@sjcrh/proteinpaint-client 2.223.0 → 2.224.1

package/dist/geneExpClustering-47HSKEFL.js

@@ -1,240 +0,0 @@
-import {
-  appInit
-} from "./chunk-UKKLAUYO.js";
-import "./chunk-VD4WX5ZG.js";
-import "./chunk-4E2F26CC.js";
-import "./chunk-FE5TCBIT.js";
-import {
-  fillTermWrapper,
-  vocabInit
-} from "./chunk-JP4IU7DO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-IRAB3OI7.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import {
-  TermTypes
-} from "./chunk-WJLRU5OF.js";
-import {
-  copyMerge
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// gdc/geneExpClustering.js
-async function init(arg, holder, genomes) {
-  try {
-    const useGenome = arg.genome || "hg38";
-    const useDslabel = arg.dslabel || "GDC";
-    const genome = genomes[useGenome];
-    if (!genome) throw useGenome + " missing";
-    const settings = arg.settings || {};
-    if (typeof settings != "object") throw "arg.settings{} not object";
-    if (!settings.hierCluster) settings.hierCluster = {};
-    if (typeof settings.hierCluster != "object") throw "arg.settings.hierCluster{} not object";
-    if (!Number.isInteger(settings.hierCluster.maxGenes)) settings.hierCluster.maxGenes = 1e3;
-    if (arg.filter0 && typeof arg.filter0 != "object") throw "arg.filter0 not object";
-    const vocabApi = await vocabInit({
-      state: { vocab: { genome: useGenome, dslabel: useDslabel } }
-    });
-    vocabApi.getTermdbConfig();
-    const plotAppApi = await appInit({
-      debug: arg.debug,
-      holder: select_default(arg.holder).select(".sja_root_holder"),
-      genome,
-      state: {
-        genome: useGenome,
-        dslabel: useDslabel,
-        termfilter: { filter0: arg.filter0 },
-        plots: [
-          // Initialize with a geneset component, in case the genes lst is empty.
-          // This will be replaced with the actual matrix/hierCluster app once
-          // a valid geneset is selected.
-          {
-            chartType: "geneset",
-            toolName: "Gene Expression Clustering",
-            settings: {
-              maxGenes: settings.hierCluster.maxGenes
-            }
-          }
-        ]
-      },
-      app: arg.opts?.app || {},
-      hierCluster: copyMerge(
-        {
-          reactsTo(action) {
-            if (action.type.startsWith("plot_")) return action.id === this.id;
-            if (action.type.startsWith("filter")) return true;
-            if (action.type == "app_refresh") return true;
-          },
-          callbacks: {
-            "firstRender.gdcHierCluster": async (hierClusterApi2) => {
-              hierClusterApi2.on("firstRender.gdcHierCluster", null);
-              if (!genesetCompApi) return;
-              plotAppApi.dispatch({
-                type: "plot_delete",
-                id: genesetCompApi.id
-              });
-              genesetCompApi = void 0;
-            }
-          }
-        },
-        arg.opts?.hierCluster || {}
-      ),
-      matrix: arg.opts?.matrix || {},
-      geneset: {
-        mode: "geneExpression",
-        // consistent with GeneSetEdit
-        genome,
-        genes: arg.genes,
-        showEditUI: arg.opts?.geneset?.showEditUI,
-        reactsTo(action) {
-          if (action.type.startsWith("plot_")) return action.id === this.id;
-          if (action.type.startsWith("filter")) return true;
-          if (action.type == "app_refresh") return true;
-        },
-        showWaitMessage(div) {
-          div.style("margin", "20px");
-          div.append("div").text("Loading genes that are top variably expressed in current cohort...");
-          div.append("div").style("font-size", ".8em").html(`
-						Only up to 1000 cases with gene expression data will be used to select genes.<br>
-						Genes are selected from all protein-coding genes, may take over 1 minute.
-					`);
-        },
-        async callback(_genesetCompApi, twlst) {
-          if (!_genesetCompApi) return;
-          genesetCompApi = _genesetCompApi;
-          if (!hierClusterApi) {
-            const plotConfig = plotAppApi.getState().plots.find((p) => p.chartType == "hierCluster");
-            if (plotConfig) hierClusterApi = plotAppApi.getComponents(`plots.${plotConfig.id}`);
-          }
-          const termgroups = [
-            {
-              name: "Gene Expression",
-              type: "hierCluster",
-              lst: twlst
