@sjcrh/proteinpaint-client 2.191.3 → 2.191.4

package/dist/chunk-SHWLROJG.js

@@ -0,0 +1,283 @@
+import {
+  NUMERIC_DICTIONARY_TERM,
+  TermTypes
+} from "./chunk-NOEAT6CX.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/hierCluster.renderers.js
+var hierCluster_renderers_exports = {};
+__export(hierCluster_renderers_exports, {
+  maySetSandboxHeader: () => maySetSandboxHeader,
+  plotDendrogramHclust: () => plotDendrogramHclust,
+  renderImage: () => renderImage
+});
+function maySetSandboxHeader(appState) {
+  if (!this.dom.header) return;
+  switch (this.config.dataType) {
+    case TermTypes.GENE_EXPRESSION:
+      const headerText = this.config?.headerText ? `${this.config.headerText} ` : "";
+      this.dom.header.text(`${headerText}Gene Expression Clustering`);
+      break;
+    case TermTypes.METABOLITE_INTENSITY:
+      this.dom.header.text("Metabolite Intensity Clustering");
+      break;
+    case TermTypes.SSGSEA:
+      this.dom.header.text("ssGSEA Clustering");
+      break;
+    case NUMERIC_DICTIONARY_TERM:
+      this.dom.header.text(
+        this.config.preBuiltPlotTitle ? this.config.preBuiltPlotTitle : appState.termdbConfig.numericDictTermCluster?.appName ? appState.termdbConfig.numericDictTermCluster.appName + " Clustering" : "Numeric Dictionary Term Clustering"
+      );
+      break;
+    case TermTypes.PROTEOME_ABUNDANCE:
+      this.dom.header.text(
+        this.config.assayCohortTitle ? `Protein Abundance Clustering (${this.config.assayCohortTitle})` : "Protein Abundance Clustering"
+      );
+      break;
+    default:
+      throw `dataType '${this.config.dataType}' not recognized`;
+  }
+}
+function plotDendrogramHclust(plotOnly) {
+  const d = this.dimensions;
+  const s = this.config.settings.matrix;
+  const xOffset = d.seriesXoffset;
+  const pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio;
+  const obj = this.hierClusterData.clustering;
+  const row = obj.row;
+  const col = obj.col;
+  const rowHeight = this.settings.matrix.clusterRowh, { xDendrogramHeight, yDendrogramHeight } = this.settings.hierCluster, colWidth = this.dimensions.dx;
+  if (plotOnly !== "left") {
+    if (!this.settings.hierCluster.clusterSamples) {
+      this.dom.topDendrogram.selectAll("*").remove();
+    } else {
+      const height2px = getHclustHeightScalefactor(col.height, yDendrogramHeight);
+      const height = yDendrogramHeight + 1e-7;
+      const width = Math.min(colWidth * col.inputOrder.length, s.imgWMax);
+      if (width <= 0 || height <= 0) {
+        console.warn(
+          "Skipping top dendrogram render: invalid dimensions.",
+          "This may indicate a zoom feedback loop issue.",
+          {
+            width,
+            height,
+            colWidth,
+            sampleCount: col.inputOrder.length,
+            yDendrogramHeight
+          }
+        );
+        this.dom.topDendrogram.selectAll("*").remove();
+        return;
+      }
+      const canvas = new OffscreenCanvas(width * pxr, height * pxr);
+      const ctx = canvas.getContext("2d");
+      ctx.scale(pxr, pxr);
+      ctx.translate(-d.xMin, 0);
+      ctx.imageSmoothingEnabled = false;
+      ctx.imageSmoothingQuality = "high";
+      ctx.strokeStyle = "black";
+      const mergedClusters = /* @__PURE__ */ new Map();
+      for (const [clusterid0, pair] of col.merge.entries()) {
+        const clusterid = clusterid0 + 1;
+        const children = [];
+        const childrenClusters = [];
+        let x1, x2, y1, y2;
+        if (pair.n1 < 0) {
+          const [name, columnNumber] = getLeafNumber(pair.n1, col.inputOrder, col.order);
+          x1 = colWidth * (columnNumber + 0.5);
+          y1 = yDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n1);
+          x1 = c.x;
+          y1 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n1);
+        }
+        if (pair.n2 < 0) {
+          const [name, columnNumber] = getLeafNumber(pair.n2, col.inputOrder, col.order);
+          x2 = colWidth * (columnNumber + 0.5);
