@sjcrh/proteinpaint-client 2.220.0 → 2.222.0

package/dist/chunk-HMTQ4M66.js

@@ -0,0 +1,305 @@
+import {
+  appear2 as appear,
+  axisstyle,
+  bwSetting,
+  disappear2 as disappear,
+  makeNumericAxisConfig,
+  rgb2hex
+} from "./chunk-4ASBDE27.js";
+import {
+  dofetch3
+} from "./chunk-4TJO2DGU.js";
+import {
+  axisLeft
+} from "./chunk-WJLRU5OF.js";
+import {
+  format,
+  linear
+} from "./chunk-4OLM3KSB.js";
+
+// src/block.tk.bigwig.js
+function bigwigfromtemplate(tk, template) {
+  tk.scale = {};
+  if (template.scale) {
+    for (const k in template.scale) {
+      tk.scale[k] = template.scale[k];
+    }
+  } else {
+    tk.scale.auto = 1;
+  }
+  if (tk.normalize) {
+  } else {
+    tk.normalize = {
+      dividefactor: 1,
+      disable: 1
+    };
+  }
+  tk.barheight = template.height || 50;
+  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
+  if (!tk.ncolor) tk.ncolor = "#BD005E";
+  if (!tk.ncolor2) tk.ncolor2 = "#5E00BD";
+  if (!tk.pcolor) tk.pcolor = "#005EBD";
+  if (!tk.pcolor2) tk.pcolor2 = "#FA7D00";
+}
+function bigwigmaketk(tk, block) {
+  tk.img = tk.glider.append("image");
+  tk.tklabel.attr("y", tk.barheight / 2);
+  tk.leftaxis = tk.gleft.append("g");
+  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
+    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+    bigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block));
+  });
+}
+async function bigwigload(tk, block) {
+  block.tkcloakon(tk);
+  const par = block.tkarg_q(tk);
+  if (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor;
+  if (tk.bgcolor) par.bgcolor = tk.bgcolor;
+  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
+  tk.img.attr("width", block.width).attr("height", tk.barheight);
+  let errtext;
+  try {
+    let data;
+    if (tk.imgData) {
+      data = tk.imgData;
+    } else {
+      data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
+    }
+    if (data.error) throw data.error;
+    if (!data.src) throw "data.src missing";
+    tk.img.attr("xlink:href", data.src);
+    if (data.minv != void 0) {
+      tk.scale.min = data.minv;
+    }
+    if (data.maxv != void 0) {
+      tk.scale.max = data.maxv;
+    }
+    const sameMinMax = tk.scale.min == tk.scale.max;
+    tk.tklabel.transition().attr("y", !data.nodata && sameMinMax ? block.labelfontsize / 2 : tk.barheight / 2);
+    tk.leftaxis.selectAll("*").remove();
+    if (data.nodata) {
+      throw "No data in view range";
+    }
+    const scale = linear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0]);
+    const axis = axisLeft().scale(scale).tickValues(sameMinMax ? [tk.scale.min] : [tk.scale.min, tk.scale.max]);
+    if (tk.integer4axis) {
+      axis.tickFormat(format("d"));
+    } else if (sameMinMax) {
+      axis.tickFormat(format("~g"));
+    }
+    axisstyle({
+      axis: tk.leftaxis.call(axis),
+      color: "black",
+      showline: true
+    });
+  } catch (err) {
+    tk.img.attr("width", 0).attr("height", 0);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+    errtext = typeof err == "string" ? err : err.message;
+  } finally {
+    block.tkcloakoff(tk, { error: errtext });
+    block.block_setheight();
+    for (const panel of tk.subpanels) {
+      bigwigloadsubpanel(tk, block, panel);
+    }
+  }
+}
+async function bigwigloadsubpanel(tk, block, panel) {
+  block.tkcloakon_subpanel(panel);
+  const par = block.tkarg_q(tk);
+  if (tk.dotplotfactor) {
+    par.dotplotfactor = tk.dotplotfactor;
+  }
+  par.width = panel.width;
+  par.rglst = [
+    {
+      chr: panel.chr,
+      start: panel.start,
+      stop: panel.stop,
+      width: panel.width
+    }
+  ];
+  delete par.percentile;
+  delete par.autoscale;
+  panel.img.attr("width", panel.width).attr("height", tk.barheight);
+  let errtext;
+  try {
+    if (tk.imgData) throw "subpanel not supported by imgData yet";
+    const data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
+    if (data.error) throw data.error;
