chart) {\n\t\tchart.chartDiv.style('margin', '20px 20px')\n\t\tchart.legendDiv = this.view.dom.mainDiv\n\t\t\t.insert('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\tchart.legendG = chart.legendDiv\n\t\t\t.append('svg')\n\t\t\t.attr('width', this.scatter.settings.svgw / 2)\n\t\t\t.attr('height', this.scatter.vm.legendHeight)\n\t\t\t.append('g')\n\t\t\t.attr('transform', 'translate(20, 20)')\n\t}\n}\n\nexport function renderContours(contourG, data, width, height, colorContours, bandwidth, thresholds) {\n\t// Create the horizontal and vertical scales.\n\n\tconst contours = contourDensity()\n\t\t.x((s: any) => s.x)\n\t\t.y((s: any) => s.y)\n\t\t.weight((s: any) => s.z)\n\t\t.size([width, height])\n\t\t.cellSize(2)\n\n\t\t.bandwidth(bandwidth)\n\t\t.thresholds(thresholds)(data)\n\n\tconst colorScale = scaleSequential()\n\t\t.domain([0, max(contours, d => d.value) as any])\n\t\t.interpolator(interpolateGreys)\n\n\t// Compute the density contours.\n\t// Append the contours.\n\tcontourG\n\t\t.attr('fill', 'none')\n\t\t.attr('stroke', 'gray') // gray to make the contours visible\n\t\t.attr('stroke-linejoin', 'round')\n\t\t.selectAll()\n\t\t.data(contours)\n\t\t.join('path')\n\t\t.attr('stroke-width', (d, i) => (i % 5 ? 0.25 : 1))\n\t\t.attr('d', geoPath())\n\t\t.attr('fill', colorContours ? d => colorScale(d.value) : 'none')\n\t\t.attr('fill-opacity', 0.05) //this is the opacity of the contour, reduce it to 0.05 to avoid hiding the points\n}\n", "import { rgb } from 'd3-color'\nimport * as THREE from 'three'\nimport { ScatterViewModel } from './scatterViewModel.js'\n\nexport class ScatterViewModel2DLarge extends ScatterViewModel {\n\tconstructor(scatter) {\n\t\tsuper(scatter)\n\t}\n\n\tasync renderSerie(chart) {\n\t\tconst DragControls = await import('three/examples/jsm/controls/DragControls.js')\n\n\t\tthis.view.dom.mainDiv.selectAll('*').remove()\n\n\t\tthis.canvas = this.view.dom.mainDiv.insert('div').style('display', 'inline-block').append('canvas').node()\n\t\tthis.canvas.width = this.scatter.settings.svgw\n\t\tthis.canvas.height = this.scatter.settings.svgh\n\t\tchart.chartDiv.style('margin', '20px 20px')\n\n\t\tconst fov = this.scatter.settings.threeFOV\n\t\tconst near = 0.1\n\t\tconst far = 1000\n\t\tconst camera = new THREE.PerspectiveCamera(fov, 1, near, far)\n\t\tconst scene = new THREE.Scene()\n\t\tcamera.position.set(0, 0, 1.5)\n\t\tcamera.lookAt(scene.position)\n\t\tcamera.updateMatrix()\n\t\tconst whiteColor = new THREE.Color('rgb(255,255,255)')\n\t\tscene.background = whiteColor\n\n\t\tconst geometry = new THREE.BufferGeometry()\n\t\tconst { vertices, colors } = this.getVertices(chart)\n\n\t\tgeometry.setAttribute('position', new THREE.Float32BufferAttribute(vertices, 3))\n\t\tgeometry.setAttribute('color', new THREE.Float32BufferAttribute(colors, 3))\n\t\tconst tex = getThreeCircle(128)\n\t\tconst material = new THREE.PointsMaterial({\n\t\t\tsize: this.scatter.settings.threeSize,\n\t\t\tsizeAttenuation: true,\n\t\t\ttransparent: true,\n\t\t\topacity: this.scatter.settings.opacity,\n\t\t\tmap: tex,\n\t\t\tvertexColors: true\n\t\t})\n\n\t\tconst particles = new THREE.Points(geometry, material)\n\n\t\tscene.add(particles)\n\t\tconst renderer = new THREE.WebGLRenderer({ antialias: true, canvas: this.canvas, preserveDrawingBuffer: true })\n\t\trenderer.setSize(this.scatter.settings.svgw, this.scatter.settings.svgh)\n\t\trenderer.setPixelRatio(window.devicePixelRatio)\n\n\t\tnew DragControls.DragControls([particles], camera, renderer.domElement)\n\n\t\tdocument.addEventListener('mousewheel', (event: any) => {\n\t\t\tif (event.ctrlKey) camera.position.z += event.deltaY / 500\n\t\t})\n\n\t\tthis.addLegendSVG(chart)\n\t\tthis.animate(camera, scene, renderer)\n\t}\n\n\tanimate(camera, scene, renderer) {\n\t\trequestAnimationFrame(() => this.animate(camera, scene, renderer))\n\t\tcamera.zoom = this.scatter.vm.scatterZoom.zoom\n\t\tcamera.updateProjectionMatrix()\n\t\trenderer.render(scene, camera)\n\t}\n\n\tgetVertices(chart) {\n\t\tconst xAxisScale = chart.xAxisScale.range([-1, 1])\n\t\tconst yAxisScale = chart.yAxisScale.range([-1, 1])\n\t\tconst vertices: any = []\n\t\tconst colors: any = []\n\t\tfor (const sample of chart.data.samples) {\n\t\t\tconst opacity = this.model.getOpacity(sample)\n\t\t\tif (opacity == 0) continue\n\t\t\tconst x = xAxisScale(sample.x)\n\t\t\tconst y = yAxisScale(sample.y)\n\t\t\tconst z = 0\n\t\t\tvertices.push(x, y, z)\n\t\t\tconst color = new THREE.Color(rgb(this.model.getColor(sample, chart)).toString())\n\t\t\tcolors.push(color.r, color.g, color.b)\n\t\t}\n\t\treturn { vertices, colors }\n\t}\n}\n\nexport function getThreeCircle(size) {\n\tconst c = document.createElement('canvas')\n\tc.width = size\n\tc.height = size\n\tconst ctx: any = c.getContext('2d')\n\tctx.clearRect(0, 0, size, size)\n\tctx.fillStyle = 'white'\n\tctx.beginPath()\n\tctx.arc(size / 2, size / 2, size / 2, 0, 2 * Math.PI)\n\tctx.fill()\n\tconst tex = new THREE.CanvasTexture(c)\n\treturn tex\n}\n", "import { getCompInit, copyMerge, deepEqual } from '../rx/index.js'\nimport { scaleLinear as d3Linear } from 'd3-scale'\nimport { dofetch3 } from '#common/dofetch'\nimport { getColors } from '#shared/common.js'\nimport { controlsInit } from './controls'\nimport { downloadSingleSVG } from '#common/svg.download'\nimport { select } from 'd3-selection'\nimport { rgb, create, extent } from 'd3'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { TermTypes } from '#shared/terms.js'\nimport {\n\tColorScale,\n\ticons as icon_functions,\n\taddGeneSearchbox,\n\trenderTable,\n\tsayerror,\n\tMenu,\n\tTabs,\n\tdownloadTable\n} from '#dom'\nimport * as THREE from 'three'\nimport { getThreeCircle } from './scatter/viewmodel/scatterViewModel2DLarge.js'\nimport { renderContours } from './scatter/viewmodel/scatterViewModel.js'\nimport { digestMessage } from '#termsetting'\n\n/*\n\nhardcoded behaviors when this.samples[].experiments[] is present:\n\n- all samples must either have or not have .experiments[]\n- experiments[] supports tracking multiple experiments done on same sample\n- an experiment must be {experimentID,sampleName} along with optional prop\n- state tracks experimentID as well as this.samples[].sample\n- in sample table, both experimentID and sampleName are shown\n\nthis\n\tsamples[]\n\t\tdatastructure returned by /termdb/singlecellSamples\n\t\t\n\t\telement structure:\n\n\t\t{\n\t\t\tsample: str\n\t\t\t<termid>: <term value>\n\t\t\texperiments?: []\n\t\t\t\texperimentID: str // required to track which table row is selected and for backend to retrieve data for\n\t\t\t\tsampleName: str // for display\n\t\t}\n\n\n\tlegendRendered=bool\n\n\tstate{}\n\t\tconfig{}\n\t\t\tsample // name of selected sample. matches to this.samples[].sample\n\t\t\texperimentID // optional. set when this.samples[].experiments[] is present. allow to match to a specific experiment of a sample that has multiples\n\n*/\n\nconst SAMPLES_TAB = 1\nconst PLOTS_TAB = 2\nconst DIFFERENTIAL_EXPRESSION_TAB = 3\nconst GENE_EXPRESSION_TAB = 4\nconst IMAGES_TAB = 5\nconst VIOLIN_TAB = 6\nconst noExpColor = '#F5F5F5' //lightGray\nconst DE_GENES_TAB = 8\nconst DE_GSEA_TAB = 7\n\nclass singleCellPlot {\n\tconstructor() {\n\t\tthis.type = 'singleCellPlot'\n\n\t\tthis.tip = new Menu({ padding: '4px', offsetX: 10, offsetY: 0 })\n\t\tthis.tip.d.style('max-height', '300px').style('overflow', 'scroll').style('font-size', '0.9em')\n\t\tthis.startGradient = {}\n\t\tthis.stopGradient = {}\n\t}\n\n\tasync init(appState) {\n\t\t// generate sample table in init() but not main() is because sample table is constant and no need to update it on dispatch\n\t\t// TODO sample table still needs to be changed when gdc (external portal) cohort changes\n\n\t\tconst state = this.getState(appState)\n\t\tif (this.opts.header) this.opts.header.html(`SINGLE CELL PLOT`).style('font-size', '0.9em')\n\n\t\t// need to set the this.samples based on the current filter0\n\n\t\tthis.tabs = []\n\t\tconst activeTab = state.config.activeTab\n\t\t// shared isVisible function for tabs that require config.sample;\n\t\t// note that tab.isVisible() will be called on tab.update(), which\n\t\t// is called in main() -> showActiveTab() below\n\t\tconst isVisible = () => this.isValidSample\n\n\t\tthis.tabs.push({\n\t\t\tlabel: 'Samples',\n\t\t\tid: SAMPLES_TAB,\n\t\t\tisVisible,\n\t\t\tactive: activeTab == SAMPLES_TAB,\n\t\t\tcallback: () => this.setActiveTab(SAMPLES_TAB)\n\t\t})\n\t\tthis.tabs.push({\n\t\t\tlabel: 'Plots',\n\t\t\tid: PLOTS_TAB,\n\t\t\tactive: activeTab == PLOTS_TAB,\n\t\t\tisVisible,\n\t\t\tcallback: () => this.setActiveTab(PLOTS_TAB)\n\t\t})\n\t\tif (state.termdbConfig.queries.singleCell.DEgenes) {\n\t\t\tthis.tabs.push({\n\t\t\t\tlabel: 'Differential Expression',\n\t\t\t\tid: DIFFERENTIAL_EXPRESSION_TAB,\n\t\t\t\tactive: activeTab == DIFFERENTIAL_EXPRESSION_TAB,\n\t\t\t\tisVisible,\n\t\t\t\tcallback: () => this.setActiveTab(DIFFERENTIAL_EXPRESSION_TAB)\n\t\t\t})\n\t\t}\n\t\tif (state.termdbConfig.queries.singleCell.geneExpression)\n\t\t\tthis.tabs.push({\n\t\t\t\tlabel: 'Gene Expression',\n\t\t\t\tid: GENE_EXPRESSION_TAB,\n\t\t\t\tactive: activeTab == GENE_EXPRESSION_TAB,\n\t\t\t\tisVisible,\n\t\t\t\tcallback: () => this.setActiveTab(GENE_EXPRESSION_TAB)\n\t\t\t})\n\n\t\t// summary tab is not limited to geneExp, as later it can be applied to cell category terms too (if there are multiple)\n\t\tthis.tabs.push({\n\t\t\tlabel: 'Summary',\n\t\t\tid: VIOLIN_TAB,\n\t\t\tactive: activeTab == VIOLIN_TAB,\n\t\t\tisVisible,\n\t\t\tcallback: () => this.setActiveTab(VIOLIN_TAB)\n\t\t})\n\n\t\tif (state.termdbConfig.queries.singleCell.images)\n\t\t\tthis.tabs.push({\n\t\t\t\tlabel: state.termdbConfig.queries.singleCell.images.label,\n\t\t\t\tid: IMAGES_TAB,\n\t\t\t\tactive: activeTab == IMAGES_TAB,\n\t\t\t\tisVisible,\n\t\t\t\tcallback: () => this.setActiveTab(IMAGES_TAB)\n\t\t\t})\n\t\tconst q = state.termdbConfig.queries\n\t\tthis.opts.holder.style('position', 'relative').style('min-height', '200px')\n\t\tthis.mainDivId = `${this.id}-sandbox`\n\t\tconst errorDiv = this.opts.holder.append('div')\n\t\tconst mainDiv = this.opts.holder\n\t\t\t.insert('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.attr('id', this.mainDivId)\n\n\t\tconst leftDiv = mainDiv.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\tconst controlsDiv = leftDiv.append('div').attr('class', 'pp-termdb-plot-controls')\n\n\t\tconst contentDiv = mainDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('padding-left', '10px')\n\t\t\t.style('min-height', '300px')\n\t\tthis.tabsComp = await new Tabs({\n\t\t\tholder: contentDiv,\n\t\t\ttabsPosition: 'horizontal',\n\t\t\ttabs: this.tabs\n\t\t})\n\t\tthis.tabsComp.main()\n\t\tconst headerDiv = contentDiv.append('div').style('display', 'inline-block').style('padding-bottom', '10px')\n\n\t\tconst samplesPromptDiv = headerDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.text('Select a sample below to see its data:')\n\t\t\t.style('padding', '0px 40px 10px 10px')\n\t\tconst showDiv = headerDiv.append('div').style('padding-bottom', '10px').style('display', 'none')\n\n\t\tif (state.config.plots.length > 1) this.renderShowPlots(showDiv, state)\n\t\t// div to show optional DE genes (precomputed by seurat for each cluster, e.g. via gdc)\n\t\tconst geDiv = headerDiv.append('div').style('display', 'none')\n\t\tconst violinSelectDiv = headerDiv.append('div').style('padding-left', '30px').style('display', 'none')\n\t\tconst deDiv = headerDiv.append('div').style('display', 'none')\n\t\tconst sampleDiv = headerDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.html(await this.getSampleDetails(state))\n\t\t\t.style('padding', '10px 20px')\n\t\tconst plotsDivParent = contentDiv.append('div')\n\t\tconst samplesTableDiv = plotsDivParent.append('div').style('padding-bottom', '10px')\n\n\t\tconst plotsDiv = plotsDivParent\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('flex-wrap', 'wrap')\n\t\t\t.style('justify-content', 'flex-start')\n\n\t\tconst loadingDiv = this.opts.holder\n\t\t\t.append('div')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('top', '0')\n\t\t\t.style('left', '0')\n\t\t\t.style('width', '100%')\n\t\t\t.style('height', '100%')\n\t\t\t.style('background-color', 'rgba(255, 255, 255, 0.95)')\n\t\t\t.style('text-align', 'center')\n\n\t\tthis.dom = {\n\t\t\tsampleDiv,\n\t\t\tsamplesPromptDiv,\n\t\t\tsamplesTableDiv,\n\t\t\tshowDiv,\n\t\t\tmainDiv,\n\t\t\tloadingDiv,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\ttooltip: new Menu({ padding: '2px', offsetX: 10, offsetY: 0 }),\n\t\t\tcontrolsHolder: controlsDiv,\n\t\t\tgeDiv,\n\t\t\tviolinSelectDiv,\n\t\t\tdeDiv,\n\t\t\tplotsDiv,\n\t\t\tplotsDivParent,\n\t\t\terrorDiv\n\t\t}\n\n\t\tif (q.singleCell?.geneExpression) this.renderGeneExpressionControls(geDiv, state)\n\n\t\tconst offsetX = 80\n\t\tthis.axisOffset = { x: offsetX, y: 30 }\n\n\t\tif (q.singleCell?.DEgenes) {\n\t\t\tconst label = this.dom.deDiv\n\t\t\t\t.append('label')\n\t\t\t\t.html('View differentially expressed genes for cells of a cluster versus rest of the cells:&nbsp;')\n\t\t\tthis.dom.deselect = label.append('select').on('change', e => {\n\t\t\t\tconst display = this.dom.deselect.node().value ? 'inline-block' : 'none'\n\t\t\t\tconst cluster = this.dom.deselect.node().value.split(' ')[1]\n\t\t\t\tthis.genes = null\n\t\t\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: { cluster, gene: null } })\n\t\t\t})\n\t\t\tthis.dom.deselect.append('option').text('')\n\t\t}\n\n\t\tthis.settings = {}\n\n\t\tdocument.addEventListener('scroll', event => this?.tip?.hide())\n\t\tselect('.sjpp-output-sandbox-content').on('scroll', event => this.tip.hide())\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\treturn {\n\t\t\tconfig,\n\t\t\tdslabel: appState.vocab.dslabel,\n\t\t\tgenome: appState.vocab.genome,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tvocab: appState.vocab\n\t\t}\n\t}\n\n\t// called in relevant dispatch when reactsTo==true\n\t// or current.state != replcament.state\n\tasync main() {\n\t\tthis.dom.mainDiv.style('display', 'block') // show the main div in case it was hidden because no data was found\n\t\tthis.dom.loadingDiv.selectAll('*').remove()\n\t\tthis.dom.loadingDiv\n\t\t\t.style('display', '')\n\t\t\t.append('div')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('top', '50%')\n\t\t\t.text('Loading...')\n\t\ttry {\n\t\t\tconst body = {\n\t\t\t\tgenome: this.state.genome,\n\t\t\t\tdslabel: this.state.dslabel,\n\t\t\t\tfilter0: this.state.termfilter.filter0 || null\n\t\t\t}\n\t\t\tconst result = await dofetch3('termdb/singlecellSamples', { body })\n\t\t\tif (result.error) throw result.error\n\t\t\tthis.samples = result.samples\n\t\t\tif (this.samples.length == 0) {\n\t\t\t\tthis.showNoMatchingDataMessage()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tthis.isValidSample = this.state.config.sample && this.samples.find(i => i.sample == this.state.config.sample)\n\t\t\tthis.colorByGene =\n\t\t\t\tthis.state.config.activeTab == GENE_EXPRESSION_TAB || this.state.config.activeTab == DIFFERENTIAL_EXPRESSION_TAB\n\t\t\tthis.config = structuredClone(this.state.config) // this config can be edited to dispatch changes\n\t\t\tcopyMerge(this.settings, this.config.settings.singleCellPlot)\n\t\t\tthis.plotColorByDivs = []\n\t\t\tthis.plots = []\n\n\t\t\tthis.legendRendered = false\n\t\t\tthis.dom.plotsDiv.selectAll('*').remove()\n\t\t\tawait this.getData()\n\t\t\tawait this.setControls()\n\t\t\tthis.dom.sampleDiv.html(await this.getSampleDetails(this.state))\n\t\t\tthis.showActiveTab()\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t} catch (e) {\n\t\t\tthis.app.tip.hide()\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t\tif (e.stack) console.log(e.stack)\n\t\t\tsayerror(this.dom.errorDiv, e)\n\t\t}\n\t}\n\n\tasync getData() {\n\t\tif (!this.state.config.sample) return\n\t\tconst plots = []\n\t\tfor (const plot of this.config.plots) {\n\t\t\tif (plot.selected) plots.push(plot.name)\n\t\t}\n\n\t\tconst body = {\n\t\t\tgenome: this.state.genome,\n\t\t\tdslabel: this.state.dslabel,\n\t\t\tplots,\n\t\t\tfilter0: this.state.termfilter.filter0\n\t\t}\n\t\t// change the sample to contains both sampleID and experimentID, so that they could\n\t\t// both be used to query data. (GDC sc gene expression only support sample uuid now)\n\t\t// a sample has already been selected\n\t\tbody.sample = {\n\t\t\teID: this.state.config.experimentID,\n\t\t\tsID: this.state.config.sample\n\t\t}\n\t\tif (\n\t\t\tthis.state.config.gene &&\n\t\t\t(this.state.config.activeTab == GENE_EXPRESSION_TAB || this.state.config.activeTab == DIFFERENTIAL_EXPRESSION_TAB)\n\t\t)\n\t\t\tbody.gene = this.state.config.gene\n\t\telse body.colorBy = this.state.config.colorBy\n\t\t//if error it will be catched on main\n\t\tconst result = await dofetch3('termdb/singlecellData', { body })\n\t\tif (result.error) throw result.error\n\t\tthis.refName = result.refName\n\t\tthis.data = result\n\t}\n\n\tasync getSampleDetails(state) {\n\t\tif (!this.samples) return ''\n\t\tconst sampleIdx = this.samples.findIndex(i => i.sample == state.config.sample)\n\t\tif (sampleIdx == -1) return ''\n\n\t\tconst extraText = [] // extra text to show alongside sample name\n\n\t\tif (state.config.experimentID) {\n\t\t\t// experimentID is tracked in state, meaning this.samples[].experiments[] is present. and the id specifies which experiment, out of potential multiple of one sample, is currently selected.