-            },
-            ...arg.termgroups || []
-          ];
-          if (hierClusterApi) {
-            plotAppApi.dispatch({
-              type: "plot_edit",
-              id: hierClusterApi.id,
-              config: { termgroups }
-            });
-          } else {
-            plotAppApi.dispatch({
-              type: "plot_create",
-              config: {
-                chartType: "hierCluster",
-                // avoid making a dictionary request when there is no gene data;
-                // if there is gene data, then the arg.termgroups can be submitted and rehydrated on app/store.init()
-                termgroups,
-                divideBy: arg.divideBy || void 0,
-                // moved default settings to gdc.hg38.js termdb[chartType].settings
-                // but can still override in the runpp() argument
-                settings,
-                dataType: TermTypes.GENE_EXPRESSION
-              }
-            });
-          }
-        }
-      },
-      recover: {
-        undoHtml: "Undo",
-        redoHtml: "Redo",
-        resetHtml: "Restore",
-        hide(state) {
-          return state.plots[0]?.chartType != "hierCluster";
-        },
-        adjustTrackedState: (state) => {
-          const s = structuredClone(state);
-          delete s.termfilter.filter0;
-          if (s.plots) {
-            for (const plot of s.plots) {
-              if (!plot.termgroups) continue;
-              for (const grp of plot.termgroups) {
-                if (!grp.lst) continue;
-                for (const tw of grp.lst) {
-                  if (!tw?.term) continue;
-                  delete tw.term.category2samplecount;
-                  delete tw.term.values;
-                }
-              }
-            }
-          }
-          return s;
-        }
-      }
-    });
-    let hierClusterApi, genesetCompApi;
-    const api = {
-      type: "hierCluster",
-      update: async (_arg) => {
-        const plotConfig = plotAppApi.getState().plots.find((p) => p.chartType == "hierCluster");
-        if (!hierClusterApi) {
-          if (plotConfig) hierClusterApi = plotAppApi.getComponents(`plots.${plotConfig.id}`);
-        }
-        if (_arg.genes) {
-          const t0 = plotConfig.termgroups.find((g) => g.type == "hierCluster");
-          plotAppApi.dispatch({
-            type: "plot_edit",
-            id: hierClusterApi.id,
-            config: {
-              termgroups: [
-                {
-                  name: t0.name,
-                  type: "hierCluster",
-                  lst: await Promise.all(
-                    _arg.genes.map(async (g) => {
-                      return await fillTermWrapper(
-                        {
-                          term: { gene: g.gene, type: "geneExpression", name: g.gene }
-                        },
-                        vocabApi
-                      );
-                    })
-                  )
-                }
-              ]
-            }
-          });
-        } else if ("filter0" in _arg) {
-          plotAppApi.dispatch({
-            type: "filter_replace",
-            filter0: _arg.filter0
-          });
-        } else if (hierClusterApi) {
-          plotAppApi.dispatch({
-            type: "plot_edit",
-            id: hierClusterApi.id,
-            config: _arg
-          });
-        }
-      },
-      triggerAbort: (_) => plotAppApi.triggerAbort(_)
-    };
-    return api;
-  } catch (e) {
-    throw e;
-  }
-}
-export {
-  init
-};
-//# sourceMappingURL=geneExpClustering-47HSKEFL.js.map

package/dist/geneExpression-GIJPTHXW.js

@@ -1,29 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-22MQLGUB.js";
-import "./chunk-JP4IU7DO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-IRAB3OI7.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=geneExpression-GIJPTHXW.js.map

package/dist/geneExpression-KPUOZ4PT.js

@@ -1,309 +0,0 @@
-import {
-  dofetch3
-} from "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import {
-  rgb_default
-} from "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/geneExpression.js
-var defaultConfig = {
-  clusterMethod: "average",
-  distanceMethod: "euclidean"
-};
-var clusterMethodLst = [
-  "average",
-  "complete",
-  "mcquitty"
-  //'single', very slow
-  //'median', 'centroid', crashes R with "No connections found!"
-  //'ward.D','ward.D2', crashes client