+    panel.img.attr("xlink:href", data.src);
+  } catch (err) {
+    panel.img.attr("width", 0).attr("height", 0);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+    errtext = typeof err == "string" ? err : err.message;
+  } finally {
+    block.tkcloakoff_subpanel(panel, { error: errtext });
+  }
+}
+function bigwigconfigpanel(tk, block, holder, loader) {
+  const config = {
+    pcolor: {},
+    ncolor: {},
+    pcolor2: {},
+    ncolor2: {},
+    // .row
+    // .lab
+    dotplot: {},
+    // .row
+    dividefactor: {}
+  };
+  {
+    const row = holder.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Height  ");
+    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
+      if (event.code != "Enter") return;
+      const s = event.target.value;
+      if (s == "") return;
+      const v = Number.parseInt(s);
+      if (Number.isNaN(v) || v <= 1) {
+        alert("track height must be positive integer");
+        return;
+      }
+      tk.barheight = v;
+      loader(bwSetting.height);
+    });
+  }
+  config.pcolor.row = holder.append("div").style("margin-bottom", "15px");
+  config.pcolor.lab = config.pcolor.row.append("span").text("Positive value color").style("padding-right", "10px");
+  config.pcolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor)).on("change", (event) => {
+    tk.pcolor = event.target.value;
+    loader(bwSetting.pcolor);
+  });
+  config.ncolor.row = holder.append("div").style("margin-bottom", "15px");
+  config.ncolor.lab = config.ncolor.row.append("span").text("Negative value color").style("padding-right", "10px");
+  config.ncolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor)).on("change", (event) => {
+    tk.ncolor = event.target.value;
+    loader(bwSetting.ncolor);
+  });
+  if (!tk.scale.auto) {
+    config.pcolor2.row = holder.append("div").style("margin-bottom", "15px");
+    config.pcolor2.lab = config.pcolor2.row.append("span").html("&ge;Max color").style("padding-right", "10px");
+    config.pcolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor2)).on("change", (event) => {
+      tk.pcolor2 = event.target.value;
+      loader(bwSetting.pcolor2);
+    });
+    config.ncolor2.row = holder.append("div").style("margin-bottom", "15px");
+    config.ncolor2.lab = config.ncolor2.row.append("span").html("&le;Min color").style("padding-right", "10px");
+    config.ncolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor2)).on("change", (event) => {
+      tk.ncolor2 = event.target.value;
+      loader(bwSetting.ncolor2);
+    });
+  }
+  {
+    const setting = {};
+    if (tk.scale.auto) {
+      setting.auto = 1;
+    } else if (tk.scale.percentile) {
+      setting.percentile = tk.scale.percentile;
+    } else {
+      setting.fixed = { min: tk.scale.min, max: tk.scale.max };
+    }
+    makeNumericAxisConfig({
+      holder: holder.append("div").style("margin-bottom", "15px"),
+      setting,
+      callback: (s) => {
+        if (s.auto) {
+          tk.scale.auto = 1;
+          loader(bwSetting.autoscale);
+          return;
+        }
+        if (s.fixed) {
+          delete tk.scale.auto;
+          delete tk.scale.percentile;
+          tk.scale.max = s.fixed.max;
+          tk.scale.min = s.fixed.min;
+          loader(bwSetting.fixedscale);
+          return;
+        }
+        delete tk.scale.auto;
+        tk.scale.percentile = s.percentile;
+        loader(bwSetting.percentilescale);
+      }
+    });
+  }
+  {
+    config.dotplot.row = holder.append("div").style("margin-bottom", "15px");
+    config.dotplot.row.append("span").html("Dot plot&nbsp;&nbsp;");
+    const s = config.dotplot.row.append("select").on("change", (event) => {
+      const i = event.target.selectedIndex;
+      if (i == 0) {
+        delete tk.dotplotfactor;
+      } else {
+        tk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML);
+      }
+      loader(i == 0 ? bwSetting.nodotplot : bwSetting.usedotplot);
