@sjcrh/proteinpaint-client 2.219.1 → 2.220.0

package/dist/chunk-LO2QBHP6.js

@@ -1,418 +0,0 @@
-import {
-  addBrushes,
-  addNewBrush
-} from "./chunk-4ENIOXIT.js";
-import {
-  escapeHtml,
-  niceNumLabels,
-  violinRenderer
-} from "./chunk-BKW35Z4U.js";
-import {
-  convertUnits,
-  getValueConversionFactor
-} from "./chunk-W5J3LTYS.js";
-import {
-  NumericRangeInput
-} from "./chunk-6XKAOSQE.js";
-import {
-  roundValueAuto
-} from "./chunk-TLT4YIG3.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// filter/tvs.numeric.js
-var handler = {
-  type: "numeric",
-  term_name_gen,
-  get_pill_label,
-  getSelectRemovePos,
-  fillMenu,
-  setTvsDefaults
-};
-function term_name_gen(d) {
-  const name = d.term.name;
-  return name.length < 26 ? escapeHtml(name) : '<label title="' + escapeHtml(name) + '">' + escapeHtml(name.substring(0, 24)) + "...</label>";
-}
-function get_pill_label(tvs) {
-  if (tvs.ranges.length == 1) {
-    const v = tvs.ranges[0];
-    if ("value" in v) {
-      if (v.label) return { txt: escapeHtml(v.label) };
-      if (tvs.term.values && tvs.term.values[v.value] && tvs.term.values[v.value].label)
-        return { txt: escapeHtml(tvs.term.values[v.value].label) };
-      console.error(`key "${v.value}" not found in values{} of ${tvs.term.name}`);
-      return { txt: escapeHtml(v.value) };
-    }
-    return { txt: format_val_text(v, tvs.term) + mafDepthText(tvs) };
-  }
-  return { txt: tvs.ranges.length + " intervals" + mafDepthText(tvs) };
-}
-function mafDepthText(tvs) {
-  if (tvs.term.mafFilterMode != "maf") return "";
-  if (!Number.isFinite(tvs.minAllelicDepth) || tvs.minAllelicDepth < 1) return "";
-  return `, Total depth &ge; ${tvs.minAllelicDepth}`;
-}
-function format_val_text(range, term) {
-  const x = '<span style="font-family:Times;font-style:italic;font-size:1em; vertical-align:top">x</span>';
-  if (range.startunbounded && range.stopunbounded) {
-    const inf = (sign = "") => `<span style='vertical-align: middle; font-size:1.1em; line-height: 0.9em'>${sign}\u221E</span>`;
-    const lt = `<span style='vertical-align: top; font-size: 0.9em'>&lt;</span>`;
-    return `<span>${inf("\uFE63")} ${lt} ${x} ${lt} ${inf("\uFE62")}</span>`;
-  }
-  const vc = term.valueConversion;
-  if (range.startunbounded)
-    return `${x} ${range.stopinclusive ? "&le;" : "&lt;"} ${vc ? convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.stop}`;
-  if (range.stopunbounded)
-    return `${x} ${range.startinclusive ? "&ge;" : "&gt;"} ${vc ? convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.start}`;
-  let startName, stopName;
-  if (vc) {
-    startName = convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-    stopName = convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-  } else {
-    ;
-    [startName, stopName] = niceNumLabels([range.start, range.stop]);
-  }
-  return `${startName} 
-			${range.startinclusive ? "&le;" : "&lt;"}
-			${x}
-			${range.stopinclusive ? "&le;" : "&lt;"}
-			${stopName}`;
-}
-function getSelectRemovePos(j, tvs) {
-  return j - tvs.ranges.slice(0, j).filter((a) => a.start || a.stop).length;
-}
-async function fillMenu(self, div, tvs) {
-  const num_parent_div = div.append("div");
-  self.num_obj = {};
-  self.num_obj.num_div = num_parent_div.append("div").attr("class", "num_div").style("padding", "5px").style("color", "#000");
-  self.num_obj.plot_size = {
-    width: 450,
-    height: 100,
-    xpad: 10,
-    ypad: 20,
-    radius: 8
-  };
-  if (typeof self.opts.vocabApi.getViolinBox == "function") {
-    try {
-      const data = await self.opts.vocabApi.getViolinBox(
-        {
-          plotType: "violin",
-          tw: { term: tvs.term, q: { mode: "continuous" } },
-          // must supply this filter and override state filter in function, so the density plot will not be limited to range defined by current numeric tvs but will show whole range
-          filter: self.filter,
-          svgw: self.num_obj.plot_size.width,