-];
-var distanceMethodLst = ["euclidean", "maximum", "manhattan", "canberra"];
-var GeneExpression = class _GeneExpression {
-  static type = "geneExpression";
-  constructor() {
-    this.type = _GeneExpression.type;
-  }
-  async init(opts) {
-    const holder = this.opts.holder.append("div");
-    this.dom = {
-      holder,
-      controlsDiv: holder.append("div"),
-      canvas: holder.append("canvas"),
-      colorScaleDiv: holder.append("div")
-    };
-    this.makeControls();
-    this.components = {};
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found`;
-    }
-    return {
-      config
-    };
-  }
-  async main() {
-    const body = this.getParam();
-    const data = await dofetch3("mds3", { body });
-    plotHeatmap_R(data, this);
-  }
-  getParam() {
-    console.log(this.state.config.genes);
-    const body = {
-      genome: this.app.opts.state.vocab.genome,
-      dslabel: this.app.opts.state.vocab.dslabel,
-      geneExpression: 1,
-      genes: this.state.config.genes,
-      clusterMethod: this.state.config.clusterMethod
-    };
-    return body;
-  }
-  makeControls() {
-    const s = this.dom.controlsDiv.append("select");
-    for (const n of clusterMethodLst) s.append("option").text(n);
-    this.dom.clusterMethodSelect = s;
-    s.on("change", () => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { clusterMethod: clusterMethodLst[s.property("selectedIndex")] }
-      });
-    });
-  }
-};
-async function getPlotConfig(opts, app) {
-  try {
-    const config = structuredClone(defaultConfig);
-    return copyMerge(config, opts);
-  } catch (e) {
-    throw `${e} [geneExpression getPlotConfig()]`;
-  }
-}
-var geneExpressionInit = getCompInit(GeneExpression);
-var componentInit = geneExpressionInit;
-function makeChartBtnMenu(holder, chartsInstance) {
-  holder.append("div").attr("class", "sja_menuoption sja_sharp_border").text("Clustering analysis").on("click", () => {
-    chartsInstance.dom.tip.hide();
-    chartsInstance.prepPlot({
-      config: {
-        chartType: "geneExpression"
-      }
-    });
-  });
-}
-function plotHeatmap_R(data, self) {
-  self.dom.clusterMethodSelect.property("selectedIndex", clusterMethodLst.indexOf(self.state.config.clusterMethod));
-  self.dom.distanceMethodSelect.property("selectedIndex", distanceMethodLst.indexOf(self.state.config.distanceMethod));
-  const obj = data.clustering;
-  console.log(obj);
-  obj.d = {
-    minColor: "#0c306b",
-    maxColor: "#ffcc00",
-    xDendrogramHeight: 150,
-    yDendrogramHeight: 150
-  };
-  obj.d.colorScale = rgb_default(obj.d.minColor, obj.d.maxColor);
-  const ctx = self.dom.canvas.node().getContext("2d");
-  obj.d.rowHeight = getRowHeight(obj);
-  obj.d.colWidth = getColWidth(obj);
-  getLabHeight(ctx, obj);
-  self.dom.canvas.attr("width", obj.d.xDendrogramHeight + obj.d.xLabHeight + obj.d.colWidth * obj.matrix[0].length).attr("height", obj.d.yDendrogramHeight + obj.d.yLabHeight + obj.d.rowHeight * obj.matrix.length);
-  plotNames(obj, ctx);
-  drawHeatmap(obj, ctx);
-  plotDendrogram_R(ctx, obj);
-  plotHmColorScale(self, obj);
-}
-function plotDendrogram_R(ctx, obj) {
-  try {
-    obj.row_dendro.map(validateRline);
-  } catch (e) {
-    throw "row_dendro error: " + e;
-  }
-  try {
-    obj.col_dendro.map(validateRline);
-  } catch (e) {
-    throw "col_dendro error: " + e;
-  }
-  for (const r of obj.row_dendro) {
-    let t = r.x1;
-    r.x1 = r.y1;
-    r.y1 = t;
-    t = r.x2;
-    r.x2 = r.y2;
-    r.y2 = t;
-  }
-  {
-    let max = 0;
-    for (const r of obj.row_dendro) max = Math.max(max, r.x1, r.x2);
-    const sf = obj.d.xDendrogramHeight / max;
-    for (const r of obj.row_dendro) {
-      r.x1 = sf * (max - r.x1);
-      r.x2 = sf * (max - r.x2);
-      r.y1 *= obj.d.rowHeight;
-      r.y2 *= obj.d.rowHeight;
-    }
-  }
-  {
-    let max = 0;
-    for (const r of obj.col_dendro) max = Math.max(max, r.y1, r.y2);
-    const sf = obj.d.yDendrogramHeight / max;
-    for (const r of obj.col_dendro) {
-      r.y1 = sf * (max - r.y1);
-      r.y2 = sf * (max - r.y2);
-      r.x1 *= obj.d.colWidth;
-      r.x2 *= obj.d.colWidth;
-    }
-  }
-  ctx.strokeStyle = "black";
-  let F = obj.d.yDendrogramHeight + obj.d.yLabHeight;
-  for (const r of obj.row_dendro) {
-    ctx.beginPath();
-    const x1 = Math.min(r.x1, r.x2), x2 = Math.max(r.x1, r.x2), y1 = Math.min(r.y1, r.y2), y2 = Math.max(r.y1, r.y2);