+    });
+    let o = s.append("option").text("no");
+    if (!tk.dotplotfactor) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("5");
+    if (tk.dotplotfactor == 5) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("10");
+    if (tk.dotplotfactor == 10) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("15");
+    if (tk.dotplotfactor == 15) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("20");
+    if (tk.dotplotfactor == 20) {
+      o.property("selected", 1);
+    }
+  }
+  config.dividefactor.row = holder.append("div");
+  {
+    const id = Math.random().toString();
+    const input = config.dividefactor.row.append("input").attr("type", "checkbox").attr("id", id);
+    if (!tk.normalize.disable) {
+      input.property("checked", 1);
+    }
+    config.dividefactor.row.append("label").html("&nbsp;Apply normalization").attr("for", id);
+    const folder = config.dividefactor.row.append("div").style("margin", "5px 10px 0px 20px").style("display", tk.normalize.disable ? "none" : "block");
+    folder.append("span").html("Divide raw value by&nbsp;");
+    const factorinput = folder.append("input").attr("type", "number").style("width", "60px").property("value", tk.normalize.dividefactor).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      const v = event.target.value;
+      if (v <= 0) {
+        return;
+      }
+      tk.normalize.dividefactor = v;
+      loader(bwSetting.usedividefactor);
+    });
+    folder.append("div").text("Enter a value above zero").style("font-size", ".7em").style("color", "#858585");
+    input.on("change", (event) => {
+      if (event.target.checked) {
+        appear(folder);
+        delete tk.normalize.disable;
+        factorinput.property("value", tk.normalize.dividefactor);
+        loader(bwSetting.usedividefactor);
+        return;
+      }
+      disappear(folder);
+      tk.normalize.disable = 1;
+      loader(bwSetting.nodividefactor);
+    });
+  }
+  return config;
+}
+
+export {
+  bigwigfromtemplate,
+  bigwigmaketk,
+  bigwigload,
+  bigwigloadsubpanel,
+  bigwigconfigpanel
+};
+//# sourceMappingURL=chunk-HMTQ4M66.js.map

package/dist/chunk-HMTQ4M66.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../src/block.tk.bigwig.js"],
+  "sourcesContent": ["import { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport * as client from './client'\nimport { dofetch3 } from '#common/dofetch'\nimport { format as d3format } from 'd3-format'\nimport { makeNumericAxisConfig } from '#dom/numericAxis'\n\n/*\nFIXME\nbigwigloadsubpanel should return promise and be tracked\n*/\n\nexport function bigwigfromtemplate(tk, template) {\n\ttk.scale = {}\n\tif (template.scale) {\n\t\tfor (const k in template.scale) {\n\t\t\ttk.scale[k] = template.scale[k]\n\t\t}\n\t} else {\n\t\ttk.scale.auto = 1\n\t}\n\n\tif (tk.normalize) {\n\t} else {\n\t\t// disable by default\n\t\ttk.normalize = {\n\t\t\tdividefactor: 1,\n\t\t\tdisable: 1\n\t\t}\n\t}\n\ttk.barheight = template.height || 50\n\ttk.height_main = tk.toppad + tk.barheight + tk.bottompad\n\tif (!tk.ncolor) tk.ncolor = '#BD005E'\n\tif (!tk.ncolor2) tk.ncolor2 = '#5E00BD'\n\tif (!tk.pcolor) tk.pcolor = '#005EBD'\n\tif (!tk.pcolor2) tk.pcolor2 = '#FA7D00'\n}\n\nexport function bigwigmaketk(tk, block) {\n\ttk.img = tk.glider.append('image')\n\ttk.tklabel.attr('y', tk.barheight / 2)\n\n\ttk.leftaxis = tk.gleft.append('g')\n\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', () => {\n\t\ttk.tkconfigtip.clear().showunder(tk.config_handle.node())\n\t\tbigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block))\n\t})\n}\n\nexport async function bigwigload(tk, block) {\n\t/*\n\tcalled by change view range\n\tor updating any rendering style, e.g. height\n\t*/\n\tblock.tkcloakon(tk)\n\tconst par = block.tkarg_q(tk)\n\tif (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor\n\tif (tk.bgcolor) par.bgcolor = tk.bgcolor // bg colors for loci with a valid numerical value, useful