+          y2 = yDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n2);
+          x2 = c.x;
+          y2 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n2);
+        }
+        const clusterY = yDendrogramHeight - col.height[clusterid0].height * height2px;
+        const highlight = this.clickedClusterIds?.includes(clusterid);
+        ctx.strokeStyle = highlight ? "red" : "black";
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(x1, clusterY);
+        ctx.lineTo(x2, clusterY);
+        ctx.lineTo(x2, y2);
+        ctx.stroke();
+        ctx.closePath();
+        mergedClusters.set(clusterid, {
+          x: (x1 + x2) / 2,
+          y: clusterY,
+          children,
+          childrenClusters,
+          clusterPosition: {
+            x1,
+            x2,
+            y1,
+            y2,
+            clusterY
+          }
+        });
+      }
+      this.renderImage(
+        this.api,
+        this.dom.topDendrogram,
+        canvas,
+        width,
+        height,
+        xDendrogramHeight + 0.5 * colWidth + d.xMin,
+        s.margin.top + s.scrollHeight
+      );
+      col.mergedClusters = mergedClusters;
+    }
+  }
+  if (plotOnly !== "top") {
+    if (!this.settings.hierCluster.clusterRows) {
+      this.dom.leftDendrogram.selectAll("*").remove();
+    } else {
+      const height2px = getHclustHeightScalefactor(row.height, xDendrogramHeight);
+      const width = xDendrogramHeight + 1e-7;
+      const height = rowHeight * row.inputOrder.length;
+      const canvasWidthPx = Number.isFinite(width) && Number.isFinite(pxr) ? Math.max(0, Math.floor(width * pxr)) : 0;
+      const canvasHeightPx = Number.isFinite(height) && Number.isFinite(pxr) ? Math.max(0, Math.floor(height * pxr)) : 0;
+      if (!Number.isFinite(width) || !Number.isFinite(height) || !Number.isFinite(pxr) || width <= 0 || height <= 0 || pxr <= 0 || canvasWidthPx < 1 || canvasHeightPx < 1) {
+        console.warn(
+          "Skipping left dendrogram render: invalid dimensions.",
+          "This may indicate a zoom feedback loop issue.",
+          {
+            width,
+            height,
+            pxr,
+            canvasWidthPx,
+            canvasHeightPx,
+            rowHeight,
+            termCount: row.inputOrder.length,
+            xDendrogramHeight
+          }
+        );
+        this.dom.leftDendrogram.selectAll("*").remove();
+        return;
+      }
+      const canvas = new OffscreenCanvas(canvasWidthPx, canvasHeightPx);
+      const ctx = canvas.getContext("2d");
+      ctx.scale(pxr, pxr);
+      ctx.imageSmoothingEnabled = false;
+      ctx.imageSmoothingQuality = "high";
+      ctx.strokeStyle = "black";
+      const mergedClusters = /* @__PURE__ */ new Map();
+      for (const [clusterid0, pair] of row.merge.entries()) {
+        const clusterid = clusterid0 + 1;
+        const children = [];
+        const childrenClusters = [];
+        let x1, x2, y1, y2;
+        if (pair.n1 < 0) {
+          const [name, rowNumber] = getLeafNumber(pair.n1, row.inputOrder, row.order);
+          y1 = rowHeight * (rowNumber + 0.5);
+          x1 = xDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n1);
+          x1 = c.x;
+          y1 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n1);
+        }
+        if (pair.n2 < 0) {
+          const [name, rowNumber] = getLeafNumber(pair.n2, row.inputOrder, row.order);
+          y2 = rowHeight * (rowNumber + 0.5);
+          x2 = xDendrogramHeight;
+          children.push({ name });
+        } else {
+          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
+          const c = mergedClusters.get(pair.n2);
+          x2 = c.x;
+          y2 = c.y;
+          children.push(...c.children);
+          childrenClusters.push(pair.n2);
+        }
+        const clusterX = xDendrogramHeight - row.height[clusterid0].height * height2px;
+        const highlight = this.clickedLeftClusterIds?.includes(clusterid);
+        ctx.strokeStyle = highlight ? "red" : "black";
+        ctx.beginPath();
+        ctx.moveTo(x1, y1);