-          radius: self.num_obj.plot_size.radius
-        },
-        self.opts.getCategoriesArguments
-      );
-      if (data.error) throw data.error;
-      if (data.max === null && data.min === null) {
-        throw `No data available under current filter conditions.`;
-      }
-      self.num_obj.density_data = data;
-    } catch (err) {
-      throw err;
-    }
-  } else {
-    self.num_obj.density_data = {};
-  }
-  if (self.num_obj.density_data.error) throw self.num_obj.density_data.error;
-  if (!self.num_obj.density_data.charts?.[""]?.plots?.[0]?.density?.bins) {
-    addRangeTableNoDensity(self, tvs);
-    return;
-  }
-  self.vr = new violinRenderer({
-    holder: self.num_obj.num_div,
-    rd: self.num_obj.density_data,
-    width: self.num_obj.plot_size.width,
-    radius: self.num_obj.plot_size.radius,
-    height: self.num_obj.plot_size.height,
-    // axis ticks are labeled in the term's user-facing unit, e.g. years and not days
-    scaleFactor: getValueConversionFactor(tvs.term)
-  });
-  self.vr.render();
-  self.num_obj.svg = self.vr.svg;
-  self.num_obj.range_table = self.num_obj.num_div.append("table").style("table-layout", "fixed").style("border-collapse", "collapse");
-  const ranges = [];
-  for (const [index, range] of tvs.ranges.entries()) {
-    range.index = index;
-    ranges.push(range);
-  }
-  self.num_obj.brush_g = self.vr.brushG.attr("class", "brush_g");
-  self.num_obj.xscale = self.vr.axisScale;
-  self.num_obj.ranges = ranges;
-  self.num_obj.brushes = [];
-  addBrushes(self);
-  addRangeTable(self);
-  if (!ranges.length) {
-    const callback = () => addRangeTable(self);
-    addNewBrush(self, "center", callback);
-  }
-  self.num_obj.brushes.forEach((brush) => brush.init());
-  await showCheckList_numeric(self, tvs, div);
-}
-function setTvsDefaults(tvs) {
-  if (!tvs.ranges) tvs.ranges = [];
-}
-function addRangeTableNoDensity(self, tvs) {
-  const termrange = tvs.term.range || {};
-  const range = tvs.ranges && tvs.ranges[0] ? tvs.ranges[0] : termrange;
-  const num_div = self.num_obj.num_div;
-  num_div.selectAll("*").remove();
-  const brush = {};
-  const holder = num_div.append("div").style("padding-left", "5px");
-  const mafFilterMode = tvs.term.mafFilterMode;
-  if (mafFilterMode == "maf" && tvs.term.child_ids?.length > 1) {
-    const ids = tvs.term.child_ids;
-    const list = ids.slice(0, -1).join(", ") + " and " + ids[ids.length - 1];
-    holder.append("div").style("margin-bottom", "8px").style("font-size", ".9em").style("opacity", 0.7).text(`MAF is computed by summing allelic depths from ${list}`);
-  }
-  const rangeRow = holder.append("div").style("display", "flex").style("align-items", "center").style("column-gap", "5px");
-  const rangeLabel = rangeRow.append("span");
-  brush.equation_div = rangeRow.append("div");
-  brush.rangeInput = new NumericRangeInput(brush.equation_div, range, () => {
-  }, {
-    width: "125px",
-    scaleFactor: getValueConversionFactor(tvs.term),
-    // without a density plot, the term's declared bounds are the only check of a typed range
-    min: tvs.term.min,
-    max: tvs.term.max
-  });
-  if (mafFilterMode == "maf") {
-    rangeLabel.text("MAF Range (0-1)");
-    const depthRow = holder.append("div").style("display", "flex").style("align-items", "center").style("column-gap", "5px").style("margin-top", "5px");
-    depthRow.append("span").text("Minimum Total Depth");
-    brush.depthInput = depthRow.append("input").attr("type", "number").attr("min", 1).attr("step", 1).style("width", "125px").property("value", Number.isFinite(tvs.minAllelicDepth) ? tvs.minAllelicDepth : "");
-    brush.apply_btn = addApplyButton(holder.append("div").style("margin-top", "10px"));
-  } else if (mafFilterMode == "value") {
-    rangeLabel.text("Range");
-    brush.apply_btn = addApplyButton(rangeRow);
-  } else if (mafFilterMode == "totalDepth" || mafFilterMode == "altDepth") {
-    rangeLabel.text(mafFilterMode == "totalDepth" ? "Total Depth" : "Alt Allele Depth");