when low values are cared about e.g. in dna methylation beta value\n\n\ttk.height_main = tk.toppad + tk.barheight + tk.bottompad\n\ttk.img.attr('width', block.width).attr('height', tk.barheight)\n\n\tlet errtext\n\ttry {\n\t\tlet data\n\t\tif (tk.imgData) {\n\t\t\tdata = tk.imgData // premade data; same structure as below\n\t\t} else {\n\t\t\tdata = await dofetch3('tkbigwig', { method: 'POST', body: JSON.stringify(par) })\n\t\t}\n\t\tif (data.error) throw data.error\n\t\tif (!data.src) throw 'data.src missing'\n\n\t\ttk.img.attr('xlink:href', data.src)\n\n\t\tif (data.minv != undefined) {\n\t\t\ttk.scale.min = data.minv\n\t\t}\n\t\tif (data.maxv != undefined) {\n\t\t\ttk.scale.max = data.maxv\n\t\t}\n\n\t\t// when min=max, the axis has a sole tick in the middle\n\t\tconst sameMinMax = tk.scale.min == tk.scale.max\n\n\t\t// in case height changed\n\t\t// with a sole tick in the middle, move the label up to not overlap with it\n\t\ttk.tklabel.transition().attr('y', !data.nodata && sameMinMax ? block.labelfontsize / 2 : tk.barheight / 2)\n\n\t\ttk.leftaxis.selectAll('*').remove()\n\n\t\tif (data.nodata) {\n\t\t\tthrow 'No data in view range'\n\t\t\t// won't update axis\n\t\t}\n\n\t\t// update axis\n\t\tconst scale = scaleLinear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0])\n\n\t\tconst axis = d3axis\n\t\t\t.axisLeft()\n\t\t\t.scale(scale)\n\t\t\t.tickValues(sameMinMax ? [tk.scale.min] : [tk.scale.min, tk.scale.max])\n\n\t\tif (tk.integer4axis) {\n\t\t\taxis.tickFormat(d3format('d'))\n\t\t} else if (sameMinMax) {\n\t\t\t// the default format of a zero-span scale shows 0 as 0.000000\n\t\t\taxis.tickFormat(d3format('~g'))\n\t\t}\n\n\t\tclient.axisstyle({\n\t\t\taxis: tk.leftaxis.call(axis),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t} catch (err) {\n\t\ttk.img.attr('width', 0).attr('height', 0)\n\t\tif (err.stack) {\n\t\t\t// error\n\t\t\tconsole.log(err.stack)\n\t\t}\n\t\terrtext = typeof err == 'string' ? err : err.message\n\t} finally {\n\t\tblock.tkcloakoff(tk, { error: errtext })\n\t\tblock.block_setheight()\n\n\t\t// also load subpanels whenever main panel updates\n\t\tfor (const panel of tk.subpanels) {\n\t\t\tbigwigloadsubpanel(tk, block, panel)\n\t\t}\n\t}\n}\n\nexport async function bigwigloadsubpanel(tk, block, panel) {\n\tblock.tkcloakon_subpanel(panel)\n\tconst par = block.tkarg_q(tk)\n\tif (tk.dotplotfactor) {\n\t\tpar.dotplotfactor = tk.dotplotfactor\n\t}\n\tpar.width = panel.width\n\tpar.rglst = [\n\t\t{\n\t\t\tchr: panel.chr,\n\t\t\tstart: panel.start,\n\t\t\tstop: panel.stop,\n\t\t\twidth: panel.width\n\t\t}\n\t]\n\tdelete par.percentile\n\tdelete par.autoscale\n\n\tpanel.img.attr('width', panel.width).attr('height', tk.barheight)\n\n\tlet errtext\n\ttry {\n\t\tif (tk.imgData) throw 'subpanel not supported by imgData yet'\n\t\tconst data = await dofetch3('tkbigwig', { method: 'POST', body: JSON.stringify(par) })\n\t\tif (data.error) throw data.error\n\t\tpanel.img.attr('xlink:href', data.src)\n\t} catch (err) {\n\t\tpanel.img.attr('width', 0).attr('height', 0)\n\t\tif (err.stack) {\n\t\t\t// error\n\t\t\tconsole.log(err.stack)\n\t\t}\n\t\terrtext = typeof err == 'string' ? err : err.message\n\t} finally {\n\t\tblock.tkcloakoff_subpanel(panel, { error: errtext })\n\t}\n}\n\nexport function bigwigconfigpanel(tk, block, holder, loader) {\n\t// provide hooks to each component, so that caller can choose to hide certain ones\n\tconst config = {\n\t\tpcolor: {},\n\t\tncolor: {},\n\t\tpcolor2: {},\n\t\tncolor2: {},\n\t\t// .row\n\t\t// .lab\n\n\t\tdotplot: {},\n\t\t// .row\n\n\t\tdividefactor: {}\n\t}\n\n\t// height\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\trow.append('span').html('Height&nbsp;&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.attr('size', 5)\n\t\t\t.property('value', tk.barheight)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter') return\n\t\t\t\tconst s = event.target.value\n\t\t\t\tif (s == '') return\n\t\t\t\tconst