-    ctx.moveTo(x1, y1 + F);
-    ctx.lineTo(x1, y2 + F);
-    if (r.x1 > r.x2 && r.y1 > r.y2 || r.x1 < r.x2 && r.y1 < r.y2) {
-      ctx.lineTo(x2, y2 + F);
-    } else {
-      ctx.moveTo(x1, y1 + F);
-      ctx.lineTo(x2, y1 + F);
-    }
-    ctx.stroke();
-    ctx.closePath();
-  }
-  F = obj.d.xDendrogramHeight + obj.d.xLabHeight;
-  for (const r of obj.col_dendro) {
-    ctx.beginPath();
-    const x1 = Math.min(r.x1, r.x2), x2 = Math.max(r.x1, r.x2), y1 = Math.min(r.y1, r.y2), y2 = Math.max(r.y1, r.y2);
-    ctx.moveTo(F + x1, y1);
-    ctx.lineTo(F + x2, y1);
-    if (r.x1 > r.x2 && r.y1 > r.y2 || r.x1 < r.x2 && r.y1 < r.y2) {
-      ctx.lineTo(F + x2, y2);
-    } else {
-      ctx.moveTo(F + x1, y1);
-      ctx.lineTo(F + x1, y2);
-    }
-    ctx.stroke();
-    ctx.closePath();
-  }
-}
-function validateRline(r) {
-  if (r.r1 < 0) throw `r.r1<0 ${r.r1}`;
-  if (r.r2 < 0) throw `r.r2<0 ${r.r2}`;
-  if (r.x1 < 1) throw `r.x1<1 ${r.x1}`;
-  if (r.x2 < 1) throw `r.x2<1 ${r.x2}`;
-  r.x1 -= 0.5;
-  r.x2 -= 0.5;
-  if (r.y1 < 0) throw `r.y1<0 ${r.y1}`;
-  if (r.y2 < 0) throw `r.y2<0 ${r.y2}`;
-}
-function plotNames(obj, ctx) {
-  if (obj.d.xLabHeight) {
-    ctx.font = obj.d.rowHeight + "px Arial";
-    ctx.textAlign = "end";
-    ctx.fillStyle = "black";
-    for (const [rowIdx, geneIdx] of obj.row_names_index.entries()) {
-      ctx.fillText(
-        obj.geneNameLst[geneIdx - 1],
-        obj.d.xDendrogramHeight + obj.d.xLabHeight,
-        obj.d.yDendrogramHeight + obj.d.yLabHeight + obj.d.rowHeight * (rowIdx + 1)
-      );
-    }
-  }
-}
-function drawHeatmap(obj, ctx) {
-  for (let i = 0; i < obj.row_names_index.length; i++) {
-    const sampleValues = obj.matrix[obj.row_names_index[i] - 1];
-    const [min, max] = getMinMax(sampleValues);
-    for (let j = 0; j < obj.col_names_index.length; j++) {
-      const v = sampleValues[obj.col_names_index[j] - 1];
-      ctx.fillStyle = obj.d.colorScale((v - min) / (max - min));
-      ctx.fillRect(
-        obj.d.xDendrogramHeight + obj.d.xLabHeight + obj.d.colWidth * j,
-        obj.d.yDendrogramHeight + obj.d.yLabHeight + obj.d.rowHeight * i,
-        obj.d.colWidth,
-        obj.d.rowHeight
-      );
-    }
-  }
-}
-function getRowHeight(obj) {
-  const h = 500 / obj.matrix.length;
-  if (h > 20) return 20;
-  if (h < 10) return 10;
-  return Math.ceil(h);
-}
-function getColWidth(obj) {
-  const w = 2e3 / obj.matrix[0].length;
-  if (w > 10) return 10;
-  return Math.ceil(w);
-}
-function getLabHeight(ctx, obj) {
-  if (obj.geneNameLst && obj.d.rowHeight >= 7) {
-    ctx.font = obj.d.rowHeight + "px Arial";
-    let max = 0;
-    for (const n of obj.geneNameLst) {
-      max = Math.max(max, ctx.measureText(n).width);
-    }
-    obj.d.xLabHeight = max;
-  } else {
-    obj.d.xLabHeight = 0;
-  }
-  if (obj.sampleNameLst && obj.d.colWidth >= 7) {
-    ctx.font = obj.d.colWidth + "px Arial";
-    let max = 0;
-    for (const n of obj.sampleNameLst) {
-      max = Math.max(max, ctx.measureText(n).width);
-    }
-    obj.d.yLabHeight = max;
-  } else {
-    obj.d.yLabHeight = 0;
-  }
-}
-function getMinMax(row) {
-  let min = null, max;
-  for (const v of row) {
-    if (min == null) {
-      min = v;
-      max = v;
-    } else {
-      min = Math.min(min, v);
-      max = Math.max(max, v);
-    }
-  }
-  return [min, max];
-}
-function plotHmColorScale(self, obj) {
-  self.dom.colorScaleDiv.selectAll("*").remove();
-  const width = 100, height = 20;
-  self.dom.colorScaleDiv.append("span").text("Min");
-  const svg = self.dom.colorScaleDiv.append("svg");
-  self.dom.colorScaleDiv.append("span").text("Max");
-  const grad = svg.append("defs").append("linearGradient").attr("id", "grad");
-  grad.append("stop").attr("offset", "0%").attr("stop-color", obj.d.minColor);
-  grad.append("stop").attr("offset", "100%").attr("stop-color", obj.d.maxColor);
-  svg.append("rect").attr("width", width).attr("height", height).attr("fill", "url(#grad)");
-  svg.attr("width", width).attr("height", height);
-}
-export {
-  componentInit,
-  geneExpressionInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=geneExpression-KPUOZ4PT.js.map

package/dist/geneExpression-KPUOZ4PT.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/geneExpression.js"],