-    brush.apply_btn = addApplyButton(rangeRow);
-  } else {
-    rangeLabel.text("Range");
-    brush.apply_btn = addApplyButton(rangeRow);
-  }
-  if (mafFilterMode) brush.rangeInput.getInput().node().focus();
-  function addApplyButton(holder2) {
-    return holder2.append("button").text("Apply").on("click", clickApply);
-  }
-  function clickApply() {
-    const r = brush.rangeInput.getRange();
-    if (!Number.isFinite(r.start) && !Number.isFinite(r.stop)) {
-      window.alert("Invalid range.");
-      return;
-    }
-    const new_tvs = { term: tvs.term, ranges: [r] };
-    if (brush.depthInput) {
-      const str = brush.depthInput.property("value").trim();
-      if (str) {
-        const minAllelicDepth = Number(str);
-        if (!Number.isFinite(minAllelicDepth)) {
-          window.alert("Minimum allelic depth must be a numeric value.");
-          return;
-        }
-        new_tvs.minAllelicDepth = Math.max(minAllelicDepth, 1);
-      }
-    }
-    self.dom.tip.hide();
-    self.opts.callback(new_tvs);
-  }
-}
-function addRangeTable(self) {
-  const brushes = self.num_obj.brushes;
-  const range_divs = self.num_obj.range_table.selectAll(".range_div").data(brushes);
-  range_divs.exit().each(function() {
-    select_default(this).style("opacity", 1).transition().duration(100).style("opacity", 0).remove();
-  });
-  range_divs.enter().append("tr").attr("class", "range_div").style("white-space", "nowrap").style("padding", "2px").transition().duration(200).each(function(brush, i) {
-    enterRange(self, this, brush, i);
-  });
-}
-function enterRange(self, tr, brush, i) {
-  if (!brush.range_tr) brush.range_tr = select_default(tr);
-  const range_tr = brush.range_tr;
-  const xscale = self.num_obj.xscale;
-  range_tr.append("td").style("margin-left", "10px").style("padding", "3px 10px").style("font-size", ".9em").text("Range " + (i + 1) + ": ");
-  brush.equation_td = range_tr.append("td").style("width", "150px");
-  brush.rangeInput = new NumericRangeInput(brush.equation_td, brush.range, apply, {
-    scaleFactor: getValueConversionFactor(self.tvs.term)
-  });
-  makeRangeButtons(self, brush);
-  if (i == 0) {
-    self.num_obj.range_table.append("tr").attr("class", "note_tr").append("td").attr("colspan", "3").append("div").style("font-size", ".8em").style("margin-left", "20px").style("font-style", "italic").style("color", "#888").html("Option 1: Drag the rectangle to select a range. Overlapping ranges will be merged.");
-  }
-  if (i == 0) {
-    self.num_obj.range_table.append("tr").attr("class", "note_tr").append("td").attr("colspan", "3").append("div").style("font-size", ".8em").style("margin-left", "20px").style("font-style", "italic").style("color", "#888").html(
-      `Option 2: Type in values to select a range.${self.tvs.term.valueConversion ? ` Values are in the unit of ${self.tvs.term.valueConversion.toUnit}.` : ""}`
-    );
-  }
-  function apply(new_range) {
-    const minvalue = self.num_obj.density_data.min;
-    const maxvalue = self.num_obj.density_data.max;
-    validateRangeInData(self, new_range);
-    brush.range = new_range;
-    const start = new_range.value != void 0 ? new_range.value : new_range.start != void 0 ? new_range.start : minvalue;
-    const stop = new_range.value != void 0 ? new_range.value : new_range.stop != void 0 ? new_range.stop : maxvalue;
-    const clamp = (v) => Math.min(Math.max(v, minvalue), maxvalue);
-    brush.elem.call(brush.d3brush).call(brush.d3brush.move, [clamp(start), clamp(stop)].map(xscale));
-  }
-  function makeRangeButtons(self2, brush2) {
-    const buttons_td = brush2.range_tr.append("td");
-    const range = brush2.range;
-    brush2.apply_btn = buttons_td.append("button").style("margin-left", "10px").text("Apply").on("click", async () => {
-      try {
-        const new_range = brush2.rangeInput.parseRange();
-        const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