v = Number.parseInt(s)\n\t\t\t\tif (Number.isNaN(v) || v <= 1) {\n\t\t\t\t\talert('track height must be positive integer')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttk.barheight = v\n\t\t\t\tloader(client.bwSetting.height)\n\t\t\t})\n\t}\n\n\t// pcolor\n\tconfig.pcolor.row = holder.append('div').style('margin-bottom', '15px')\n\tconfig.pcolor.lab = config.pcolor.row.append('span').text('Positive value color').style('padding-right', '10px')\n\tconfig.pcolor.row\n\t\t.append('input')\n\t\t.attr('type', 'color')\n\t\t.property('value', client.rgb2hex(tk.pcolor))\n\t\t.on('change', event => {\n\t\t\ttk.pcolor = event.target.value\n\t\t\tloader(client.bwSetting.pcolor)\n\t\t})\n\n\t// ncolor\n\tconfig.ncolor.row = holder.append('div').style('margin-bottom', '15px')\n\tconfig.ncolor.lab = config.ncolor.row.append('span').text('Negative value color').style('padding-right', '10px')\n\tconfig.ncolor.row\n\t\t.append('input')\n\t\t.attr('type', 'color')\n\t\t.property('value', client.rgb2hex(tk.ncolor))\n\t\t.on('change', event => {\n\t\t\ttk.ncolor = event.target.value\n\t\t\tloader(client.bwSetting.ncolor)\n\t\t})\n\n\tif (!tk.scale.auto) {\n\t\t// pcolor2\n\t\tconfig.pcolor2.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.pcolor2.lab = config.pcolor2.row.append('span').html('&ge;Max color').style('padding-right', '10px')\n\t\tconfig.pcolor2.row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.property('value', client.rgb2hex(tk.pcolor2))\n\t\t\t.on('change', event => {\n\t\t\t\ttk.pcolor2 = event.target.value\n\t\t\t\tloader(client.bwSetting.pcolor2)\n\t\t\t})\n\t\t// ncolor2\n\t\tconfig.ncolor2.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.ncolor2.lab = config.ncolor2.row.append('span').html('&le;Min color').style('padding-right', '10px')\n\t\tconfig.ncolor2.row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.property('value', client.rgb2hex(tk.ncolor2))\n\t\t\t.on('change', event => {\n\t\t\t\ttk.ncolor2 = event.target.value\n\t\t\t\tloader(client.bwSetting.ncolor2)\n\t\t\t})\n\t}\n\n\t// y-scale\n\t{\n\t\tconst setting = {}\n\t\tif (tk.scale.auto) {\n\t\t\tsetting.auto = 1\n\t\t} else if (tk.scale.percentile) {\n\t\t\tsetting.percentile = tk.scale.percentile\n\t\t} else {\n\t\t\tsetting.fixed = { min: tk.scale.min, max: tk.scale.max }\n\t\t}\n\t\tmakeNumericAxisConfig({\n\t\t\tholder: holder.append('div').style('margin-bottom', '15px'),\n\t\t\tsetting,\n\t\t\tcallback: s => {\n\t\t\t\tif (s.auto) {\n\t\t\t\t\ttk.scale.auto = 1\n\t\t\t\t\tloader(client.bwSetting.autoscale)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (s.fixed) {\n\t\t\t\t\tdelete tk.scale.auto\n\t\t\t\t\tdelete tk.scale.percentile\n\t\t\t\t\ttk.scale.max = s.fixed.max\n\t\t\t\t\ttk.scale.min = s.fixed.min\n\t\t\t\t\tloader(client.bwSetting.fixedscale)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tdelete tk.scale.auto\n\t\t\t\ttk.scale.percentile = s.percentile\n\t\t\t\tloader(client.bwSetting.percentilescale)\n\t\t\t}\n\t\t})\n\t}\n\n\t// dot plot\n\t{\n\t\tconfig.dotplot.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.dotplot.row.append('span').html('Dot plot&nbsp;&nbsp;')\n\t\tconst s = config.dotplot.row.append('select').on('change', event => {\n\t\t\tconst i = event.target.selectedIndex\n\t\t\tif (i == 0) {\n\t\t\t\tdelete tk.dotplotfactor\n\t\t\t} else {\n\t\t\t\ttk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML)\n\t\t\t}\n\t\t\tloader(i == 0 ? client.bwSetting.nodotplot : client.bwSetting.usedotplot)\n\t\t})\n\t\tlet o = s.append('option').text('no')\n\t\tif (!tk.dotplotfactor) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('5')\n\t\tif (tk.dotplotfactor == 5) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('10')\n\t\tif (tk.dotplotfactor == 10) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('15')\n\t\tif (tk.dotplotfactor == 15) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('20')\n\t\tif (tk.dotplotfactor == 20) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t}\n\n\t// normalization using a divide-by factor\n\tconfig.dividefactor.row = holder.append('div')\n\t//.style('margin-bottom','15px')\n\t{\n\t\tconst id = Math.random().toString()\n\t\tconst input = config.dividefactor.row.append('input').attr('type', 'checkbox').attr('id', id)\n\t\tif (!tk.normalize.disable) {\n\t\t\tinput.property('checked', 1)\n\t\t}\n\t\tconfig.dividefactor.row.append('label').html('&nbsp;Apply normalization').attr('for', id)\n\n\t\tconst folder = config.dividefactor.row\n\t\t\t.append('div')\n\t\t\t.style('margin', '5px 10px 0px 20px')\n\t\t\t.style('display', tk.normalize.disable ? 'none' : 'block')\n\t\tfolder.append('span').html('Divide raw value by&nbsp;')\n\t\tconst factorinput = folder\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.style('width', '60px')\n\t\t\t.property('value', tk.normalize.dividefactor)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\tconst v = event.target.value\n\t\t\t\tif (v <= 0) {\n\t\t\t\t\t// don't allow\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttk.normalize.dividefactor = v\n\t\t\t\tloader(client.bwSetting.usedividefactor)\n\t\t\t})\n\t\tfolder.append('div').text('Enter a value above zero').style('font-size', '.7em').style('color', '#858585')\n\t\tinput.on('change', event => {\n\t\t\tif (event.target.checked) {\n\t\t\t\tclient.appear(folder)\n\t\t\t\tdelete tk.normalize.disable\n\t\t\t\tfactorinput.property('value', tk.normalize.dividefactor)\n\t\t\t\tloader(client.bwSetting.usedividefactor)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tclient.disappear(folder)\n\t\t\ttk.normalize.disable = 1\n\t\t\tloader(client.bwSetting.nodividefactor)\n\t\t})\n\t}\n\treturn config\n}\n"],
+  "mappings": 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+  "names": []
+}

package/dist/chunk-IQO3VZCP.js

@@ -0,0 +1,255 @@
+import {
+  first_genetrack_tolist
+} from "./chunk-4ASBDE27.js";
+import {
+  HYPER_COLOR,
+  HYPO_COLOR
+} from "./chunk-4TJO2DGU.js";
+
+// plots/dmr/settings/defaults.ts
+function getDefaultDMRSettings(opts) {
+  const overrides = opts.settings || {};
+  const dm = opts?.app?.vocabApi?.termdbConfig?.queries?.dnaMethylation;
+  const chr = opts?.coordinateOverride?.chr;
+  const elementScale = dm?.regionAnalysis == "element" || Array.isArray(dm?.cpgChroms) && !!chr && !dm.cpgChroms.includes(chr);
+  const defaults = {
+    blockWidth: 800,
+    pad: elementScale ? 1e5 : 2e3,
+    lambda: elementScale ? 5e4 : 1e3,
+    C: 2,
+    fdr_cutoff: 0.05,
+    colors: {
+      group1: "#3b5ee6",
+      group2: "#c04e00",
+      hyper: HYPER_COLOR,
+      hypo: HYPO_COLOR
+    },
+    maxLoessRegion: 25e4,
+    minProbesForCi: 10,
+    backend: "rust",
+    maxRegionSize: 5e6
+  };
+  if (overrides.colors) {
+    Object.assign(defaults.colors, overrides.colors);
+    delete overrides.colors;
+  }
+  return Object.assign(defaults, overrides);
+}
+
+// plots/dmr/viewModel/DmrViewModel.ts
+var CCRE_TRACK_NAME = "ENCODE cCREs";
+var DmrViewModel = class {
+  constructor(dmrResult, config, genomeObj, queryChr, queryStart, queryStop) {
+    const { settings } = config;
+    const dmrBedItems = this.makeDmrBedItems(dmrResult, settings);
+    const sigCpgBedItems = this.makeSigCpgBedItems(dmrResult, settings, queryChr, queryStart, queryStop);
+    const xRange = (queryStop ?? 0) - (queryStart ?? 0);
+    const loess = dmrResult.diagnostic?.loess;
+    const showLoess = !!(loess && loess.group1_fitted.length > 0 && loess.group2_fitted.length > 0);
+    const showDots = xRange <= settings.dmr.maxLoessRegion;
+    const betaTrackResult = dmrResult.diagnostic ? this.renderBetaTrack(
+      dmrResult.diagnostic,
+      config,
+      settings.dmr.blockWidth,
+      showLoess,
+      showDots,
+      queryStart,
+      queryStop
+    ) : void 0;
+    this.viewData = {
+      tklst: this.buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackResult?.img),