\n\t\t\t// in such case, experiments[].sampleName should also be present, and display the sampleName next to config.sample which is actually person id\n\t\t\textraText.push(\n\t\t\t\t'<span style=\"margin-left:15px;font-size:.7em\">SAMPLE</span> ' +\n\t\t\t\t\tthis.samples[sampleIdx].experiments?.find(i => i.experimentID == state.config.experimentID)?.sampleName\n\t\t\t)\n\t\t} else if (this.samples[sampleIdx].experiments) {\n\t\t\t// experimentID not in state, but sample carries exp array; this is possible when app launches. simply show first experiment of this sample\n\t\t\textraText.push(\n\t\t\t\t'<span style=\"margin-left:15px;font-size:.7em\">SAMPLE</span> ' +\n\t\t\t\t\tthis.samples[sampleIdx].experiments[0].sampleName\n\t\t\t)\n\t\t}\n\n\t\tif (state.termdbConfig.queries.singleCell.samples.extraSampleTabLabel) {\n\t\t\t// value is a term id. get the term name\n\t\t\tconst termname = (\n\t\t\t\tawait this.app.vocabApi.getterm(state.termdbConfig.queries.singleCell.samples.extraSampleTabLabel)\n\t\t\t).name\n\t\t\t// get the term value from current sample\n\t\t\tconst sampleValue = this.samples[sampleIdx][state.termdbConfig.queries.singleCell.samples.extraSampleTabLabel]\n\t\t\textraText.push(`<span style=\"margin-left:15px;font-size:.7em\">${termname.toUpperCase()}</span> ${sampleValue}`)\n\t\t}\n\n\t\treturn `<span style=\"font-size:.7em\">${state.config.settings.singleCellPlot.uiLabels.sample.toUpperCase()}</span>\n\t\t\t${this.samples[sampleIdx].sample}\n\t\t\t${extraText.join('')}`\n\t}\n\n\tasync getSampleFilename(state) {\n\t\tconst sampleIdx = this.samples.findIndex(i => i.sample == state.config.sample)\n\t\tif (sampleIdx == -1) return ''\n\n\t\tconst extraText = [] // extra text to show alongside sample name\n\n\t\tif (state.config.experimentID) {\n\t\t\t// experimentID is tracked in state, meaning this.samples[].experiments[] is present. and the id specifies which experiment, out of potential multiple of one sample, is currently selected.\n\t\t\t// in such case, experiments[].sampleName should also be present, and display the sampleName next to config.sample which is actually person id\n\t\t\textraText.push(\n\t\t\t\t'SAMPLE_' +\n\t\t\t\t\tthis.samples[sampleIdx].experiments?.find(i => i.experimentID == state.config.experimentID)?.sampleName\n\t\t\t)\n\t\t} else if (this.samples[sampleIdx].experiments) {\n\t\t\t// experimentID not in state, but sample carries exp array; this is possible when app launches. simply show first experiment of this sample\n\t\t\textraText.push('SAMPLE_' + this.samples[sampleIdx].experiments[0].sampleName)\n\t\t}\n\n\t\tif (state.termdbConfig.queries.singleCell.samples.extraSampleTabLabel) {\n\t\t\t// value is a term id. get the term name\n\t\t\tconst termname = (\n\t\t\t\tawait this.app.vocabApi.getterm(state.termdbConfig.queries.singleCell.samples.extraSampleTabLabel)\n\t\t\t).name\n\t\t\t// get the term value from current sample\n\t\t\tconst sampleValue = this.samples[sampleIdx][state.termdbConfig.queries.singleCell.samples.extraSampleTabLabel]\n\t\t\textraText.push(`${termname.toUpperCase()}_${sampleValue}`)\n\t\t}\n\t\tif (this.state.config.activeTab == GENE_EXPRESSION_TAB) extraText.push(this.state.config.gene)\n\t\tif (this.state.config.activeTab == DIFFERENTIAL_EXPRESSION_TAB) extraText.push(this.state.config.cluster)\n\t\tif (this.state.config.activeTab == VIOLIN_TAB && this.dom.expressionBySelect)\n\t\t\textraText.push(this.dom.expressionBySelect.node().value)\n\n\t\tconst filename = `${state.config.settings.singleCellPlot.uiLabels.sample.toUpperCase()}_\n\t\t\t${this.samples[sampleIdx].sample}_\n\t\t\t${extraText.join('_')}`\n\n\t\treturn filename.replace(/[^0-9a-z_]/gi, '')\n\t}\n\n\trenderShowPlots(showDiv, state) {\n\t\tshowDiv.append('label').text('Plots:').style('font-size', '1.1em')\n\n\t\tfor (const plot of state.config.plots) {\n\t\t\tconst id = plot.name.replace(/\\s+/g, '')\n\t\t\tconst key = `show${id}`\n\t\t\tshowDiv\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.attr('id', key)\n\t\t\t\t.property('checked', plot.selected)\n\t\t\t\t.on('change', e => {\n\t\t\t\t\tlet plots = structuredClone(this.state.config.plots)\n\t\t\t\t\tplots.find(p => p.name == plot.name).selected = e.target.checked\n\t\t\t\t\tconst selectedCount = plots.filter(p => p.selected).length\n\t\t\t\t\tconst defaultSettings = getDefaultSingleCellSettings()\n\t\t\t\t\tlet settings = { svgw: defaultSettings.svgw, svgh: defaultSettings.svgh }\n\n\t\t\t\t\tif (selectedCount > 1) {\n\t\t\t\t\t\tconst width = 800\n\t\t\t\t\t\tconst height = 800\n\t\t\t\t\t\tsettings.svgh = width / selectedCount\n\t\t\t\t\t\tsettings.svgw = height / selectedCount\n\t\t\t\t\t\tsettings.contourBandwidth = 10\n\t\t\t\t\t}\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: { plots, settings: { singleCellPlot: settings } }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\tshowDiv.append('label').attr('for', key).text(plot.name)\n\t\t}\n\t}\n\n\trenderGeneExpressionControls(geDiv, state) {\n\t\tthis.dom.searchboxDiv = geDiv.append('div').style('display', 'inline-block')\n\t\tthis.dom.geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: this.app.opts.genome,\n\t\t\trow: this.dom.searchboxDiv,\n\t\t\tsearchOnly: 'gene',\n\t\t\tplaceholder: state.config.gene || 'Gene',\n\t\t\tcallback: () => this.colorByGeneExp(),\n\t\t\temptyInputCallback: () => this.colorByGeneExp(),\n\t\t\thideHelp: true,\n\t\t\tfocusOff: true\n\t\t})\n\t\tthis.dom.searchbox = this.dom.geneSearch?.searchbox\n\t}\n\n\tasync setActiveTab(tab) {\n\t\tif (!this.state) return\n\t\tawait this.app.dispatch({ type: 'plot_edit', id: this.id, config: { activeTab: tab } })\n\t}\n\n\tasync showActiveTab() {\n\t\tlet id = this.state.config.activeTab || this.tabs[0].id\n\t\tif (!this.isValidSample && id != SAMPLES_TAB) {\n\t\t\tid = SAMPLES_TAB\n\t\t\tthis.config.activeTab = SAMPLES_TAB\n\t\t}\n\t\tconst index = this.tabs.findIndex(t => t.id == id)\n\t\tconst tab = this.tabs[index]\n\t\ttab.active = true\n\t\tthis.tabsComp.update(index)\n\n\t\tthis.dom.deDiv.style('display', 'none')\n\t\tthis.dom.geDiv.style('display', 'none')\n\t\tthis.dom.showDiv.style('display', 'none')\n\t\tthis.dom.violinSelectDiv.style('display', 'none')\n\t\tthis.dom.samplesTableDiv.style('display', 'none')\n\t\tthis.dom.samplesPromptDiv.style('display', 'none')\n\t\tthis.dom.controlsHolder.style('display', 'none')\n\t\tswitch (id) {\n\t\t\tcase SAMPLES_TAB:\n\t\t\t\tthis.dom.samplesTableDiv.style('display', 'block')\n\t\t\t\tthis.dom.samplesPromptDiv.style('display', 'inline-block')\n\t\t\t\tthis.renderSamplesTable()\n\t\t\t\tbreak\n\t\t\tcase PLOTS_TAB:\n\t\t\t\tawait this.renderPlots()\n\t\t\t\tthis.dom.showDiv.style('display', 'inline-block')\n\t\t\t\tthis.dom.controlsHolder.style('display', 'block')\n\t\t\t\tbreak\n\n\t\t\tcase GENE_EXPRESSION_TAB:\n\t\t\t\tthis.dom.controlsHolder.style('display', 'block')\n\t\t\t\tawait this.renderPlots()\n\t\t\t\tthis.dom.geDiv.style('display', 'inline-block')\n\t\t\t\tthis.dom.searchbox.node().focus()\n\t\t\t\tif (this.state.config.gene) this.dom.searchbox.node().value = this.state.config.gene\n\t\t\t\tbreak\n\t\t\tcase DIFFERENTIAL_EXPRESSION_TAB:\n\t\t\t\tthis.dom.deDiv.style('display', 'inline-block')\n\t\t\t\tthis.renderDETable()\n\t\t\t\tbreak\n\n\t\t\tcase IMAGES_TAB:\n\t\t\t\tthis.renderImage()\n\t\t\t\tbreak\n\t\t\tcase VIOLIN_TAB:\n\t\t\t\tthis.dom.geDiv.style('display', 'inline-block')\n\t\t\t\tthis.renderViolinTab()\n\t\t\t\tthis.dom.searchbox.node().focus()\n\t\t\t\tbreak\n\t\t}\n\t}\n\n\taddZoomIcons(iconsDiv, plot) {\n\t\tconst zoomInDiv = iconsDiv.append('div').style('margin', '20px 0px')\n\t\ticon_functions['zoomIn'](zoomInDiv, {\n\t\t\thandler: () => {\n\t\t\t\tplot.particles.position.z += 0.1\n\t\t\t},\n\t\t\ttitle: 'Zoom in. You can also zoom in moving the mouse wheel with the Ctrl key pressed.'\n\t\t})\n\t\tconst zoomOutDiv = iconsDiv.append('div').style('margin', '20px 0px')\n\t\ticon_functions['zoomOut'](zoomOutDiv, {\n\t\t\thandler: () => {\n\t\t\t\tplot.particles.position.z -= 0.1\n\t\t\t},\n\t\t\ttitle: 'Zoom out. You can also zoom out moving the mouse wheel with the Ctrl key pressed.'