-  "sourcesContent": ["import { getCompInit, copyMerge } from '#rx'\nimport { dofetch3 } from '#common/dofetch'\nimport { interpolateRgb } from 'd3-interpolate'\n\nconst defaultConfig = {\n\tclusterMethod: 'average',\n\tdistanceMethod: 'euclidean'\n}\n\nconst clusterMethodLst = [\n\t'average',\n\t'complete',\n\t'mcquitty'\n\t//'single', very slow\n\t//'median', 'centroid', crashes R with \"No connections found!\"\n\t//'ward.D','ward.D2', crashes client\n]\n\nconst distanceMethodLst = ['euclidean', 'maximum', 'manhattan', 'canberra']\n\nclass GeneExpression {\n\tstatic type = 'geneExpression'\n\n\tconstructor() {\n\t\tthis.type = GeneExpression.type\n\t}\n\n\tasync init(opts) {\n\t\tconst holder = this.opts.holder.append('div')\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\tcontrolsDiv: holder.append('div'),\n\t\t\tcanvas: holder.append('canvas'),\n\t\t\tcolorScaleDiv: holder.append('div')\n\t\t}\n\t\tthis.makeControls()\n\t\tthis.components = {}\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='${this.id}' found`\n\t\t}\n\t\treturn {\n\t\t\tconfig\n\t\t}\n\t}\n\n\tasync main() {\n\t\tconst body = this.getParam()\n\t\tconst data = await dofetch3('mds3', { body })\n\t\tplotHeatmap_R(data, this)\n\t}\n\n\tgetParam() {\n\t\tconsole.log(this.state.config.genes)\n\t\tconst body = {\n\t\t\tgenome: this.app.opts.state.vocab.genome,\n\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\tgeneExpression: 1,\n\t\t\tgenes: this.state.config.genes,\n\t\t\tclusterMethod: this.state.config.clusterMethod\n\t\t}\n\t\treturn body\n\t}\n\n\tmakeControls() {\n\t\tconst s = this.dom.controlsDiv.append('select')\n\t\tfor (const n of clusterMethodLst) s.append('option').text(n)\n\t\tthis.dom.clusterMethodSelect = s\n\t\ts.on('change', () => {\n\t\t\tthis.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.id,\n\t\t\t\tconfig: { clusterMethod: clusterMethodLst[s.property('selectedIndex')] }\n\t\t\t})\n\t\t})\n\t}\n}\n\nexport async function getPlotConfig(opts, app) {\n\ttry {\n\t\tconst config = structuredClone(defaultConfig)\n\n\t\treturn copyMerge(config, opts)\n\t} catch (e) {\n\t\tthrow `${e} [geneExpression getPlotConfig()]`\n\t}\n}\n\nexport const geneExpressionInit = getCompInit(GeneExpression)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = geneExpressionInit\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\t/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n        termdbConfig is accessible at chartsInstance.state.termdbConfig{}\n        mass option is accessible at chartsInstance.app.opts{}\n\t*/\n\n\t// to fill in menu, create options in holder\n\t/*\n\tholder.append('div')\n\t\t.attr('class','sja_menuoption sja_sharp_border')\n\t\t.text('Single gene expression')\n\t\t.on('click',()=>{\n\t\t\tchartsInstance.dom.tip.hide()\n\t\t\t\n\t\t})\n\t\t*/\n\n\tholder\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t.text('Clustering analysis')\n\t\t.on('click', () => {\n\t\t\tchartsInstance.dom.tip.hide()\n\t\t\tchartsInstance.prepPlot({\n\t\t\t\tconfig: {\n\t\t\t\t\tchartType: 'geneExpression'\n\t\t\t\t}\n\t\t\t})\n\t\t})\n}\n\n// connect with output from R\nfunction plotHeatmap_R(data, self) {\n\t/* data={\n\t\tgeneNameLst,sampleNameLst,matrix,\n\t\trow_dendro [ {id1, x1, y1, id2, x2, y2} ... ]\n\t\trow_children [ {id:0, children:[1]}, ...]\n\t\trow_names_index [3,1,2]\n\t\tcol_dendro\n\t\tcol_children\n\t\tcol_names_index\n\t}\n\t*/\n\tself.dom.clusterMethodSelect.property('selectedIndex', clusterMethodLst.indexOf(self.state.config.clusterMethod))\n\tself.dom.distanceMethodSelect.property('selectedIndex', distanceMethodLst.indexOf(self.state.config.distanceMethod))\n\tconst obj = data.clustering\n\tconsole.log(obj)\n\tobj.d = {\n\t\tminColor: '#0c306b',\n\t\tmaxColor: '#ffcc00',\n\t\txDendrogramHeight: 150,\n\t\tyDendrogramHeight: 150\n\t}\n\tobj.d.colorScale = interpolateRgb(obj.d.minColor, obj.d.maxColor)\n\tconst ctx = self.dom.canvas.node().getContext('2d')\n\n\tobj.d.rowHeight = getRowHeight(obj)\n\tobj.d.colWidth = getColWidth(obj)\n\n\tgetLabHeight(ctx, obj) // set obj.d.xLabHeight obj.d.yLabHeight\n\n\tself.dom.canvas\n\t\t.attr('width', obj.d.xDendrogramHeight + obj.d.xLabHeight + obj.d.colWidth * obj.matrix[0].length)\n\t\t.attr('height', obj.d.yDendrogramHeight + obj.d.yLabHeight + obj.d.rowHeight * obj.matrix.length)\n\n\tplotNames(obj, ctx)\n\tdrawHeatmap(obj, ctx)\n\tplotDendrogram_R(ctx, obj)\n\tplotHmColorScale(self, obj)\n}\n\n/*\nin both row_dendro[] and