+      legendRows: this.buildLegendData(
+        config,
+        dmrResult.dmrs,
+        sigCpgBedItems,
+        showLoess,
+        showDots,
+        betaTrackResult?.showCi ?? false
+      ),
+      diagnostic: dmrResult.diagnostic,
+      dmrs: dmrResult.dmrs,
+      dmrBedItems,
+      showLoess,
+      showDots
+    };
+  }
+  buildTrackList(dmrBedItems, sigCpgBedItems, genomeObj, betaTrackImg) {
+    const tklst = [];
+    first_genetrack_tolist(genomeObj, tklst);
+    const ccre = (genomeObj?.tracks || []).find((t) => t.name == CCRE_TRACK_NAME);
+    if (ccre) tklst.push(structuredClone(ccre));
+    tklst.push({ type: "bedj", name: "DMRs", bedItems: dmrBedItems });
+    tklst.push({ type: "bedj", name: "Sig. CpGs", bedItems: sigCpgBedItems });
+    if (betaTrackImg) {
+      tklst.push({
+        type: "bigwig",
+        name: "Per-CpG Means",
+        height: 150,
+        imgData: betaTrackImg
+      });
+    }
+    return tklst;
+  }
+  buildLegendData(config, dmrs, sigCpgBedItems, showLoess, showDots, showCi) {
+    const { colors } = config.settings.dmr;
+    const g1 = config.group1Name || "Group 1";
+    const g2 = config.group2Name || "Group 2";
+    const meansItems = [];
+    if (showDots) {
+      meansItems.push({ text: `${g1} (control)`, color: colors.group1 }, { text: `${g2} (case)`, color: colors.group2 });
+    }
+    if (showLoess) {
+      const ciLabel = showCi ? " + 95% CI" : "";
+      meansItems.push(
+        { text: `${g1} LOESS trend${ciLabel}`, color: colors.group1, style: showCi ? "shaded" : "dashed" },
+        { text: `${g2} LOESS trend${ciLabel}`, color: colors.group2, style: showCi ? "shaded" : "dashed" }
+      );
+    }
+    const rows = [{ label: "Per-CpG Means", items: meansItems }];
+    const hasHyper = dmrs.some((d) => d.direction === "hyper");
+    const hasHypo = dmrs.some((d) => d.direction === "hypo");
+    if (hasHyper || hasHypo) {
+      const items = [];
+      if (hasHyper) items.push({ text: "Hypermethylated", color: colors.hyper });
+      if (hasHypo) items.push({ text: "Hypomethylated", color: colors.hypo });
+      rows.push({ label: "DMR", items });
+    }
+    if (sigCpgBedItems.length) {
+      const items = [];
+      const hasHyperCpg = sigCpgBedItems.some((b) => b.color === colors.hyper);
+      const hasHypoCpg = sigCpgBedItems.some((b) => b.color === colors.hypo);
+      if (hasHyperCpg) items.push({ text: "Hyper (FDR sig.)", color: colors.hyper });
+      if (hasHypoCpg) items.push({ text: "Hypo (FDR sig.)", color: colors.hypo });
+      rows.push({ label: "Sig. CpGs", items });
+    }
+    return rows;
+  }
+  /**
+   * Render the per-CpG means scatter plot to an offscreen canvas and return
+   * a data URI suitable for the bigwig imgData track.
+   */
+  renderBetaTrack(diagnostic, config, blockWidth, showLoess, showDots, queryStart, queryStop) {
+    const { probes } = diagnostic;
+    if (!probes.positions.length) return void 0;
+    const { colors, fdr_cutoff, minProbesForCi } = config.settings.dmr;
+    const dpr = typeof window !== "undefined" && window.devicePixelRatio > 1 ? window.devicePixelRatio : 1;
+    const width = blockWidth;
+    const height = 150;
+    const canvas = document.createElement("canvas");
+    canvas.width = width * dpr;
+    canvas.height = height * dpr;
+    const ctx = canvas.getContext("2d");
+    if (!ctx) return void 0;
+    ctx.scale(dpr, dpr);
+    const xMin = queryStart ?? probes.positions[0];
+    const xMax = queryStop ?? probes.positions[probes.positions.length - 1];
+    const xRange = xMax - xMin || 1;
+    const scaleX = (val) => (val - xMin) / xRange * width;
+    const scaleY = (val) => height - val * height;
+    ctx.clearRect(0, 0, width, height);
+    let showCi = false;
+    if (showLoess && diagnostic.loess) {
+      const { loess } = diagnostic;
+      const firstProbePos = probes.positions[0];
+      const lastProbePos = probes.positions[probes.positions.length - 1];