\n\t\t})\n\t\tconst identityDiv = iconsDiv.append('div').style('margin', '20px 0px')\n\t\ticon_functions['restart'](identityDiv, {\n\t\t\thandler: () => {\n\t\t\t\tplot.particles.position.z = 0\n\t\t\t\tplot.particles.position.x = 0\n\t\t\t\tplot.particles.position.y = 0\n\t\t\t},\n\t\t\ttitle: 'Reset plot to defaults'\n\t\t})\n\t}\n\n\tasync renderImage() {\n\t\tconst sample = this.state.config.sample || this.samples[0].sample\n\t\tconst i = this.state.termdbConfig.queries.singleCell.images\n\t\tconst result = await dofetch3(`img?file=${i.folder}${i.folder.endsWith('/') ? '' : '/'}${sample}/${i.fileName}`)\n\t\tif (!result.src || result.error) {\n\t\t\tsayerror(this.dom.plotsDiv, 'Cannot load image: ' + (result.error || ''))\n\t\t\treturn\n\t\t}\n\t\tthis.dom.plotsDiv.append('img').attr('src', result.src).attr('height', 400)\n\t}\n\n\tasync renderViolinTab() {\n\t\tif (!this.state.config.gene) return\n\t\tconst selectDiv = this.dom.violinSelectDiv.style('display', 'inline-block')\n\t\tselectDiv.selectAll('*').remove()\n\t\tconst plotDiv = this.dom.plotsDiv.append('div').style('width', '100%')\n\n\t\tconst options = new Set()\n\t\tlet selectedOption = ''\n\t\tfor (const plot of this.data.plots) {\n\t\t\tconst colorBy = this.state.config.colorBy?.[plot.name] || plot.colorColumns[0]\n\t\t\tif (!selectedOption) selectedOption = colorBy\n\t\t\tfor (const c of plot.colorColumns) options.add(c)\n\t\t}\n\n\t\tif (options.size > 1) {\n\t\t\tselectDiv.append('label').text('Show expression by: ')\n\t\t\tconst expressionBySelect = selectDiv.append('select').on('change', async e => {\n\t\t\t\tconst expressionBy = e.target.value\n\t\t\t\tviolinDiv.selectAll('*').remove()\n\t\t\t\tthis.renderViolin(expressionBy, violinDiv)\n\t\t\t})\n\t\t\tthis.dom.expressionBySelect = expressionBySelect\n\t\t\texpressionBySelect\n\t\t\t\t.selectAll('option')\n\t\t\t\t.data(Array.from(options))\n\t\t\t\t.enter()\n\t\t\t\t.append('option')\n\t\t\t\t.attr('value', d => d)\n\t\t\t\t.attr('selected', d => (d == selectedOption ? d : null))\n\t\t\t\t.html(d => d)\n\t\t} else selectDiv.append('label').text(`Expression by ${selectedOption}:`)\n\t\tconst violinDiv = this.dom.plotsDiv.append('div')\n\t\tthis.renderViolin(selectedOption, violinDiv)\n\t}\n\n\tasync renderViolin(colorBy, violinDiv) {\n\t\tconst gene = this.state.config.gene\n\t\tconst plot = this.data.plots.find(p => p.colorColumns.find(c => c == colorBy))\n\t\tthis.initPlot(plot)\n\t\tconst values = {}\n\t\tfor (const cluster of plot.clusters) {\n\t\t\tvalues[cluster] = { key: cluster, value: cluster }\n\t\t}\n\t\tconst downloadFilename = (await this.getSampleFilename(this.state)) + '_VIOLIN'\n\t\tconst opts = {\n\t\t\tholder: violinDiv,\n\t\t\tstate: {\n\t\t\t\tvocab: this.state.vocab,\n\t\t\t\tplots: [\n\t\t\t\t\t{\n\t\t\t\t\t\tchartType: 'violin',\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t$id: await digestMessage(`${gene}-${this.state.config.sample}-${this.state.config.experimentID}`),\n\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\ttype: TermTypes.SINGLECELL_GENE_EXPRESSION,\n\t\t\t\t\t\t\t\tid: gene,\n\t\t\t\t\t\t\t\tgene,\n\t\t\t\t\t\t\t\tname: gene,\n\t\t\t\t\t\t\t\tsample: {\n\t\t\t\t\t\t\t\t\tsID: this.state.config.sample,\n\t\t\t\t\t\t\t\t\teID: this.state.config.experimentID\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t\t},\n\t\t\t\t\t\tterm2: {\n\t\t\t\t\t\t\t$id: await digestMessage(`${colorBy}-${this.state.config.sample}-${this.state.config.experimentID}`),\n\n\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\ttype: TermTypes.SINGLECELL_CELLTYPE,\n\t\t\t\t\t\t\t\tid: colorBy,\n\t\t\t\t\t\t\t\tname: colorBy,\n\t\t\t\t\t\t\t\tsample: {\n\t\t\t\t\t\t\t\t\tsID: this.state.config.sample,\n\t\t\t\t\t\t\t\t\teID: this.state.config.experimentID\n\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t//plot and color by are used to read the sample categories from the plot\n\t\t\t\t\t\t\t\tplot: plot.name,\n\t\t\t\t\t\t\t\tcolorBy,\n\t\t\t\t\t\t\t\tvalues\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\tdownloadFilename\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t}\n\t\tconst plotImport = await import('#plots/plot.app.js')\n\t\tconst plotAppApi = await plotImport.appInit(opts)\n\t}\n\n\tasync renderGSEA(holder) {\n\t\tconst gsea_params = {\n\t\t\tgenes: this.genes,\n\t\t\tfold_change: this.fold_changes,\n\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome\n\t\t}\n\t\tconst downloadFilename = (await this.getSampleFilename(this.state)) + '_GSEA'\n\t\tconst config = {\n\t\t\tchartType: 'gsea',\n\t\t\tgsea_params: gsea_params,\n\t\t\t// if getPlotHolder is defined, use this.mainDivId as insertBefore,\n\t\t\t// so that in GDC frontend framework, plots that are launched from scRNAseq\n\t\t\t// will be inserted before it. TODO: may insert after the scRNAseq plot instead???\n\t\t\tinsertBefore: this.app.opts?.app?.getPlotHolder ? this.mainDivId : this.id,\n\t\t\tdownloadFilename\n\t\t}\n\t\tconst opts = {\n\t\t\tgenome: this.app.opts.genome,\n\t\t\tholder,\n\t\t\tstate: {\n\t\t\t\tvocab: this.state.vocab,\n\t\t\t\tplots: [config]\n\t\t\t}\n\t\t}\n\t\tconst plotImport = await import('#plots/plot.app.js')\n\t\tconst plotAppApi = await plotImport.appInit(opts)\n\t}\n\n\tasync renderDETable() {\n\t\t//first plot\n\t\tthis.dom.deselect.selectAll('*').remove()\n\t\tthis.dom.deselect.append('option').text('')\n\t\tconst plot = this.data.plots[0]\n\t\tthis.initPlot(plot)\n\t\tfor (const cluster of plot.clusters) this.dom.deselect.append('option').text(cluster)\n\t\tconst categoryName = this.state.config.cluster\n\t\tthis.dom.deselect.node().value = categoryName != undefined ? `Cluster ${categoryName}` : ''\n\t\tif (!categoryName) return\n\t\tconst columnName = this.state.termdbConfig.queries.singleCell.DEgenes.termId\n\t\tconst sample =\n\t\t\tthis.state.config.experimentID || this.state.config.sample || this.samples?.[0]?.experiments[0]?.experimentID\n\n\t\tconst DEContentDiv = this.dom.plotsDiv.append('div').style('width', '100%')\n\n\t\tconst tabsDiv = DEContentDiv.append('div')\n\t\tconst tableDiv = DEContentDiv.append('div')\n\t\tconst GSEADiv = DEContentDiv.append('div').style('display', 'none')\n\n\t\tlet result\n\t\ttry {\n\t\t\tconst args = { genome: this.state.genome, dslabel: this.state.dslabel, categoryName, sample, columnName }\n\t\t\tresult = await dofetch3('termdb/singlecellDEgenes', { body: args })\n\t\t\tif (result.error) {\n\t\t\t\ttableDiv.text(result.error)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (!result.data || !result?.data?.length) {\n\t\t\t\ttableDiv.text('No differentially expressed genes found.')\n\t\t\t\treturn\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tif (e.stack) console.error(e.stack)\n\t\t\telse throw `Error fetching DE genes: ${e.message || e} [singleCellPlot.renderDETable()]`\n\t\t\treturn\n\t\t}\n\n\t\tconst tabs = [\n\t\t\t{\n\t\t\t\tlabel: 'Differentially Expressed Genes',\n\t\t\t\tid: DE_GENES_TAB,\n\t\t\t\tactive: true,\n\t\t\t\tcallback: () => showActiveDETab(DE_GENES_TAB)\n\t\t\t}\n\t\t]\n\t\tif (this.app.opts.genome.termdbs) {\n\t\t\t// assumption is that can run gsea on the differential genes, when the genome-level termdb is available (which is right now geneset dbs)\n\t\t\ttabs.push({\n\t\t\t\tlabel: 'Gene Set Enrichment Analysis (GSEA)',\n\t\t\t\tid: DE_GSEA_TAB,\n\t\t\t\tactive: false,\n\t\t\t\tcallback: () => showActiveDETab(DE_GSEA_TAB)\n\t\t\t})\n\t\t}\n\n\t\tfunction showActiveDETab(id) {\n\t\t\ttableDiv.style('display', 'none')\n\t\t\tGSEADiv.style('display', 'none')\n\t\t\tif (id == DE_GENES_TAB) tableDiv.style('display', 'block')\n\t\t\tif (id == DE_GSEA_TAB) GSEADiv.style('display', 'block')\n\t\t}\n\t\tif (tabs.length > 1) {\n\t\t\tconst deTabs = await new Tabs({\n\t\t\t\tholder: tabsDiv,\n\t\t\t\ttabsPosition: 'horizontal',\n\t\t\t\ttabs\n\t\t\t})\n\t\t\tdeTabs.main()\n\t\t}\n\n\t\ttableDiv.append('div').style('padding-bottom', '10px').text('Select a gene to view its expression:')\n\n\t\tconst tableDivContent = tableDiv.append('div').style('padding-bottom', '10px')\n\t\tconst columns = [\n\t\t\t{ label: 'Gene', width: '15vw' },\n\t\t\t{ label: 'Log2FC', width: '12vw', barplot: {} },\n\t\t\t{ label: 'Adjusted P-value', width: '12vw' }\n\t\t]\n\t\tconst rows = []\n\t\tthis.genes = []\n\t\tthis.fold_changes = []\n\t\tresult.data.sort((a, b) => b.fold_change - a.fold_change)\n\t\tconst selectedRows = []\n\t\tlet i = 0\n\t\tfor (const gene of result.data) {\n\t\t\tconst row = [\n\t\t\t\t{ value: gene.gene_name },\n\t\t\t\t{ value: gene.fold_change },\n\t\t\t\t{ value: roundValueAuto(gene.adjusted_p_value) }\n\t\t\t]\n\t\t\trows.push(row)\n\t\t\tthis.genes.push(gene.gene_name)\n\t\t\tthis.fold_changes.push(gene.fold_change)\n\t\t\tif (gene.gene_name == this.state.config.gene) selectedRows.push(i)\n\t\t\ti++\n\t\t}\n\t\tthis.DETable = { rows, columns }\n\t\tconst downloadFilename = `${await this.getSampleFilename(this.state)}_DE_GENES.tsv`\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tmaxHeight: '50vh',\n\t\t\tdiv: tableDivContent,\n\t\t\tsingleMode: true,\n\t\t\tnoButtonCallback: (i, node) => {\n\t\t\t\tconst gene = result.data[i].gene_name\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tgene,\n\t\t\t\t\t\tsample: this.state.config.sample || this.samples?.