-        delete new_tvs.groupset_label;
-        if (self2.num_obj.ranges.length > 1) new_tvs.ranges = mergeOverlapRanges(self2, new_range);
-        else new_tvs.ranges[range.index] = new_range;
-        validateNumericTvs(new_tvs);
-        self2.dom.tip.hide();
-        self2.opts.callback(new_tvs);
-      } catch (ex) {
-        alert(ex);
-      }
-    });
-    buttons_td.append("button").attr("class", "sja_filter_tag_btn sjpp_delete_btn").style("display", self2.num_obj.ranges.length > 1 ? "inline-block" : "none").style("margin-left", "10px").style("text-transform", "uppercase").text("Delete").on("click", async () => {
-      const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
-      new_tvs.ranges.splice(range.index, 1);
-      self2.num_obj.ranges.pop();
-      self2.num_obj.brushes.pop();
-      self2.num_obj.num_div.select(".note_tr").remove();
-      addBrushes(self2);
-      addRangeTable(self2);
-      if (new_tvs.ranges.length) self2.opts.callback(new_tvs);
-    });
-  }
-}
-function mergeOverlapRanges(self, new_range) {
-  let ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
-  let merged_flag = false;
-  for (const [i, range] of ranges.entries()) {
-    if (!range.value && new_range.index != i) {
-      if (new_range.start <= range.start && new_range.stop >= range.stop) {
-        range.start = new_range.start;
-        range.stop = new_range.stop;
-        merged_flag = true;
-      } else if (new_range.start <= range.stop && new_range.stop >= range.stop) {
-        range.stop = new_range.stop;
-        merged_flag = true;
-      } else if (new_range.stop >= range.start && new_range.start <= range.start) {
-        range.start = new_range.start;
-        merged_flag = true;
-      } else if (new_range.start >= range.start && new_range.stop <= range.stop) {
-        merged_flag = true;
-      } else if (new_range.startunbounded) {
-        if (new_range.stop > range.stop) {
-          range.stop = new_range.stop;
-        }
-        delete range.start;
-        range.startunbounded = true;
-        merged_flag = true;
-      } else if (new_range.stopunbounded) {
-        if (new_range.start < range.start) {
-          range.start = new_range.start;
-        }
-        delete range.stop;
-        range.stopunbounded = true;
-        merged_flag = true;
-      }
-    }
-  }
-  if (merged_flag) {
-    if (new_range.index <= ranges.length - 1) ranges.splice(new_range.index, 1);
-  } else {
-    ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
-    if (new_range.index) ranges[new_range.index] = new_range;
-    else ranges.push(new_range);
-  }
-  return ranges;
-}
-async function showCheckList_numeric(self, tvs, div) {
-  if (!tvs.term.values) {
-    return;
-  }
-  const values = await self.opts.vocabApi.getNumericUncomputableCategories(tvs.term, self.filter);
-  const unannotated_cats = [];
-  const lst = values?.lst || values;
-  for (const cat of lst) {
-    const key = "key" in cat ? cat.key : cat.value;
-    if (!("key" in cat)) cat.key = key;
-    if (!("value" in cat)) cat.value = key;
-    if (key in tvs.term.values) {
-      cat.label = tvs.term.values[key].label;
-      unannotated_cats.push(cat);
-    }
-  }
-  const sortedVals = unannotated_cats.sort((a, b) => {
-    return b.samplecount - a.samplecount;
-  });
-  const unanno_div = div.append("div").style("padding", "5px").style("color", "#000");
-  const callback = (indexes) => {
-    try {
-      const new_tvs = JSON.parse(JSON.stringify(tvs));
-      delete new_tvs.groupset_label;
-      new_tvs.ranges = [
-        ...new_tvs.ranges.filter((r) => !("value" in r)),
-        ...indexes.map((i) => ({ value: sortedVals[i].value, label: sortedVals[i].label }))
-      ];
-      self.dom.tip.hide();
-      if (new_tvs.ranges.length == 0) throw "select at least one range or category";
-      if (JSON.parse(JSON.stringify(tvs) != new_tvs)) {
-        try {
-          validateNumericTvs(new_tvs);
-        } catch (e) {
