@sjcrh/proteinpaint-client 2.213.0 → 2.214.0

package/dist/chunk-7AOA5WZY.js

@@ -1,274 +0,0 @@
-import {
-  termType2label
-} from "./chunk-RU2UHH7M.js";
-import {
-  TermTypes
-} from "./chunk-57Z4VYLM.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.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;
-  const dataType = this.config.dataType;
-  const headerText = this.config?.headerText ? `${this.config.headerText} ` : "";
-  let title;
-  if (this.config.preBuiltPlotTitle) {
-    title = this.config.preBuiltPlotTitle;
-  } else if (this.config.appName) {
-    title = `${headerText}${this.config.appName} Clustering`;
-  } else if (dataType == TermTypes.PROTEOME_ABUNDANCE) {
-    title = this.config.assayCohortTitle ? `Protein Abundance Clustering (${this.config.assayCohortTitle})` : "Protein Abundance Clustering";
-  } else {
-    title = `${headerText}${termType2label(dataType)} Clustering`;
-  }
-  this.dom.header.text(title);
-}
-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-7AOA5WZY.js.map

package/dist/chunk-7HPICVA4.js

@@ -1,178 +0,0 @@
-import {
-  __glob
-} from "./chunk-HS5PO5ZQ.js";
-
-// import("../plots/**/*.js") in plots/importPlot.js
-var globImport_plots_js = __glob({
-  "../plots/controls.btns.js": () => import("./controls.btns-6AKLIWOG.js"),
-  "../plots/controls.config.js": () => import("./controls.config-UPE6TAHK.js"),
-  "../plots/controls.js": () => import("./controls-2R2OQAX2.js"),
-  "../plots/dictionary.js": () => import("./dictionary-GYN7OXWQ.js"),
-  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-JOIKBWVC.js"),
-  "../plots/geneExpression.js": () => import("./geneExpression-NP2N4CRU.js"),
-  "../plots/geneORA.js": () => import("./geneORA-ZWZCCBL7.js"),
-  "../plots/geneset.js": () => import("./geneset-LZNALH2H.js"),
-  "../plots/hierCluster.js": () => import("./hierCluster-M6R4CH22.js"),
-  "../plots/importPlot.js": () => import("./importPlot-LKMMP7ZV.js"),
-  "../plots/matrix.js": () => import("./matrix-UAU7QUP2.js"),
-  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-DBQYJXML.js"),
-  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-EKKKYVEP.js"),
-  "../plots/matrix/hierCluster.js": () => import("./hierCluster-DCESQECE.js"),
-  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-DUDSHKDT.js"),
-  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-QKWO5EP4.js"),
-  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-RH4BOM5F.js"),
-  "../plots/matrix/matrix.config.js": () => import("./matrix.config-HZ3TORDS.js"),
-  "../plots/matrix/matrix.data.js": () => import("./matrix.data-D77IGADO.js"),
-  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-3Z5PNSKJ.js"),
-  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-XW2G5BJH.js"),
-  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-OIKLY2O6.js"),
-  "../plots/matrix/matrix.js": () => import("./matrix-U7PGR4MD.js"),
-  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-ICBZ5PCU.js"),
-  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-C3MQRAZJ.js"),
-  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-PN56PKD3.js"),
-  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-SNMIQFKB.js"),
-  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-WHVUSUJZ.js"),
-  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-UKANNCZM.js"),
-  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-DPXTME5W.js"),
-  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-7QLCJO26.js"),
-  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-IQOMDVVS.js"),
-  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-JCN62VCG.js"),
-  "../plots/matrix/test/matrix.unit.spec.js": () => import("./matrix.unit.spec-JASP2ZH6.js"),
-  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-43PZ4CLH.js"),
-  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-6I4HHUMD.js"),
-  "../plots/plot.disco.js": () => import("./plot.disco-BOWNCFJV.js"),
-  "../plots/plot.ssgq.js": () => import("./plot.ssgq-6STRLDEG.js"),
-  "../plots/singleCellPlot.js": () => import("./singleCellPlot-3V47EUB4.js"),
-  "../plots/stattable.js": () => import("./stattable-EXOWMETP.js"),
-  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-EO5KAFDQ.js"),
-  "../plots/table.js": () => import("./table-DFSX7XYJ.js"),
-  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-2TWLDD2S.js"),
-  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-2DE653PH.js"),
-  "../plots/volcano/test/testData.js": () => import("./testData-DRM5HWQB.js")
-});
-
-// plots/importPlot.js
-async function importPlot(chartType, notFoundMessage = "") {
-  switch (chartType) {
-    case "aggMatrixInput":
-      return await import("./AggMatrixInput-QA2FHMSY.js");
-    case "aggregateMatrix":
-      return await import("./AggregateMatrix-XGVKDN2K.js");
-    case "animatedBubbleChart":
-      return await import("./animatedBubbleChart-C57NY3PX.js");