[0]?.sample,\n\t\t\t\t\t\texperimentID: this.state.config.experimentID || this.samples?.[0].experiments?.[0]?.experimentID,\n\t\t\t\t\t\tactiveTab: GENE_EXPRESSION_TAB\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t},\n\t\t\tselectedRows,\n\t\t\tresize: true,\n\t\t\tdownload: { fileName: downloadFilename }\n\t\t})\n\t\tthis.renderGSEA(GSEADiv)\n\t}\n\n\tcolorByGeneExp() {\n\t\tconst gene = this.dom.searchbox.node().value\n\n\t\tfor (const div of this.plotColorByDivs) div.style('display', 'none')\n\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: {\n\t\t\t\tgene,\n\t\t\t\tsample: this.state.config.sample || this.samples?.[0]?.sample,\n\t\t\t\texperimentID: this.state.config.experimentID || this.samples?.[0].experiments?.[0]?.experimentID\n\t\t\t}\n\t\t})\n\t}\n\n\tasync setControls() {\n\t\tthis.dom.controlsHolder.selectAll('*').remove()\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\tlabel: 'Chart width',\n\t\t\t\ttitle: 'Chart width',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\tsettingsKey: 'svgw',\n\t\t\t\tmin: 300,\n\t\t\t\tmax: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Chart height',\n\t\t\t\ttitle: 'Chart height',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\tsettingsKey: 'svgh',\n\t\t\t\tmin: 300,\n\t\t\t\tmax: 1000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Dot size',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\tsettingsKey: 'sampleSizeThree',\n\t\t\t\ttitle: 'Dot size',\n\t\t\t\tmin: 0.001,\n\t\t\t\tmax: 0.1,\n\t\t\t\tstep: 0.001\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Dot opacity',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\tsettingsKey: 'opacity',\n\t\t\t\ttitle: 'Dot opacity',\n\t\t\t\tmin: 0.1,\n\t\t\t\tmax: 1,\n\t\t\t\tstep: 0.1\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Show grid',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\tsettingsKey: 'showGrid',\n\t\t\t\ttitle: 'Show grid'\n\t\t\t}\n\t\t]\n\t\tconst enableContour = this.state.config.activeTab == GENE_EXPRESSION_TAB && this.state.config.gene\n\t\tif (enableContour)\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Show contour map',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\tsettingsKey: 'showContour',\n\t\t\t\ttitle:\n\t\t\t\t\t'Shows the density of point clouds. It uses gene expression to weight the points when calculating the density contours.'\n\t\t\t})\n\t\tif (enableContour && this.settings.showContour)\n\t\t\t//enabled and active\n\t\t\tinputs.push(\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Color contours',\n\t\t\t\t\tboxLabel: '',\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\t\tsettingsKey: 'colorContours'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Contour bandwidth',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\t\tsettingsKey: 'contourBandwidth',\n\t\t\t\t\ttitle: 'Reduce to increase resolution. ',\n\t\t\t\t\tmin: 5,\n\t\t\t\t\tmax: 50,\n\t\t\t\t\tstep: 5\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Contour thresholds',\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\t\tsettingsKey: 'contourThresholds',\n\t\t\t\t\ttitle: 'Dot size',\n\t\t\t\t\tmin: 5,\n\t\t\t\t\tmax: 30,\n\t\t\t\t\tstep: 5\n\t\t\t\t}\n\t\t\t)\n\t\tif (\n\t\t\t(this.state.config.activeTab == GENE_EXPRESSION_TAB ||\n\t\t\t\tthis.state.config.activeTab == DIFFERENTIAL_EXPRESSION_TAB) &&\n\t\t\tthis.state.config.gene\n\t\t)\n\t\t\tinputs.unshift({\n\t\t\t\tlabel: 'Show unexpressed cells',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\tsettingsKey: 'showNoExpCells',\n\t\t\t\ttitle: 'Show cells not expressing the selected gene'\n\t\t\t})\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controlsHolder,\n\t\t\t\tinputs\n\t\t\t})\n\t\t}\n\t\tthis.components.controls.on('downloadClick.singleCellPlot', async () => {\n\t\t\tif (!this.state) return\n\t\t\tconst filename = await this.getSampleFilename(this.state)\n\t\t\tif (this.state.config.activeTab == GENE_EXPRESSION_TAB || this.state.config.activeTab == PLOTS_TAB)\n\t\t\t\tfor (const plot of this.plots) this.downloadPlot(plot, filename)\n\t\t})\n\t}\n\n\tdownloadSCTable(name, table) {\n\t\tdownloadTable(table.rows, table.columns, name)\n\t}\n\n\tdownloadPlot(plot, filename) {\n\t\tdownloadSingleSVG(plot.legendSVG, filename + '_LEGEND.svg', this.opts.holder.node())\n\t\tconst downloadImgName = plot.name\n\t\tconst a = document.createElement('a')\n\t\tdocument.body.appendChild(a)\n\t\tconst dataURL = plot.canvas.toDataURL()\n\n\t\ta.addEventListener(\n\t\t\t'click',\n\t\t\t() => {\n\t\t\t\t// Download the image\n\t\t\t\ta.download = filename + '_' + downloadImgName + '.png'\n\t\t\t\ta.href = dataURL\n\t\t\t\tdocument.body.removeChild(a)\n\t\t\t},\n\t\t\tfalse\n\t\t)\n\t\ta.click()\n\t}\n\n\tshowNoMatchingDataMessage() {\n\t\tthis.dom.mainDiv.style('display', 'none')\n\t\tthis.dom.loadingDiv.selectAll('*').remove()\n\t\tthis.dom.loadingDiv.style('display', '').append('div').style('font-size', '1.2em').html('No matching cohort data.')\n\t}\n\n\trenderPlots() {\n\t\tconst result = this.data\n\t\tif (result.nodata) return\n\t\tfor (const plot of result.plots) {\n\t\t\tif (\n\t\t\t\t(this.state.config.activeTab == DIFFERENTIAL_EXPRESSION_TAB ||\n\t\t\t\t\tthis.state.config.activeTab == GENE_EXPRESSION_TAB) &&\n\t\t\t\tthis.state.config.gene &&\n\t\t\t\t!plot.expCells.length\n\t\t\t)\n\t\t\t\tcontinue\n\n\t\t\tthis.renderPlot(plot)\n\t\t}\n\t\tif (this.plots.length == 0) this.dom.plotsDiv.append('div').text('No data to plot')\n\t}\n\n\trenderPlot(plot) {\n\t\tif (!plot.plotDiv) {\n\t\t\tconst plotDiv = this.dom.plotsDiv.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\t\t\tconst leftDiv = plotDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.style('padding-top', '30px')\n\t\t\tplot.plotDiv = plotDiv.append('div').style('display', 'inline-block')\n\t\t\tthis.addZoomIcons(leftDiv, plot)\n\t\t}\n\t\tconst colorMap = {}\n\t\tthis.initPlot(plot)\n\n\t\tconst cat2Color = getColors(plot.clusters.length + 2) //Helps to use the same color scheme in different samples\n\t\tfor (const cluster of plot.clusters)\n\t\t\tcolorMap[cluster] = plot.colorMap?.[cluster] ? plot.colorMap[cluster] : cat2Color(cluster)\n\n\t\tplot.colorMap = colorMap\n\n\t\t//used to plot the cells\n\t\tthis.initAxes(plot)\n\n\t\t//.style('flex-grow', 1)\n\t\tplot.headerDiv = plot.plotDiv.append('div')\n\t\tplot.headerDiv.append('label').text(plot.name).style('font-size', '1.2em').style('margin-right', '10px')\n\t\tif (this.colorByGene && this.state.config.gene) {\n\t\t\t// for gene expression sc plot, needs to add colorGenerator to plot even\n\t\t\t// when legend is not needed for the plot\n\t\t\tif (!this.config.startColor[plot.name]) this.config.startColor[plot.name] = '#fffee0'\n\t\t\tif (!this.config.stopColor[plot.name]) this.config.stopColor[plot.name] = 'red'\n\t\t\tconst startColor = this.config.startColor[plot.name]\n\t\t\tconst stopColor = this.config.stopColor[plot.name]\n\t\t\tlet min, max\n\t\t\tconst expCells = plot.expCells\n\n\t\t\tconst values = expCells.map(cell => cell.geneExp).sort()\n\t\t\tplot.colorValues = values\n\t\t\tif (values.length == 0) {\n\t\t\t\tplot.colorGenerator = null\n\t\t\t} else {\n\t\t\t\tswitch (this.settings.colorScaleMode) {\n\t\t\t\t\t// Fixed mode: Use user-defined min/max values\n\t\t\t\t\t// This is useful when you want consistent scaling across different views\n\t\t\t\t\tcase 'fixed':\n\t\t\t\t\t\tmin = this.settings.colorScaleMinFixed\n\t\t\t\t\t\tmax = this.settings.colorScaleMaxFixed\n\t\t\t\t\t\tbreak\n\n\t\t\t\t\tcase 'percentile':\n\t\t\t\t\t\t// Percentile mode: Scale based on data distribution\n\t\t\t\t\t\tmin = values[0] // Start at the first value of the array for percentile mode\n\t\t\t\t\t\t// Calculate the value at the specified percentile\n\t\t\t\t\t\t// This helps handle outliers by focusing on the main distribution\n\t\t\t\t\t\tconst index = Math.floor((values.length * this.settings.colorScalePercentile) / 100)\n\t\t\t\t\t\tmax = values[index]\n\t\t\t\t\t\tbreak\n\n\t\t\t\t\tcase 'auto':\n\t\t\t\t\tdefault:\n\t\t\t\t\t\t// Auto mode (default): Use the full range of the data\n\t\t\t\t\t\t// This gives the most accurate representation of the actual data distribution\n\t\t\t\t\t\tmin = values[0]\n\t\t\t\t\t\tmax = values[values.length - 1] // Since the values are already sorted in ascending\n\t\t\t\t\t\t// order just get the first and last values\n\t\t\t\t\t\tbreak\n\t\t\t\t}\n\n\t\t\t\tplot.colorGenerator = d3Linear().domain([min, max]).range([startColor, stopColor])\n\t\t\t}\n\t\t}\n\t\tthis.renderLargePlotThree(plot)\n\t\tthis.renderLegend(plot)\n\t}\n\n\tinitPlot(plot) {\n\t\tthis.plots.push(plot)\n\t\tconst expCells = plot.expCells.sort((a, b) => a.geneExp - b.geneExp)\n\t\tplot.cells = [...plot.noExpCells, ...expCells]\n\t\tplot.id = plot.name.replace(/\\s+/g, '')\n\t\tlet clusters = new Set(plot.cells.map(c => c.category))\n\n\t\tplot.clusters = Array.from(clusters).sort((a, b) => {\n\t\t\tconst num1 = parseInt(a.split(' ')[1])\n\t\t\tconst num2 = parseInt(b.split(' ')[1])\n\t\t\treturn num1 - num2\n\t\t})\n\t}\n\n\tgetOpacity(d) {\n\t\tif (this.config.hiddenClusters[d.category]) return 0\n\t\tif (this.colorByGene && this.state.config.gene && !d.geneExp)\n\t\t\treturn this.settings.showNoExpCells ? this.settings.opacity : 0\n\t\treturn this.settings.opacity\n\t}\n\n\tgetColor(d, plot) {\n\t\tlet color = plot.colorMap[d.category]\n\t\tif (this.colorByGene && this.state.config.gene) {\n\t\t\tif (!d.geneExp) color = noExpColor\n\t\t\telse if (d.geneExp > plot.max) color = plot.colorGenerator(plot.max)\n\t\t\telse color = plot.colorGenerator(d.geneExp)\n\t\t}\n\t\treturn color\n\t}\n\n\thandleZoom(e, plot) {\n\t\tplot.mainG.attr('transform', e.transform)\n\t}\n\n\tinitAxes(plot) {\n\t\tif (!plot.cells.length) return\n\t\tconst s0 = plot.cells[0]\n\t\tconst [xMin, xMax, yMin, yMax] = plot.cells.reduce(\n\t\t\t(s, d) => [d.x < s[0] ? d.x : s[0], d.x > s[1] ? d.x : s[1], d.y < s[2] ? d.y : s[2], d.y > s[3] ? d.y : s[3]],\n\t\t\t[s0.x, s0.x, s0.y, s0.y]\n\t\t)\n\t\tplot.xAxisScale = d3Linear().domain([xMin, xMax]).range([-1, 1])\n\t\tplot.yAxisScale = d3Linear().domain([yMin, yMax]).range([-1, 1])\n\t}\n\n\trenderLegend(plot) {\n\t\tconst colorMap = plot.colorMap\n\t\tlet legendSVG = plot.legendSVG\n\t\tconst clustersHeight = 20 * Object.keys(colorMap).length + 50 //added 50 for the title and padding\n\t\tconst height = Math.max(this.settings.svgh, clustersHeight)\n\t\tif (!plot.legendSVG) {\n\t\t\tconst activeTab = this.tabs.find(tab => tab.active)\n\t\t\tif (activeTab.id == PLOTS_TAB) {\n\t\t\t\tconst app = this.app\n\n\t\t\t\tif (plot.colorColumns.length > 1) {\n\t\t\t\t\tconst plotColorByDiv = plot.headerDiv\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t\t.style('padding-bottom', '20px')\n\t\t\t\t\tplotColorByDiv.append('label').text('Color by:').style('margin-right', '5px')\n\t\t\t\t\tconst colorBySelect = plotColorByDiv.append('select')\n\t\t\t\t\tthis.plotColorByDivs.push(plotColorByDiv)\n\t\t\t\t\tcolorBySelect\n\t\t\t\t\t\t.selectAll('option')\n\t\t\t\t\t\t.data(plot.colorColumns)\n\t\t\t\t\t\t.enter()\n\t\t\t\t\t\t.append('option')\n\t\t\t\t\t\t.attr('value', d => d)\n\t\t\t\t\t\t.property('selected', d => d == this.state.config.colorBy?.[plot.name])\n\t\t\t\t\t\t.html(d => d)\n\t\t\t\t\tcolorBySelect.on('change', () => {\n\t\t\t\t\t\tconst colorBy = colorBySelect.node().value\n\t\t\t\t\t\tapp.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\tconfig: { colorBy: { [plot.name]: colorBy } }\n\t\t\t\t\t\t})\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tlegendSVG = plot.plotDiv\n\t\t\t\t.append('svg')\n\t\t\t\t.attr('width', 250)\n\t\t\t\t.attr('height', height)\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('vertical-align', 'top')\n\t\t\t\t.style('font-size', '0.9em')\n\n\t\t\tplot.legendSVG = legendSVG\n\t\t}\n\t\tlegendSVG.selectAll('*').remove()\n\n\t\tthis.legendRendered = true\n\n\t\tif (\n\t\t\t(this.state.config.activeTab == GENE_EXPRESSION_TAB ||\n\t\t\t\tthis.state.config.activeTab == DIFFERENTIAL_EXPRESSION_TAB) &&\n\t\t\tthis.state.config.gene\n\t\t) {\n\t\t\tthis.renderColorGradient(plot)\n\t\t\treturn\n\t\t}\n\t\tlet x = 20\n\n\t\tplot.legendSVG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(${x}, ${25})`)\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.text(`${plot.colorBy}`)\n\t\tlet step = 25\n\t\tif (height < 500) {\n\t\t\tplot.legendSVG.style('font-size', '0.8em')\n\t\t\tstep = 20\n\t\t}\n\t\tlet y = 50\n\t\tconst configPlot = this.state.config.plots.find(p => p.name == plot.name)\n\t\tconst aliases = configPlot.colorColumns.find(c => c.name == plot.colorBy)?.aliases\n\t\tfor (const cluster in colorMap) {\n\t\t\tconst clusterCells = plot.cells.filter(item => item.category == cluster)\n\t\t\tconst hidden = this.config.hiddenClusters?.[cluster]\n\t\t\tconst n = clusterCells.length\n\t\t\tconst color = colorMap[cluster]\n\t\t\tconst itemG = plot.legendSVG.append('g').attr('transform', c => `translate(${x}, ${y})`)\n\t\t\titemG.append('circle').attr('r', 5).attr('fill', color)\n\t\t\titemG\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', `translate(15, 5)`)\n\t\t\t\t.append('text')\n\t\t\t\t.text(\n\t\t\t\t\t`${\n\t\t\t\t\t\tcluster == 'ref'\n\t\t\t\t\t\t\t? this.state.termdbConfig.queries.singleCell.data.refName\n\t\t\t\t\t\t\t: cluster == 'query'\n\t\t\t\t\t\t\t? this.state.config.sample || this.samples[0].sample\n\t\t\t\t\t\t\t: aliases\n\t\t\t\t\t\t\t? aliases[cluster]\n\t\t\t\t\t\t\t: cluster\n\t\t\t\t\t} n=${n}`\n\t\t\t\t)\n\t\t\t\t.style('text-decoration', hidden ? 'line-through' : 'none')\n\t\t\t\t.on('click', e => this.showLegendItemMenu(e, cluster, plot))\n\t\t\ty += step\n\t\t}\n\t}\n\n\thideCategory(key, hidden) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { hiddenClusters: { [key]: hidden } }\n\t\t})\n\t}\n\n\tshowLegendItemMenu(e, key, plot) {\n\t\tlet hiddenCount = 0\n\t\tfor (const cluster in this.state.config.hiddenClusters) if (this.state.config.hiddenClusters[cluster]) hiddenCount++\n\t\tconst hidden = this.state.config.hiddenClusters?.[key]\n\t\tif (hidden && hiddenCount == 1) {\n\t\t\t//show hidden category and skip menu\n\t\t\tthis.hideCategory(key, false, plot.legendSVG)\n\t\t\treturn\n\t\t}\n\t\tconst menu = this.tip.clear()\n\t\tconst div = menu.d.append('div')\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text(hidden ? 'Show' : 'Hide')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.hideCategory(key, !hidden, plot.legendSVG)\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text('Show only')\n\t\t\t.on('click', () => {\n\t\t\t\tfor (const cluster in plot.colorMap) if (key != cluster) this.hideCategory(cluster, true, plot.legendSVG)\n\t\t\t\tthis.hideCategory(key, false, plot.legendSVG)\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t\tif (hiddenCount > 1)\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t\t.text('Show all')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tmenu.hide()\n\t\t\t\t\tfor (const mapKey in plot.colorMap) this.hideCategory(mapKey, false, plot.legendSVG)\n\t\t\t\t})\n\t\tmenu.showunder(e.target)\n\t}\n\n\trenderColorGradient(plot) {\n\t\tif (plot.cells.length == 0 || !plot.colorGenerator) return\n\t\tconst colors = [this.config.startColor[plot.name], this.config.stopColor[plot.name]]\n\t\tconst gene = this.state.config.gene\n\t\tlet offsetY = 20\n\t\tconst barwidth = 100\n\t\tplot.legendSVG\n\t\t\t.append('g')\n\t\t\t.attr('transform', `translate(${20}, ${offsetY})`)\n\t\t\t.append('text')\n\t\t\t.text(`${gene} expression`)\n\t\tconst legendG = plot.legendSVG.append('g').attr('transform', `translate(20, ${2 * offsetY})`)\n\t\tconst colorScale = new ColorScale({\n\t\t\tholder: legendG,\n\t\t\tbarwidth,\n\t\t\tbarheight: 20,\n\t\t\tcolors,\n\t\t\tdomain: plot.colorGenerator.domain(),\n\n\t\t\tposition: '0, 20',\n\t\t\tticks: 4,\n\t\t\ttickSize: 5,\n\t\t\ttopTicks: true,\n\t\t\tsetColorsCallback: (val, idx) => {\n\t\t\t\tthis.changeGradientColor(plot, val, idx)\n\t\t\t},\n\t\t\tnumericInputs: {\n\t\t\t\tcutoffMode: this.settings.colorScaleMode,\n\t\t\t\tdefaultPercentile: this.settings.colorScalePercentile,\n\t\t\t\tcallback: obj => {\n\t\t\t\t\tlet min, max\n\t\t\t\t\tconst colorValues = plot.colorValues\n\t\t\t\t\t// Handle different modes for color scaling\n\t\t\t\t\tif (obj.cutoffMode === 'auto') {\n\t\t\t\t\t\tmin = colorValues[0]\n\t\t\t\t\t\tmax = colorValues[colorValues.length - 1]\n\t\t\t\t\t} else if (obj.cutoffMode === 'fixed') {\n\t\t\t\t\t\tmin = obj.min\n\t\t\t\t\t\tmax = obj.max\n\t\t\t\t\t} else if (obj.cutoffMode === 'percentile') {\n\t\t\t\t\t\tmin = colorValues[0]\n\t\t\t\t\t\tconst index = Math.floor((colorValues.length * obj.percentile) / 100)\n\t\t\t\t\t\tmax = colorValues[index]\n\t\t\t\t\t}\n\n\t\t\t\t\t// Dispatch the updated config\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\tsingleCellPlot: {\n\t\t\t\t\t\t\t\t\tcolorScaleMode: obj.cutoffMode,\n\t\t\t\t\t\t\t\t\tcolorScaleMinFixed: obj.cutoffMode === 'fixed' ? min : null,\n\t\t\t\t\t\t\t\t\tcolorScaleMaxFixed: obj.cutoffMode === 'fixed' ? max : null,\n\t\t\t\t\t\t\t\t\tcolorScalePercentile:\n\t\t\t\t\t\t\t\t\t\tobj.cutoffMode === 'percentile' ? obj.percentile : this.settings.colorScalePercentile\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\tcolorScale.updateScale()\n\t}\n\n\tchangeGradientColor = function (plot, newColor, idx) {\n\t\tconst colorKey = idx == 0 ? 