+        ctx.lineTo(clusterX, y1);
+        ctx.lineTo(clusterX, y2);
+        ctx.lineTo(x2, y2);
+        ctx.stroke();
+        ctx.closePath();
+        mergedClusters.set(clusterid, {
+          x: clusterX,
+          y: (y1 + y2) / 2,
+          children,
+          childrenClusters,
+          clusterPosition: {
+            x1,
+            x2,
+            y1,
+            y2,
+            clusterX
+          }
+        });
+      }
+      const t = this.termOrder.find((t2) => t2.grp.type == "hierCluster" || t2.grp.name == this.hcTermGroup.name);
+      const y = (
+        // t.labelOffset is commented out because it is already handled in adjustSvgDimensions
+        t.grpIndex * s.rowgspace + t.prevGrpTotalIndex * s.rowh + t.totalHtAdjustments + s.margin.top + s.scrollHeight + // left dendrogram image must be lower than the top dendrogram image height
+        yDendrogramHeight
+      );
+      this.renderImage(this.api, this.dom.leftDendrogram, canvas, width, height, 0, y);
+      row.mergedClusters = mergedClusters;
+    }
+  }
+}
+async function renderImage(componentApi, g, canvas, width, height, x, y) {
+  const sequenceId = componentApi.getSequenceId();
+  const reader = new FileReader();
+  reader.addEventListener(
+    "load",
+    () => {
+      if (componentApi.isStaleSequenceId(sequenceId)) return;
+      g.selectAll("*").remove();
+      g.append("image").attr("x", x + 0.033).attr("y", y + 0.033).attr("xlink:href", reader.result).attr("width", width).attr("height", height);
+    },
+    false
+  );
+  const blob = await canvas.convertToBlob({ quality: 1 });
+  reader.readAsDataURL(blob);
+}
+function getHclustHeightScalefactor(lst, ph) {
+  let max = lst[0].height;
+  for (const h of lst) max = Math.max(max, h.height);
+  return ph / max;
+}
+function getLeafNumber(minus, inputOrder, order) {
+  const name = inputOrder[-minus - 1];
+  if (!name) throw "minus not in inputOrder";
+  const i = order.findIndex((j) => j.name == name);
+  if (i == -1) throw "name not found in hc$order";
+  return [name, i];
+}
+
+export {
+  maySetSandboxHeader,
+  plotDendrogramHclust,
+  renderImage,
+  hierCluster_renderers_exports
+};
+//# sourceMappingURL=chunk-SHWLROJG.js.map

package/dist/chunk-SKREEF3H.js

@@ -0,0 +1,184 @@
+import {
+  __glob
+} from "./chunk-HFNDKYVF.js";
+
+// import("../plots/**/*.js") in plots/importPlot.js
+var globImport_plots_js = __glob({
+  "../plots/barchart.data.js": () => import("./barchart.data-Z2E72EET.js"),
+  "../plots/barchart.events.js": () => import("./barchart.events-NUYQBI5S.js"),
+  "../plots/barchart.js": () => import("./barchart-VDOP6FQU.js"),
+  "../plots/bars.renderer.js": () => import("./bars.renderer-JHCZDSM6.js"),
+  "../plots/bars.settings.js": () => import("./bars.settings-SDU7PZOS.js"),
+  "../plots/brainImaging.js": () => import("./brainImaging-65QDNR4D.js"),
+  "../plots/controls.btns.js": () => import("./controls.btns-AP67YWKW.js"),
+  "../plots/controls.config.js": () => import("./controls.config-C535H5DL.js"),
+  "../plots/controls.js": () => import("./controls-YEEW46C6.js"),
+  "../plots/cuminc.js": () => import("./cuminc-II7NFIFP.js"),
+  "../plots/dataDownload.js": () => import("./dataDownload-ZQYLXN6D.js"),
+  "../plots/dictionary.js": () => import("./dictionary-RYM4WP2W.js"),
+  "../plots/dziviewer/plot.dzi.js": () => import("./plot.dzi-T3GPUH36.js"),
+  "../plots/facet.js": () => import("./facet-2FBUAD7P.js"),
+  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-DJIRW2X7.js"),
+  "../plots/geneExpression.js": () => import("./geneExpression-2OPFWV2K.js"),
+  "../plots/geneORA.js": () => import("./geneORA-S3KQMBYL.js"),
+  "../plots/geneset.js": () => import("./geneset-SNM4M6UM.js"),
+  "../plots/gsea.js": () => import("./gsea-SPTQJW67.js"),
+  "../plots/hierCluster.js": () => import("./hierCluster-KDE5SMYP.js"),
+  "../plots/importPlot.js": () => import("./importPlot-YH7ZY6RJ.js"),
+  "../plots/matrix.js": () => import("./matrix-DZJXYRYN.js"),