col_dendro[], elements are: {id1,x1,y1, id2,x2,y2}\nis one line traversing between a parent and a child\nid1/2 can either be parent or child, it's mixed\nx1/2 is row/column node index, 1-based\ny1/2 is depth\n*/\nfunction plotDendrogram_R(ctx, obj) {\n\ttry {\n\t\tobj.row_dendro.map(validateRline)\n\t} catch (e) {\n\t\tthrow 'row_dendro error: ' + e\n\t}\n\ttry {\n\t\tobj.col_dendro.map(validateRline)\n\t} catch (e) {\n\t\tthrow 'col_dendro error: ' + e\n\t}\n\n\t// hardcoding gene to be on rows, swap x/y for row dendrogram\n\tfor (const r of obj.row_dendro) {\n\t\tlet t = r.x1\n\t\tr.x1 = r.y1\n\t\tr.y1 = t\n\t\tt = r.x2\n\t\tr.x2 = r.y2\n\t\tr.y2 = t\n\t}\n\n\t// replace node x/y values with on-screen #pixel for plotting\n\t{\n\t\tlet max = 0\n\t\tfor (const r of obj.row_dendro) max = Math.max(max, r.x1, r.x2)\n\t\tconst sf = obj.d.xDendrogramHeight / max\n\t\tfor (const r of obj.row_dendro) {\n\t\t\tr.x1 = sf * (max - r.x1) // for row dendrogram, x is now depth\n\t\t\tr.x2 = sf * (max - r.x2)\n\t\t\tr.y1 *= obj.d.rowHeight // y is number of row items\n\t\t\tr.y2 *= obj.d.rowHeight\n\t\t}\n\t}\n\t{\n\t\tlet max = 0\n\t\tfor (const r of obj.col_dendro) max = Math.max(max, r.y1, r.y2)\n\t\tconst sf = obj.d.yDendrogramHeight / max\n\t\tfor (const r of obj.col_dendro) {\n\t\t\tr.y1 = sf * (max - r.y1) // for col dendrogram, y is depth\n\t\t\tr.y2 = sf * (max - r.y2)\n\t\t\tr.x1 *= obj.d.colWidth // x is number of column items\n\t\t\tr.x2 *= obj.d.colWidth\n\t\t}\n\t}\n\n\tctx.strokeStyle = 'black'\n\n\t// plot row dendrogram\n\n\tlet F = obj.d.yDendrogramHeight + obj.d.yLabHeight // yoffset applied to y coord when plotting x dendrogram\n\n\tfor (const r of obj.row_dendro) {\n\t\tctx.beginPath()\n\n\t\t// r is a line between two points. get extreme x/y\n\t\tconst x1 = Math.min(r.x1, r.x2),\n\t\t\tx2 = Math.max(r.x1, r.x2),\n\t\t\ty1 = Math.min(r.y1, r.y2),\n\t\t\ty2 = Math.max(r.y1, r.y2)\n\n\t\t// always one way to plot vertical line\n\t\tctx.moveTo(x1, y1 + F)\n\t\tctx.lineTo(x1, y2 + F)\n\n\t\t// two ways to plot horizontal line\n\t\tif ((r.x1 > r.x2 && r.y1 > r.y2) || (r.x1 < r.x2 && r.y1 < r.y2)) {\n\t\t\t// one point is on lower right of another, the horizontal line is based on *max y*\n\t\t\tctx.lineTo(x2, y2 + F)\n\t\t} else {\n\t\t\t// one point is on upper right of another, the horizontal line is based on *min y*\n\t\t\tctx.moveTo(x1, y1 + F)\n\t\t\tctx.lineTo(x2, y1 + F)\n\t\t}\n\t\tctx.stroke()\n\t\tctx.closePath()\n\t}\n\n\t// plot column dendrogram\n\tF = obj.d.xDendrogramHeight + obj.d.xLabHeight // xoffset applied to x coord when plotting y dendrogram\n\tfor (const r of obj.col_dendro) {\n\t\tctx.beginPath()\n\t\tconst x1 = Math.min(r.x1, r.x2),\n\t\t\tx2 = Math.max(r.x1, r.x2),\n\t\t\ty1 = Math.min(r.y1, r.y2),\n\t\t\ty2 = Math.max(r.y1, r.y2)\n\t\tctx.moveTo(F + x1, y1)\n\t\tctx.lineTo(F + x2, y1) // hline\n\t\tif ((r.x1 > r.x2 && r.y1 > r.y2) || (r.x1 < r.x2 && r.y1 < r.y2)) {\n\t\t\t// vline at max x\n\t\t\tctx.lineTo(F + x2, y2)\n\t\t} else {\n\t\t\t// vline at min x\n\t\t\tctx.moveTo(F + x1, y1)\n\t\t\tctx.lineTo(F + x1, y2)\n\t\t}\n\t\tctx.stroke()\n\t\tctx.closePath()\n\t}\n}\nfunction validateRline(r) {\n\t// a line between parent and child, {id1,x1,y1, id2,x2,y2}\n\n\t// r1/2 is node id, 0-based, currently not used\n\tif (r.r1 < 0) throw `r.r1<0 ${r.r1}`\n\tif (r.r2 < 0) throw `r.r2<0 ${r.r2}`\n\n\t// x1/2 is matrix row/column entity index, 1-based; parent node can get non-integer value\n\tif (r.x1 < 1) throw `r.x1<1 ${r.x1}`\n\tif (r.x2 < 1) throw `r.x2<1 ${r.x2}`\n\tr.x1 -= 0.5 // since the values are 1-based, subtract 0.5 to point to middle of row/column when rendering\n\tr.x2 -= 0.5\n\n\t// y1/2 is dendrogram node depth, non-negative\n\tif (r.y1 < 0) throw `r.y1<0 ${r.y1}`\n\tif (r.y2 < 0) throw `r.y2<0 ${r.y2}`\n}\n\n// connect with output from rust/src/cluster\nfunction plotHeatmap(data, self) {\n\tself.dom.clusterMethodSelect.property('selectedIndex', clusterMethodLst.indexOf(self.state.config.clusterMethod))\n\tself.dom.distanceMethodSelect.property('selectedIndex', distanceMethodLst.indexOf(self.state.config.distanceMethod))\n\t// data={geneNameLst,sampleNameLst,matrix,rowIdxLst,sorted_sample_coordinates,sorted_gene_coordinates}\n\tconst obj = data.clustering\n\tconsole.log(obj)\n\tobj.d = {\n\t\tminColor: '#0c306b',\n\t\tmaxColor: '#ffcc00',\n\t\txDendrogramHeight: 