'startColor' : 'stopColor'\n\t\tthis.config[colorKey][plot.name] = newColor\n\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: this.config\n\t\t})\n\t}\n\n\tdistance(x1, y1, x2, y2, plot) {\n\t\tconst x = plot.xAxisScale(x2) - plot.xAxisScale(x1)\n\t\tconst y = plot.yAxisScale(y2) - plot.yAxisScale(y1)\n\t\tconst distance = Math.sqrt(Math.pow(x, 2) + Math.pow(y, 2))\n\t\treturn distance\n\t}\n\n\tshowTooltip(event, plot) {\n\t\tif (this.onClick && event.type == 'click') {\n\t\t\tthis.onClick = false\n\t\t\tthis.tip.hide()\n\t\t\treturn\n\t\t}\n\t\tif (event.target.tagName == 'circle') {\n\t\t\tthis.onClick = event.type == 'click'\n\n\t\t\tconst d = event.target.__data__\n\n\t\t\tconst menu = this.tip.clear()\n\t\t\tconst table = menu.d.append('table')\n\t\t\tlet tr = table.append('tr')\n\t\t\ttr.append('td').style('color', '#aaa').text(plot.colorBy)\n\n\t\t\tlet td = tr.append('td')\n\t\t\ttd.text(d.category)\n\n\t\t\tif ('geneExp' in d) {\n\t\t\t\ttr = table.append('tr')\n\t\t\t\ttr.append('td').style('color', '#aaa').text('Gene expression')\n\t\t\t\ttd = tr.append('td')\n\t\t\t\tconst svg = td.append('svg').attr('width', 150).attr('height', 20)\n\t\t\t\tconst x = 10\n\t\t\t\tconst y = 12\n\t\t\t\tconst g = svg.append('g').attr('transform', `translate(${x}, ${y})`)\n\t\t\t\tg.append('circle').attr('fill', this.getColor(d, plot)).attr('r', 4)\n\t\t\t\tsvg\n\t\t\t\t\t.append('g')\n\t\t\t\t\t.attr('transform', `translate(${x + 15}, ${y + 4})`)\n\t\t\t\t\t.append('text')\n\t\t\t\t\t.text(roundValueAuto(d.geneExp))\n\t\t\t}\n\t\t\tmenu.show(event.clientX, event.clientY, true, true)\n\t\t} else this.onMouseOut(event)\n\t}\n\n\tonMouseOut(event) {\n\t\tthis.tip.hide()\n\t}\n\n\tasync renderSamplesTable() {\n\t\tconst state = this.state\n\t\t// need to do this after the this.samples has been set\n\n\t\tconst div = this.dom.samplesTableDiv\n\n\t\tdiv.selectAll('*').remove()\n\t\tconst [rows, columns] = await this.getTableData(state)\n\t\tif (columns.length > 5) div.style('font-size', '0.9em')\n\t\tconst selectedRows = []\n\t\tconst i = this.samples.findIndex(i => i.sample == state.config.sample)\n\t\tif (i != -1) selectedRows.push(i)\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tresize: true,\n\t\t\tsingleMode: true,\n\t\t\tdiv,\n\t\t\tmaxWidth: columns.length > 3 ? '98vw' : '40vw',\n\t\t\tmaxHeight: '50vh',\n\t\t\tnoButtonCallback: index => {\n\t\t\t\t// NOTE that \"index\" is not array index of this.samples[]\n\t\t\t\tconst sample = rows[index][0].value\n\t\t\t\tconst hiddenClusters = {}\n\t\t\t\t// reset hidden clusters when changing sample\n\t\t\t\tfor (const cluster in this.config.hiddenClusters) hiddenClusters[cluster] = false\n\t\t\t\t// reset these settings when changing sample\n\t\t\t\tconst settings = {\n\t\t\t\t\tcolorScaleMode: 'auto',\n\t\t\t\t\tcolorScaleMinFixed: null,\n\t\t\t\t\tcolorScaleMaxFixed: null,\n\t\t\t\t\tcolorScalePercentile: 95,\n\t\t\t\t\tshowNoExpCells: false,\n\t\t\t\t\tshowContour: false,\n\t\t\t\t\tcolorContours: false,\n\t\t\t\t\tcontourBandwidth: 15,\n\t\t\t\t\tcontourThresholds: 10\n\t\t\t\t}\n\t\t\t\tconst config = {\n\t\t\t\t\tchartType: 'singleCellPlot',\n\t\t\t\t\tsample, // track sample name to identify it in this.samples[]\n\t\t\t\t\tactiveTab: PLOTS_TAB, // on selecting a sample from table, auto switch to plots to directly show this sample's plots, to save user a click\n\t\t\t\t\tcluster: null, // reset cluster\n\t\t\t\t\thiddenClusters, // reset hidden clusters\n\t\t\t\t\tsettings: { singleCellPlot: settings }\n\t\t\t\t}\n\t\t\t\tthis.genes = null // reset DE genes\n\t\t\t\tif (rows[index][0].__experimentID) {\n\t\t\t\t\tconfig.experimentID = rows[index][0].__experimentID\n\t\t\t\t}\n\n\t\t\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config })\n\t\t\t},\n\t\t\tselectedRows,\n\t\t\tstriped: true,\n\t\t\theader: { style: { 'text-transform': 'capitalize' } } // to show header in title case; if it results in a conflict (e.g. a sample name showing in 1st tab has to be lower case), then use sampleColumns[].columnHeader as override of term name\n\t\t})\n\t}\n\n\tasync getTableData(state) {\n\t\tconst { uiLabels } = state.config.settings.singleCellPlot\n\t\tconst s = state.termdbConfig.queries?.singleCell?.samples || {}\n\t\tconst samples = this.samples\n\t\tconst rows = []\n\t\tconst hasExperiments = samples.some(i => i.experiments)\n\t\t// first column is sample and is hardcoded\n\t\tconst columns = [{ label: uiLabels.Sample }]\n\t\tif (hasExperiments) columns.push({ label: 'Sample' }) //add after the case column\n\n\t\t// add in optional sample columns\n\t\tfor (const c of s.sampleColumns || []) {\n\t\t\tlet label = c.termid\n\t\t\ttry {\n\t\t\t\tlabel = (await this.app.vocabApi.getterm(c.termid)).name\n\t\t\t} catch (e) {\n\t\t\t\t/* term not found by c.termid, in such case ignore and just show termid as column header\n\t\t\t\tthis is due to practical constrain that gdc needs to supply analysis.workflow_type as 'Library',\n\t\t\t\tbut this is not a term in gdc dictionary\n\t\t\t\t*/\n\t\t\t}\n\t\t\tcolumns.push({ label, width: '14vw' })\n\t\t}\n\n\t\t// if samples are using experiments, add the hardcoded experiment column at the end\n\t\tif (hasExperiments) columns.push({ label: 'Experiment' }) // corresponds to this.samples[].experiments[].experimentID\n\n\t\tfor (const sample of samples) {\n\t\t\tif (hasExperiments)\n\t\t\t\t//GDC\n\t\t\t\tfor (const exp of sample.experiments) {\n\t\t\t\t\t// first cell is always sample name. sneak in experiment object to be accessed in click callback\n\t\t\t\t\tconst row = [{ value: sample.sample, __experimentID: exp.experimentID }]\n\t\t\t\t\t// hardcode to expect exp.sampleName and add this as a column\n\t\t\t\t\trow.push({ value: exp.sampleName })\n\t\t\t\t\t// optional sample and experiment columns\n\t\t\t\t\tfor (const c of s.sampleColumns || []) {\n\t\t\t\t\t\trow.push({ value: sample[c.termid] })\n\t\t\t\t\t}\n\n\t\t\t\t\t// hardcode to always add in experiment id column\n\t\t\t\t\tconst urlTemp = this.state.termdbConfig?.urlTemplates?.scrnaExperimentId\n\t\t\t\t\tif (urlTemp) row.push({ value: exp.experimentID, url: `${urlTemp.base}${exp.experimentID}` })\n\t\t\t\t\telse row.push({ value: exp.experimentID })\n\t\t\t\t\trows.push(row)\n\t\t\t\t}\n\t\t\telse {\n\t\t\t\t// sample does not use experiment\n\n\t\t\t\t// first cell is sample name\n\t\t\t\tconst row = [{ value: sample.sample }]\n\n\t\t\t\t// optional sample columns\n\t\t\t\tfor (const c of s.sampleColumns || []) {\n\t\t\t\t\trow.push({ value: sample[c.termid] })\n\t\t\t\t}\n\t\t\t\trows.push(row)\n\t\t\t}\n\t\t}\n\n\t\t//const index = columnNames.length == 1 ? 0 : columnNames.length - 1\n\t\t//columns[index].width = '25vw'\n\t\treturn [rows, columns]\n\t}\n\n\trenderLargePlotThree = async function (plot) {\n\t\tif (!plot.canvas) {\n\t\t\tconst canvas = plot.plotDiv.append('canvas').style('display', 'inline-block').style('vertical-align', 'top')\n\t\t\tplot.canvas = canvas.node()\n\t\t\tplot.canvas.width = this.settings.svgw\n\t\t\tplot.canvas.height = this.settings.svgh\n\t\t\tplot.renderer = new THREE.WebGLRenderer({ antialias: true, canvas: plot.canvas, preserveDrawingBuffer: true })\n\t\t} else plot.renderer.clear()\n\n\t\tconst renderer = plot.renderer\n\n\t\t//WebGLRenderer.outputColorSpace property determines the color space of the final rendered output. By default this is set to THREE.SRGBColorSpace, so that the rendered image is correctly displayed on standard monitors.\n\t\t//There are times where you may want to set the output color space to THREE.LinearSRGBColorSpace, so that color information is not altered before post processing effects are applied.