+  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-VNEEJCKJ.js"),
+  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-DKBSJ644.js"),
+  "../plots/matrix/hierCluster.js": () => import("./hierCluster-XG4YLVL3.js"),
+  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-OG6LZAT7.js"),
+  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-PT7S74QP.js"),
+  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-NU5CYRUT.js"),
+  "../plots/matrix/matrix.config.js": () => import("./matrix.config-2ORCUWKX.js"),
+  "../plots/matrix/matrix.data.js": () => import("./matrix.data-C6VPQJJ4.js"),
+  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-F7AN3QGE.js"),
+  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-CEOCG2CT.js"),
+  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-GFLIFIER.js"),
+  "../plots/matrix/matrix.js": () => import("./matrix-Y5345QQG.js"),
+  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-DOVDHTDX.js"),
+  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-JE4ZSLP7.js"),
+  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-GPUJQ7KF.js"),
+  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-REE4DCSR.js"),
+  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-VD5URUWY.js"),
+  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-VQYY6KBK.js"),
+  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-SSDN7LSH.js"),
+  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-U4B3JB6N.js"),
+  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-4IOFVHJN.js"),
+  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-V5O2EJBX.js"),
+  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-RLIVVVD6.js"),
+  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-KV72PAON.js"),
+  "../plots/plot.disco.js": () => import("./plot.disco-OUE4RFHL.js"),
+  "../plots/plot.ssgq.js": () => import("./plot.ssgq-WJHGMXW5.js"),
+  "../plots/regression.inputs.js": () => import("./regression.inputs-QOSBAGL6.js"),
+  "../plots/regression.inputs.term.js": () => import("./regression.inputs.term-HMUMPY7X.js"),
+  "../plots/regression.inputs.values.table.js": () => import("./regression.inputs.values.table-VMCTZHLG.js"),
+  "../plots/regression.js": () => import("./regression-ZPDPLI6G.js"),
+  "../plots/regression.results.js": () => import("./regression.results-5XC6M67C.js"),
+  "../plots/sampleView.js": () => import("./sampleView-SVTLSWRG.js"),
+  "../plots/scatter/test/scatter.integration.spec.js": () => import("./scatter.integration.spec-3EYTPY5B.js"),
+  "../plots/singleCellPlot.js": () => import("./singleCellPlot-ZUAWK5RE.js"),
+  "../plots/stattable.js": () => import("./stattable-MDABSW3F.js"),
+  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-7IWBTPJG.js"),
+  "../plots/table.js": () => import("./table-FQAIXKLE.js"),
+  "../plots/test/barchart.integration.spec.js": () => import("./barchart.integration.spec-COVZPXMH.js"),
+  "../plots/test/cuminc.integration.spec.js": () => import("./cuminc.integration.spec-B4N6OMBJ.js"),
+  "../plots/test/dataDownload.integration.spec.js": () => import("./dataDownload.integration.spec-2PKYZ2AY.js"),
+  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-UJO2R3CW.js"),
+  "../plots/test/regression.integration.spec.js": () => import("./regression.integration.spec-RP74JTAA.js"),
+  "../plots/test/regression.spec.js": () => import("./regression.spec-EZYM24J7.js"),
+  "../plots/test/sampleScatter.spec.js": () => import("./sampleScatter.spec-CD52FEOC.js"),
+  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-ZLRIA7G2.js"),
+  "../plots/test/violin.integration.spec.js": () => import("./violin.integration.spec-RJATDLQH.js"),
+  "../plots/violin.interactivity.js": () => import("./violin.interactivity-SKF5H7MN.js"),
+  "../plots/violin.js": () => import("./violin-6VKRUQV3.js"),
+  "../plots/violin.renderer.js": () => import("./violin.renderer-GB4TPX3B.js"),
+  "../plots/volcano/test/testData.js": () => import("./testData-LEJ53F2K.js"),
+  "../plots/wsiviewer/plot.wsi.js": () => import("./plot.wsi-2MU5BDG3.js")
+});
+