150,\n\t\tyDendrogramHeight: 150\n\t}\n\tobj.d.colorScale = interpolateRgb(obj.d.minColor, obj.d.maxColor)\n\n\tconst ctx = self.dom.canvas.node().getContext('2d')\n\n\tobj.d.rowHeight = getRowHeight(obj)\n\tobj.d.colWidth = getColWidth(obj)\n\n\t//parseDendrogram(obj)\n\n\t{\n\t\tconst r = parseDendrogram2(obj.rowSteps, obj.matrix.length)\n\t\tobj.rowIdxLst = r.idxLst\n\t\tobj.xId2coord = r.id2coord\n\t\tlet max = 0\n\t\tfor (const n of obj.xId2coord.values()) {\n\t\t\tmax = Math.max(max, n.x)\n\t\t}\n\t\tfor (const n of obj.xId2coord.values()) {\n\t\t\tn.x = max - n.x\n\t\t\tn.y *= obj.d.rowHeight\n\t\t\tn.y += obj.d.rowHeight / 2\n\t\t}\n\t\tconst scale = obj.d.xDendrogramHeight / max\n\t\tfor (const n of obj.xId2coord.values()) {\n\t\t\tn.x *= scale\n\t\t}\n\t}\n\t{\n\t\tconst r = parseDendrogram2(obj.colSteps, obj.matrix[0].length)\n\t\tobj.colIdxLst = r.idxLst\n\t\tobj.yId2coord = r.id2coord\n\t\tlet max = 0\n\t\tfor (const n of obj.yId2coord.values()) {\n\t\t\tconst t = n.x\n\t\t\tn.x = n.y\n\t\t\tn.y = t\n\t\t\tmax = Math.max(max, n.y)\n\t\t}\n\t\tfor (const n of obj.yId2coord.values()) {\n\t\t\tn.y = max - n.y\n\t\t\tn.x *= obj.d.colWidth\n\t\t}\n\t\tconst scale = obj.d.yDendrogramHeight / max\n\t\tfor (const n of obj.yId2coord.values()) {\n\t\t\tn.y *= scale\n\t\t}\n\t}\n\n\tgetLabHeight(ctx, obj)\n\t// set obj.d.xLabHeight obj.d.yLabHeight\n\n\tself.dom.canvas\n\t\t.attr('width', obj.d.xDendrogramHeight + obj.d.xLabHeight + obj.d.colWidth * obj.colIdxLst.length)\n\t\t.attr('height', obj.d.yDendrogramHeight + obj.d.yLabHeight + obj.d.rowHeight * obj.rowIdxLst.length)\n\n\tplotNames(obj, ctx)\n\tdrawHeatmap(obj, ctx)\n\tplotDendrogram(ctx, obj)\n\tplotHmColorScale(self, obj)\n}\nfunction plotNames(obj, ctx) {\n\tif (obj.d.xLabHeight) {\n\t\t// can plot gene name as row label, do first loop\n\t\tctx.font = obj.d.rowHeight + 'px Arial'\n\t\tctx.textAlign = 'end'\n\t\tctx.fillStyle = 'black'\n\t\tfor (const [rowIdx, geneIdx] of obj.row_names_index.entries()) {\n\t\t\tctx.fillText(\n\t\t\t\tobj.geneNameLst[geneIdx - 1],\n\t\t\t\tobj.d.xDendrogramHeight + obj.d.xLabHeight,\n\t\t\t\tobj.d.yDendrogramHeight + obj.d.yLabHeight + obj.d.rowHeight * (rowIdx + 1)\n\t\t\t)\n\t\t}\n\t}\n\t// col names are not plotted yet\n}\nfunction drawHeatmap(obj, ctx) {\n\tfor (let i = 0; i < obj.row_names_index.length; i++) {\n\t\tconst sampleValues = obj.matrix[obj.row_names_index[i] - 1] // row of matrix, that are sample values for this gene\n\t\t// min/max of this gene, to convert to [0,1] for mapping to color\n\t\tconst [min, max] = getMinMax(sampleValues)\n\t\tfor (let j = 0; j < obj.col_names_index.length; j++) {\n\t\t\tconst v = sampleValues[obj.col_names_index[j] - 1]\n\t\t\tctx.fillStyle = obj.d.colorScale((v - min) / (max - min))\n\t\t\tctx.fillRect(\n\t\t\t\tobj.d.xDendrogramHeight + obj.d.xLabHeight + obj.d.colWidth * j,\n\t\t\t\tobj.d.yDendrogramHeight + obj.d.yLabHeight + obj.d.rowHeight * i,\n\t\t\t\tobj.d.colWidth,\n\t\t\t\tobj.d.rowHeight\n\t\t\t)\n\t\t}\n\t}\n}\nfunction getRowHeight(obj) {\n\tconst h = 500 / obj.matrix.length\n\tif (h > 20) return 20\n\tif (h < 10) return 10\n\treturn Math.ceil(h)\n}\nfunction getColWidth(obj) {\n\tconst w = 2000 / obj.matrix[0].length\n\tif (w > 10) return 10\n\treturn Math.ceil(w)\n}\nfunction getLabHeight(ctx, obj) {\n\tif (obj.geneNameLst && obj.d.rowHeight >= 7) {\n\t\tctx.font = obj.d.rowHeight + 'px Arial'\n\t\tlet max = 0\n\t\tfor (const n of obj.geneNameLst) {\n\t\t\tmax = Math.max(max, ctx.measureText(n).width)\n\t\t}\n\t\tobj.d.xLabHeight = max\n\t} else {\n\t\tobj.d.xLabHeight = 0\n\t}\n\n\tif (obj.sampleNameLst && obj.d.colWidth >= 7) {\n\t\tctx.font = obj.d.colWidth + 'px Arial'\n\t\tlet max = 0\n\t\tfor (const n of obj.sampleNameLst) {\n\t\t\tmax = Math.max(max, ctx.measureText(n).width)\n\t\t}\n\t\tobj.d.yLabHeight = max\n\t} else {\n\t\tobj.d.yLabHeight = 0\n\t}\n}\nfunction getMinMax(row) {\n\tlet min = null,\n\t\tmax\n\tfor (const v of row) {\n\t\tif (min == null) {\n\t\t\tmin = v\n\t\t\tmax = v\n\t\t} else {\n\t\t\tmin = Math.min(min, v)\n\t\t\tmax = Math.max(max, v)\n\t\t}\n\t}\n\treturn [min, max]\n}\n\n// not in use\nfunction parseDendrogram(obj) {\n\t// if isX=true, collect max y from all nodes; otherwise collect max x\n\tobj.xId2coord = new Map()\n\tlet max = null\n\tfor (const n of obj.sorted_gene_coordinates) {\n\t\t// convert to on-canvas