\n\t\t//This fixes the issue where the colors are washed out and look lighter than in the legend\n\t\trenderer.outputColorSpace = THREE.LinearSRGBColorSpace\n\t\tconst DragControls = await import('three/examples/jsm/controls/DragControls.js')\n\n\t\tconst fov = this.settings.threeFOV\n\t\tconst near = 0.1\n\t\tconst far = 1000\n\t\tconst camera = new THREE.PerspectiveCamera(fov, 1, near, far)\n\t\tconst scene = new THREE.Scene()\n\t\tcamera.position.set(0, 0, 2)\n\t\tcamera.lookAt(scene.position)\n\t\tcamera.updateMatrix()\n\t\tconst whiteColor = new THREE.Color('rgb(255,255,255)')\n\t\tscene.background = whiteColor\n\n\t\tconst geometry = new THREE.BufferGeometry()\n\t\tconst { vertices, colors } = this.getVertices(plot)\n\n\t\tgeometry.setAttribute('position', new THREE.Float32BufferAttribute(vertices, 3))\n\t\tgeometry.setAttribute('color', new THREE.Float32BufferAttribute(colors, 3))\n\t\tconst tex = getThreeCircle(256)\n\t\tconst material = new THREE.PointsMaterial({\n\t\t\tsize: this.settings.sampleSizeThree,\n\t\t\tsizeAttenuation: true,\n\t\t\ttransparent: true,\n\t\t\topacity: this.settings.opacity,\n\t\t\tmap: tex,\n\t\t\tvertexColors: true\n\t\t})\n\n\t\tconst particles = new THREE.Points(geometry, material)\n\t\tplot.particles = particles\n\t\tscene.add(particles)\n\n\t\trenderer.setSize(this.settings.svgw, this.settings.svgh)\n\t\trenderer.setPixelRatio(window.devicePixelRatio)\n\n\t\tplot.canvas.addEventListener('mousewheel', event => {\n\t\t\tif (!event.ctrlKey) return\n\t\t\tevent.preventDefault()\n\t\t\tparticles.position.z -= event.deltaY / 500\n\t\t})\n\n\t\tif (this.settings.showContour && this.state.config.gene && this.state.config.activeTab == GENE_EXPRESSION_TAB) {\n\t\t\tconst cells = plot.expCells.length > 0 ? plot.expCells : plot.cells\n\t\t\tconst xAxisScale = plot.xAxisScale.range([0, this.settings.svgw])\n\t\t\tconst yAxisScale = plot.yAxisScale.range([this.settings.svgh, 0])\n\t\t\tlet zAxisScale\n\t\t\tif (plot.expCells.length > 0) {\n\t\t\t\tconst [min, max] = extent(plot.expCells, d => d.geneExp)\n\t\t\t\tzAxisScale = d3Linear().domain([min, max]).range([0, 1])\n\t\t\t}\n\n\t\t\tconst xCoords = cells.map(c => xAxisScale(c.x))\n\t\t\tconst yCoords = cells.map(c => yAxisScale(c.y))\n\t\t\tconst zCoords = cells.map(c => (zAxisScale ? zAxisScale(c.geneExp) : 1))\n\t\t\tawait this.renderContourMap(scene, xCoords, yCoords, zCoords, plot)\n\t\t}\n\n\t\tconst controls = new DragControls.DragControls([particles], camera, renderer.domElement)\n\n\t\tfunction animate() {\n\t\t\trequestAnimationFrame(animate)\n\t\t\trenderer.render(scene, camera)\n\t\t}\n\t\tanimate()\n\t\tif (this.settings.showGrid) this.renderThreeGrid(scene)\n\t}\n\n\tasync renderContourMap(scene, xCoords, yCoords, zCoords, plot) {\n\t\tconst data = xCoords.map((x, i) => ({ x, y: yCoords[i], z: zCoords[i] }))\n\t\t// Create the data URL\n\t\tconst imageUrl = getContourImage(\n\t\t\tdata,\n\t\t\tthis.settings.svgw,\n\t\t\tthis.settings.svgh,\n\t\t\tthis.settings.colorContours,\n\t\t\tthis.settings.contourBandwidth,\n\t\t\tthis.settings.contourThresholds\n\t\t)\n\t\tconst loader = new THREE.TextureLoader()\n\t\tloader.load(imageUrl, texture => {\n\t\t\t// Create a plane geometry\n\t\t\tconst geometry = new THREE.PlaneGeometry(2, 2)\n\t\t\t// Create a material using the loaded texture\n\t\t\t// the transparent parameter is needed to keep the contours transparent, otherwise the background will be black\n\t\t\t// the color parameter is needed to make the contours darker, otherwise they are light gray\n\t\t\tconst material = new THREE.MeshBasicMaterial({ map: texture, transparent: true, color: 0x141414 })\n\t\t\t// Create a mesh with the geometry and material\n\t\t\tconst plane = new THREE.Mesh(geometry, material)\n\t\t\t// Add the plane to the scene\n\t\t\tscene.add(plane)\n\t\t\tplot.plane = plane\n\t\t\tplane.position.z = 0.00001 //makes the plane be on top of the particles\n\t\t\tplot.particles.add(plane) //makes the plane move with the particles\n\t\t})\n\t}\n\n\trenderThreeGrid(scene) {\n\t\tlet x = -1\n\t\t// Line Geometry\n\t\tconst lineMaterial = new THREE.LineBasicMaterial({ color: 0xffd3d3d3 })\n\n\t\tconst lines = 10\n\t\tconst step = 2 / lines\n\n\t\tfor (let i = 0; i < lines; i++) {\n\t\t\tlet points = []\n\t\t\tpoints.push(new THREE.Vector3(x, 1.5, 0))\n\t\t\tpoints.push(new THREE.Vector3(x, -1.5, 0))\n\t\t\tlet lineGeometry = new THREE.BufferGeometry().setFromPoints(points)\n\t\t\tlet line = new THREE.Line(lineGeometry, lineMaterial)\n\t\t\tline.position.z = 1\n\n\t\t\tscene.add(line)\n\t\t\tpoints = []\n\t\t\tpoints.push(new THREE.Vector3(-1.5, x, 0))\n\t\t\tpoints.push(new THREE.Vector3(1.5, x, 0))\n\t\t\tlineGeometry = new THREE.BufferGeometry().setFromPoints(points)\n\t\t\tline = new THREE.Line(lineGeometry, lineMaterial)\n\t\t\tscene.add(line)\n\t\t\tx += step\n\t\t\tline.position.z = 1\n\t\t}\n\t}\n\n\tgetVertices(plot) {\n\t\tconst vertices = []\n\t\tconst colors = []\n\t\tfor (const c of plot.cells) {\n\t\t\tconst opacity = this.getOpacity(c)\n\t\t\tif (opacity == 0) continue\n\t\t\tlet x = plot.xAxisScale(c.x)\n\t\t\tlet y = plot.yAxisScale(c.y)\n\t\t\tconst rgbColor = rgb(this.getColor(c, plot))\n\t\t\tvertices.push(x, y, 0)\n\t\t\tcolors.push(rgbColor.r / 255, rgbColor.g / 255, rgbColor.b / 255)\n\t\t}\n\t\treturn { vertices, colors }\n\t}\n}\n\nexport function getContourImage(data, width, height, colorContours, bandwidth, thresholds) {\n\tconst svg = create('svg').attr('width', width).attr('height', height)\n\n\trenderContours(svg.append('g'), data, width, height, colorContours, bandwidth, thresholds)\n\n\t// Serialize the SVG element\n\tconst svgString = new XMLSerializer().serializeToString(svg.node())\n\n\t// Encode the SVG string\n\tconst encodedSvg = encodeURIComponent(svgString)\n\n\t// Create the data URL\n\tconst imageUrl = 'data:image/svg+xml;charset=utf-8,' + encodedSvg\n\treturn imageUrl\n}\n\n// Function to get mouse position in normalized device coordinates (-1 to +1)\nexport function getMouseNDC(event, rect) {\n\t//const rect = renderer.domElement.getBoundingClientRect()\n\treturn new THREE.Vector2(\n\t\t((event.clientX - rect.left) / rect.width) * 2 - 1,\n\t\t(-(event.clientY - rect.top) / rect.height) * 2 + 1\n\t)\n}\n\nexport const scatterInit = getCompInit(singleCellPlot)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = scatterInit\n\nexport async function getPlotConfig(opts, app) {\n\ttry {\n\t\tconst data = app.vocabApi.termdbConfig?.queries?.singleCell?.data\n\t\tconst plots = data?.plots\n\t\tlet settings = getDefaultSingleCellSettings()\n\t\tif (data.settings)\n\t\t\tfor (const key in data.settings) {\n\t\t\t\tsettings[key] = data.settings[key]\n\t\t\t}\n\n\t\tconst config = {\n\t\t\thiddenClusters: {},\n\t\t\tsettings: {\n\t\t\t\tsingleCellPlot: settings,\n\t\t\t\tcontrols: { isOpen: false }\n\t\t\t},\n\t\t\tstartColor: {},\n\t\t\tstopColor: {},\n\t\t\tplots,\n\t\t\thidePlotFilter: true\n\t\t}\n\t\t// may apply term-specific changes to the default object\n\t\tconst result = copyMerge(config, opts)\n\t\treturn result\n\t} catch (e) {\n\t\tconsole.log(e)\n\t\tthrow `${e} [singleCellPlot getPlotConfig()]`\n\t}\n}\n\nexport function getDefaultSingleCellSettings() {\n\treturn {\n\t\tsvgw: 600,\n\t\tsvgh: 600,\n\t\tshowGrid: true,\n\t\tsampleSize: 1.5,\n\t\tsampleSizeThree: 0.04,\n\t\tthreeFOV: 60,\n\t\topacity: 0.8,\n\t\tshowNoExpCells: false,\n\t\tshowContour: false,\n\t\tcolorContours: false,\n\t\tcontourBandwidth: 15,\n\t\tcontourThresholds: 10,\n\t\tuiLabels: {\n\t\t\t// allow customized user interface labels (buttons, menus, etc) by dataset override,\n\t\t\t// for example in GDC, use 'Case' instead of 'Sample'\n\t\t\t// TODO: different plots should use the same uiLabels override,\n\t\t\t// should not need to define separately for matrix, single cell, etc\n\t\t\tSamples: 'Samples',\n\t\t\tsamples: 'samples',\n\t\t\tSample: 'Sample',\n\t\t\tsample: 'sample'\n\t\t},\n\t\tcolorScaleMode: 'auto', // Default to automatic scaling based on data range\n\t\t// Other options: 'fixed' (user-defined range) or\n\t\t// 'percentile' (scale based on data distribution)\n\n\t\tcolorScalePercentile: 95, // Default percentile for percentile mode\n\t\t// This means we'll scale colors based on values\n\t\t// up to the 95th percentile by default\n\t\tcolorScaleMinFixed: null, // User-defined minimum value for fixed mode\n\t\t// Null indicates this hasn't been set yet\n\t\tcolorScaleMaxFixed: null // User-defined maximum value for fixed mode\n\t}\n}\n"],
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