@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/geneExpClustering-PJA6Y5GW.js

@@ -1,244 +0,0 @@
-import {
-  appInit
-} from "./chunk-CPIPN5F6.js";
-import "./chunk-MSSPT5YM.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import {
-  fillTermWrapper,
-  vocabInit
-} from "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import {
-  TermTypes
-} from "./chunk-4EZLVENZ.js";
-import {
-  copyMerge
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.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-PJA6Y5GW.js.map

package/dist/geneExpression-EMLVPVNK.js

@@ -1,310 +0,0 @@
-import {
-  dofetch3
-} from "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.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-EMLVPVNK.js.map

package/dist/geneExpression-JMGYBT53.js

@@ -1,33 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-VO7Q4WMM.js";
-import "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=geneExpression-JMGYBT53.js.map