-    case "brainImaging":
-      return await import("./brainImaging-J4HK4JON.js");
-    case "brainRegions":
-      return await import("./brainRegions-RH4EXEQ7.js");
-    case "barchart":
-      return await import("./barchart-7MOHGOPW.js");
-    case "boxplot":
-      return await import("./BoxPlot-IVO7VBQZ.js");
-    case "bubbleHeatmap":
-      return await import("./bubbleHeatmap-R2CNWOAJ.js");
-    case "cellTypeBubbleHeatmap":
-      return await import("./cellTypeBubbleHeatmap-KJSNP4A3.js");
-    case "correlationVolcano":
-      return await import("./CorrelationVolcano-2XD5OH2S.js");
-    case "cuminc":
-      return await import("./Cuminc-ECQ56PKO.js");
-    case "dataDownload":
-      return await import("./dataDownload-PYQX2BWN.js");
-    case "DEinput":
-      return await import("./DEinput-ZP6CYIRN.js");
-    case "dictionary":
-      return await import("./dictionary-GYN7OXWQ.js");
-    case "differentialAnalysis":
-      return await import("./DifferentialAnalysis-6SIKR566.js");
-    case "Disco":
-      return await import("./Disco-LVRT7T3B.js");
-    case "dmr":
-      return await import("./DmrPlot-ZZYKJ4UH.js");
-    case "facet":
-      return await import("./facet-4O65ZSBQ.js");
-    case "GeneExpInput":
-      return await import("./GeneExpInput-CQSORTKI.js");
-    case "geneRanking":
-      return await import("./geneRanking-UZXH5SLT.js");
-    case "genomeBrowser":
-      return await import("./GB-WR6SENAZ.js");
-    case "geomap":
-      return await import("./Geomap-CGJ7EIMD.js");
-    case "grin2":
-      return await import("./grin2-GFZ5REPY.js");
-    case "gsea":
-      return await import("./GSEA-U2GFOHWT.js");
-    case "imagePlot":
-      return await import("./imagePlot-XXSCMNUV.js");
-    case "numericDictTermCluster":
-      return await import("./numericDictTermCluster-MJK6SIWE.js");
-    case "profileBarchart2":
-      return await import("./barchart2-NOWNROMN.js");
-    case "profileForms":
-      return await import("./profileForms-WU7UNK7Y.js");
-    case "profilePlot":
-      return await import("./profilePlot-KW7UITCT.js");
-    case "profilePolar2":
-      return await import("./polar2-QQ2ZYQ3I.js");
-    case "profileRadar2":
-      return await import("./radar2-G75NIN2N.js");
-    case "profileRadarFacility2":
-      return await import("./radarFacility2-OOAUSL6F.js");
-    case "proteinView":
-      return await import("./proteinView-ET75MKLU.js");
-    case "proteomeAbundance":
-      return await import("./proteomeAbundance-NH3Y4YC7.js");
-    case "proteomeCohortCompare":
-      return await import("./proteomeCohortCompare-SDX5D26O.js");
-    case "ProteomeInput":
-      return await import("./ProteomeInput-AC5TRXHE.js");
-    case "regression":
-      return await import("./Regression-MHGQ2ECB.js");
-    case "report":
-      return await import("./report-UKB7676O.js");
-    case "runChart2":
-    //See frequencyChart
-    case "frequencyChart":
-      return await import("./RunChart2-6VSXLBNE.js");
-    case "sampleView":
-      return await import("./sampleView-JGWU2E5H.js");
-    case "sampleScatter":
-      return await import("./scatter-JXBGEKLF.js");
-    case "sc":
-      return await import("./SC-KPIQR5JQ.js");
-    case "studyCatalog":
-      return await import("./studyCatalog-OAGHQXKY.js");
-    case "summarizeCnvGeneexp":
-      return await import("./summarizeCnvGeneexp-K6XO5YEP.js");
-    case "summarizeGeneexpSurvival":
-      return await import("./summarizeGeneexpSurvival-WTAGCCU4.js");
-    case "summarizeMutationDiagnosis":
-      return await import("./summarizeMutationDiagnosis-ACFWADSQ.js");
-    case "summarizeMutationSurvival":
-      return await import("./summarizeMutationSurvival-XPFPN4N5.js");
-    case "summarizeMutationCnv":
-      return await import("./summarizeMutationCnv-QKIDS3LI.js");
-    case "summaryInput":
-      return await import("./summaryInput-GO75OPLA.js");
-    case "summary":
-      return await import("./summary-VCU2NTIZ.js");
-    case "survival":
-      return await import("./survival-BEP7JNML.js");
-    case "table":
-      return await import("./table-DFSX7XYJ.js");
-    case "violin":
-      return await import("./Violin-6BRIIZAY.js");
-    case "volcano":
-      return await import("./Volcano-TNNAVPVQ.js");
-    case "wsi":
-      return await import("./Wsi-JRAK47YP.js");
-    default:
-      if (notFoundMessage) throw notFoundMessage;
-      return await globImport_plots_js(`../plots/${chartType}.js`);
-  }
-}
-
-export {
-  importPlot
-};
-//# sourceMappingURL=chunk-7HPICVA4.js.map

package/dist/chunk-7PBHM4JU.js

@@ -1,14 +0,0 @@
-// src/block.lazyload.js
-var Block;
-async function blocklazyload(arg) {
-  if (!Block) {
-    const b = await import("./block-PRB7FXIC.js");
-    Block = b.Block;
-  }
-  return new Block(arg);
-}
-
-export {
-  blocklazyload
-};
-//# sourceMappingURL=chunk-7PBHM4JU.js.map