-          window.alert(e);
-          return;
-        }
-        self.opts.callback(new_tvs);
-      }
-    } catch (e) {
-      window.alert(e);
-    }
-  };
-  const values_table = self.makeValueTable(unanno_div, tvs, sortedVals, callback).node();
-}
-function validateRangeInData(self, range) {
-  if (range.value != void 0) return;
-  const { min, max } = self.num_obj.density_data;
-  if (!Number.isFinite(min) || !Number.isFinite(max)) return;
-  const aboveMax = !range.startunbounded && (range.start > max || range.start == max && !range.startinclusive);
-  const belowMin = !range.stopunbounded && (range.stop < min || range.stop == min && !range.stopinclusive);
-  if (!aboveMax && !belowMin) return;
-  const sf = getValueConversionFactor(self.tvs.term);
-  const [minLabel, maxLabel] = [min, max].map((v) => roundValueAuto(v * sf));
-  throw `The range is outside of the data, which ranges from ${minLabel} to ${maxLabel}`;
-}
-function validateNumericTvs(tvs) {
-  if (!tvs.term) throw "tvs.term is not defined";
-  if (!tvs.ranges) throw `.values[] missing for a term ${tvs.term.name}`;
-  if (!Array.isArray(tvs.ranges)) throw `.values[] is not an array for a term ${tvs.term.name}`;
-  if (!tvs.ranges.length) throw `no categories selected for ${tvs.term.name}`;
-  for (const range of tvs.ranges) {
-    if (range.value != void 0) {
-      if (!range.label) throw `.label missing for special category for a term ${tvs.term.name}`;
-    } else {
-      if (range.startunbounded) {
-        if (range.stopunbounded) throw `both start & stop are unbounded for a term ${tvs.term.name}`;
-        if (!Number.isFinite(range.stop)) throw `.stop undefined when start is unbounded for a term ${tvs.term.name}`;
-      } else if (range.stopunbounded) {
-        if (!Number.isFinite(range.start)) throw `.start undefined when stop is unbounded for a term ${tvs.term.name}`;
-      } else {
-        if (!Number.isFinite(range.start))
-          throw `.start undefined when start is not unbounded for a term ${tvs.term.name}`;
-        if (!Number.isFinite(range.stop)) throw `.stop undefined when stop is not unbounded for a term ${tvs.term.name}`;
-        if (range.start >= range.stop) throw `.start is not lower than stop for a term ${tvs.term.name}`;
-      }
-    }
-  }
-}
-
-export {
-  handler,
-  format_val_text
-};
-//# sourceMappingURL=chunk-LO2QBHP6.js.map

package/dist/chunk-LSRFRZNP.js

@@ -1,59 +0,0 @@
-import {
-  plotColor
-} from "./chunk-ME3HB3V6.js";
-
-// plots/scatter/settings/defaults.ts
-function getDefaultScatterSettings(opts = {}) {
-  const overrides = opts?.overrides || {};
-  const defaults = {
-    size: 0.8,
-    minShapeSize: 0.5,
-    maxShapeSize: 4,
-    scaleDotOrder: "Ascending",
-    refSize: 0.8,
-    svgw: 600,
-    svgh: 600,
-    svgd: 600,
-    axisTitleFontSize: 16,
-    showAxes: true,
-    showRef: true,
-    opacity: 0.6,
-    defaultColor: plotColor,
-    regression: "None",
-    fov: 50,
-    threeSize: 5e-3,
-    threeFOV: 70,
-    maxSvgSamplesCutoff: 2e4,
-    // if a cohort is larger than this, switch from svg to webgl/canvas rendering
-    //ColorScale settings
-    colorScaleMode: "auto",
-    colorScalePercentile: 95,
-    colorScaleMinFixed: null,
-    colorScaleMaxFixed: null,
-    noExpColor: "#F5F5F5",
-    // light gray, for dots with no gene expression value
-    expColor: "#ff000d",
-    // default color for the maximum gene expression value
-    //3D Plot settings
-    showContour: false,
-    colorContours: false,
-    contourBandwidth: 30,
-    contourThresholds: 10,
-    duration: 500,
-    useGlobalMinMax: true,
-    saveZoomTransform: false,
-    // Axis scale settings
-    minXScale: null,
-    maxXScale: null,
-    minYScale: null,
-    maxYScale: null,
-    itemLabel: opts?.singleCellPlot ? "Cell" : "Sample",
-    maxTooltipRows: 5
-  };
-  return Object.assign(defaults, overrides);
-}
-
-export {
-  getDefaultScatterSettings
-};
-//# sourceMappingURL=chunk-LSRFRZNP.js.map