+      showCi = probes.positions.length >= minProbesForCi;
+      for (const [fitted, ciLower, ciUpper, color] of [
+        [loess.group1_fitted, loess.group1_ci_lower, loess.group1_ci_upper, colors.group1],
+        [loess.group2_fitted, loess.group2_ci_lower, loess.group2_ci_upper, colors.group2]
+      ]) {
+        if (!fitted.length) continue;
+        const lPos = loess.positions;
+        let iStart = 0;
+        let iEnd = lPos.length - 1;
+        while (iStart < lPos.length && lPos[iStart] < firstProbePos) iStart++;
+        while (iEnd >= 0 && lPos[iEnd] > lastProbePos) iEnd--;
+        if (iStart > iEnd) continue;
+        if (showCi) {
+          ctx.globalAlpha = 0.12;
+          ctx.fillStyle = color;
+          ctx.beginPath();
+          for (let i = iStart; i <= iEnd; i++) {
+            ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciUpper[i]))));
+          }
+          for (let i = iEnd; i >= iStart; i--) {
+            ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, ciLower[i]))));
+          }
+          ctx.closePath();
+          ctx.fill();
+        }
+        ctx.globalAlpha = 0.8;
+        ctx.strokeStyle = color;
+        ctx.lineWidth = 2;
+        ctx.setLineDash(showCi ? [] : [6, 4]);
+        ctx.beginPath();
+        for (let i = iStart; i <= iEnd; i++) {
+          ctx.lineTo(scaleX(lPos[i]), scaleY(Math.max(0, Math.min(1, fitted[i]))));
+        }
+        ctx.stroke();
+        ctx.setLineDash([]);
+      }
+    }
+    if (!showDots) {
+      ctx.globalAlpha = 1;
+      return { img: { minv: 0, maxv: 1, src: canvas.toDataURL("image/png") }, showCi };
+    }
+    for (let i = 0; i < probes.positions.length; i++) {
+      const x = scaleX(probes.positions[i]);
+      const isSig = probes.fdr[i] < fdr_cutoff;
+      const alpha = isSig ? 0.85 : 0.3;
+      ctx.globalAlpha = alpha;
+      ctx.fillStyle = colors.group1;
+      const m1 = probes.mean_group1[i];
+      if (m1 != null) {
+        ctx.beginPath();
+        ctx.arc(x, scaleY(m1), 4, 0, Math.PI * 2);
+        ctx.fill();
+      }
+      ctx.fillStyle = colors.group2;
+      const m2 = probes.mean_group2[i];
+      if (m2 != null) {
+        ctx.beginPath();
+        ctx.arc(x, scaleY(m2), 4, 0, Math.PI * 2);
+        ctx.fill();
+      }
+    }
+    ctx.globalAlpha = 1;
+    return { img: { minv: 0, maxv: 1, src: canvas.toDataURL("image/png") }, showCi };
+  }
+  makeDmrBedItems(dmrResult, settings) {
+    return dmrResult.dmrs.map((dmr) => {
+      const negLog = -Math.log10(Math.max(dmr.min_smoothed_fdr, 1e-300));
+      const alpha = Math.round(Math.min(255, Math.max(50, negLog / 10 * 255)));
+      const hex = alpha.toString(16).padStart(2, "0");
+      const base = dmr.direction === "hyper" ? settings.dmr.colors.hyper : settings.dmr.colors.hypo;
+      return { chr: dmr.chr, start: dmr.start, stop: dmr.stop, color: base + hex };
+    });
+  }
+  makeSigCpgBedItems(dmrResult, settings, chr, queryStart, queryStop) {
+    const diag = dmrResult.diagnostic;
+    if (!diag) return [];
+    const { probes } = diag;
+    const items = [];
+    const minDeltaBeta = 0.05;
+    for (let i = 0; i < probes.positions.length; i++) {
+      if (probes.fdr[i] >= settings.dmr.fdr_cutoff) continue;
+      const pos = probes.positions[i];
+      if (queryStart != null && queryStop != null && (pos < queryStart || pos > queryStop)) continue;
+      const mg1 = probes.mean_group1[i];
+      const mg2 = probes.mean_group2[i];
+      if (mg1 == null || mg2 == null) continue;
+      const deltaBeta = mg2 - mg1;
+      if (Math.abs(deltaBeta) < minDeltaBeta) continue;
+      const color = deltaBeta >= 0 ? settings.dmr.colors.hyper : settings.dmr.colors.hypo;
+      items.push({ chr, start: pos, stop: pos + 1, color });
+    }
+    return items;
+  }
+};
+
+export {
+  getDefaultDMRSettings,
+  CCRE_TRACK_NAME,
+  DmrViewModel
+};
+//# sourceMappingURL=chunk-IQO3VZCP.js.map