position\n\t\tn.node_coordinates.x *= obj.d.dFactor\n\t\tn.node_coordinates.y *= obj.d.rowHeight\n\t\tn.node_coordinates.y += obj.d.rowHeight / 2\n\n\t\tobj.xId2coord.set(n.node_id, n.node_coordinates)\n\t\tconst v = n.node_coordinates.x\n\t\tif (max == null) max = v\n\t\telse max = Math.max(max, v)\n\t}\n\tobj.d.xDendrogramHeight = max\n\n\tobj.yId2coord = new Map()\n\tmax = null\n\tfor (const n of obj.sorted_sample_coordinates) {\n\t\t// convert\n\t\tn.node_coordinates.x *= obj.d.colWidth\n\t\tn.node_coordinates.y *= obj.d.dFactor\n\n\t\tobj.yId2coord.set(n.node_id, n.node_coordinates)\n\t\tconst v = n.node_coordinates.y\n\t\tif (max == null) max = v\n\t\telse max = Math.max(max, v)\n\t}\n\tobj.d.yDendrogramHeight = max\n}\n\nfunction parseDendrogram2(steps, leafCount) {\n\tconst idxLst = [] // list of leaf idx, sorted by steps\n\tconst id2coord = new Map() // k: node idx, v: {x,y,children[]}\n\n\tlet currentRowIdx = 0 // cumulative row number, to derive y position of each node\n\tconst parentHeap = [] // heap of parent nodes, last in, first out\n\n\tfor (const [i, step] of steps.entries()) {\n\t\t// collect leaf id by the order of appearance in rowSteps[], into rowIdxLst\n\t\tif (step.size == 2) {\n\t\t\t// both leaf\n\n\t\t\tidxLst.push(step.cluster1)\n\t\t\tidxLst.push(step.cluster2)\n\n\t\t\tconst y1 = currentRowIdx++,\n\t\t\t\ty2 = currentRowIdx++\n\t\t\tid2coord.set(step.cluster1, { x: 0, y: y1 })\n\t\t\tid2coord.set(step.cluster2, { x: 0, y: y2 })\n\t\t\t// a free parent node is generated with these two leaves, and is cached in the array (it has no id yet)\n\t\t\tparentHeap.push({\n\t\t\t\tx: step.dissimilarity,\n\t\t\t\ty: (y1 + y2) / 2,\n\t\t\t\tchildren: [step.cluster1, step.cluster2]\n\t\t\t})\n\t\t\tcontinue\n\t\t}\n\n\t\t// at least one node is parent; may have a leaf\n\t\t// for every parent node, consume one earlier parent from the heap\n\n\t\tlet leafId = null,\n\t\t\tparentId\n\t\tif (step.cluster1 < leafCount) {\n\t\t\tleafId = step.cluster1\n\t\t\tif (step.cluster2 < leafCount) throw 'cluster2 also leaf'\n\t\t\tparentId = step.cluster2\n\t\t} else if (step.cluster2 < leafCount) {\n\t\t\tleafId = step.cluster2\n\t\t\tparentId = step.cluster1\n\t\t}\n\n\t\tif (leafId != null) {\n\t\t\t// this is a link between a parent and a leaf\n\t\t\tidxLst.push(leafId)\n\t\t\tconst y1 = currentRowIdx++\n\t\t\tid2coord.set(leafId, { x: 0, y: y1 })\n\t\t\tif (parentHeap.length == 0) throw 'empty heap, expecting 1'\n\t\t\tconst p = parentHeap.pop()\n\t\t\tid2coord.set(parentId, p)\n\t\t\t// generate a new parent\n\t\t\tparentHeap.push({\n\t\t\t\tx: step.dissimilarity,\n\t\t\t\ty: (y1 + p.y) / 2,\n\t\t\t\tchildren: [step.cluster1, step.cluster2]\n\t\t\t})\n\t\t\tcontinue\n\t\t}\n\n\t\t// both are parent\n\t\tif (parentHeap.length < 2) throw 'heap has less than 2'\n\t\tconst p1 = parentHeap.pop(),\n\t\t\tp2 = parentHeap.pop()\n\t\tid2coord.set(step.cluster1, p1)\n\t\tid2coord.set(step.cluster2, p2)\n\t\t// generate new parent\n\t\tparentHeap.push({\n\t\t\tx: step.dissimilarity,\n\t\t\ty: (p1.y + p2.y) / 2,\n\t\t\tchildren: [step.cluster1, step.cluster2]\n\t\t})\n\t}\n\n\tif (parentHeap.length != 1) throw '1 last parent not in heap'\n\tid2coord.set(leafCount * 2, parentHeap[0])\n\treturn { idxLst, id2coord }\n}\n\nfunction plotDendrogram(ctx, obj) {\n\tctx.strokeStyle = 'black'\n\n\tlet F = obj.d.yDendrogramHeight + obj.d.yLabHeight // yoffset applied to y coord when plotting x dendrogram\n\n\tfor (const n of obj.xId2coord.values()) {\n\t\tif (!n.children) continue\n\t\tif (n.children.length != 2) throw 'gene child_nodes length!=2'\n\t\tconst [c1, c2] = n.children\n\t\tconst p1 = obj.xId2coord.get(c1),\n\t\t\tp2 = obj.xId2coord.get(c2)\n\t\tif (!p1 || !p2) throw 'coord not found for gene child nodes'\n\n\t\t/*\n\t\t|-------p1\n\t\t|\n\t\tn\n\t\t|\n\t\t|-------p2\n\t\t*/\n\t\tctx.beginPath()\n\t\t// h line from n to p1\n\t\tctx.moveTo(n.x, p1.y + F)\n\t\tctx.lineTo(p1.x, p1.y + F)\n\t\t// h line from n to p2\n\t\tctx.moveTo(n.x, p2.y + F)\n\t\tctx.lineTo(p2.x, p2.y + F)\n\t\t// v line through n, from p1 to p2\n\t\tctx.moveTo(n.x, p1.y + F)\n\t\tctx.lineTo(n.x, p2.y + F)\n\t\t// end\n\t\tctx.stroke()\n\t\tctx.closePath()\n\t}\n\n\tF = obj.d.xDendrogramHeight + obj.d.xLabHeight // xoffset applied to x coord when plotting y dendrogram\n\n\tfor (const n of 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