+// plots/importPlot.js
+async function importPlot(chartType, notFoundMessage = "") {
+  switch (chartType) {
+    case "AIProjectAdmin":
+      return await import("./AIProjectAdmin-2OQOQXH4.js");
+    case "barchart":
+      return await import("./barchart-VDOP6FQU.js");
+    case "boxplot":
+      return await import("./BoxPlot-PUZKHACO.js");
+    case "correlationVolcano":
+      return await import("./CorrelationVolcano-RO6CFLZA.js");
+    case "DEinput":
+      return await import("./DEinput-MRUQW6X6.js");
+    case "dictionary":
+      return await import("./dictionary-RYM4WP2W.js");
+    case "differentialAnalysis":
+      return await import("./DifferentialAnalysis-5YQQLJKR.js");
+    case "Disco":
+      return await import("./Disco-4FTOJBLG.js");
+    case "dmr":
+      return await import("./DmrPlot-FPJJHTM5.js");
+    case "DziViewer":
+      return await import("./DziViewer-6737GC22.js");
+    case "GeneExpInput":
+      return await import("./GeneExpInput-Q42COANS.js");
+    case "genomeBrowser":
+      return await import("./GB-H6JETPRC.js");
+    case "grin2":
+      return await import("./grin2-RKJXYWJ5.js");
+    case "gsea":
+      return await import("./gsea-SPTQJW67.js");
+    case "imagePlot":
+      return await import("./imagePlot-M5JSHEY4.js");
+    case "report":
+      return await import("./report-ZOVQCOGQ.js");
+    case "runChart2":
+    //See frequencyChart
+    case "frequencyChart":
+      return await import("./RunChart2-N7AZVQXJ.js");
+    case "profileBarchart2":
+      return await import("./barchart2-KMSU4ROO.js");
+    case "profileForms":
+      return await import("./profileForms-OV3I6RK7.js");
+    case "profileForms2":
+      return await import("./forms2-ZBT5BZW3.js");
+    case "profilePlot":
+      return await import("./profilePlot-OMVO3K4H.js");
+    case "profilePolar2":
+      return await import("./polar2-YCWPBPFU.js");
+    case "profileRadar2":
+      return await import("./radar2-KREAMGVV.js");
+    case "profileRadarFacility2":
+      return await import("./radarFacility2-DBPEV7VC.js");
+    case "proteinView":
+      return await import("./proteinView-OAR2RC6U.js");
+    case "numericDictTermCluster":
+      return await import("./numericDictTermCluster-TFXBBUVI.js");
+    case "proteomeAbundance":
+      return await import("./proteomeAbundance-NQ4635NL.js");
+    case "geneRanking":
+      return await import("./geneRanking-UZ36XAL7.js");
+    case "ProteomeInput":
+      return await import("./ProteomeInput-5KMNE3PZ.js");
+    case "sampleScatter":
+      return await import("./scatter-WNRTPSEE.js");
+    case "sc":
+      return await import("./SC-M6RGALZM.js");
+    case "summarizeCnvGeneexp":
+      return await import("./summarizeCnvGeneexp-RRP6JUV6.js");
+    case "summarizeGeneexpSurvival":
+      return await import("./summarizeGeneexpSurvival-AFLHDD6Q.js");
+    case "summarizeMutationDiagnosis":
+      return await import("./summarizeMutationDiagnosis-2LQ7JU3K.js");
+    case "summarizeMutationSurvival":
+      return await import("./summarizeMutationSurvival-3WBT5TXG.js");
+    case "summarizeMutationCnv":
+      return await import("./summarizeMutationCnv-NABUYHMX.js");
+    case "summaryInput":
+      return await import("./summaryInput-4JO6MHP4.js");
+    case "summary":
+      return await import("./summary-FRDKOFXW.js");
+    case "survival":
+      return await import("./survival-IF5NI3A6.js");
+    case "table":
+      return await import("./table-FQAIXKLE.js");
+    case "violin":
+      return await import("./violin-6VKRUQV3.js");
+    case "volcano":
+      return await import("./Volcano-YH4RJTT5.js");
+    case "WSISamplesPlot":
+      return await import("./WsiSamplesPlot-QPPB7OOD.js");
+    case "WSIViewer":
+      return await import("./WSIViewer-7LOVM3AU.js");
+    default:
+      if (notFoundMessage) throw notFoundMessage;
+      return await globImport_plots_js(`../plots/${chartType}.js`);
+  }
+}
+
+export {
+  importPlot
+};
+//# sourceMappingURL=chunk-SKREEF3H.js.map