@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/chunk-HJARHSDC.js

@@ -1,274 +0,0 @@
-import {
-  termType2label
-} from "./chunk-AMW5LCUB.js";
-import {
-  TermTypes
-} from "./chunk-ZPWBYHNE.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-HJARHSDC.js.map

package/dist/chunk-HWNQOADC.js

@@ -1,182 +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-WQHVQAIJ.js"),
-  "../plots/controls.js": () => import("./controls-JQCMGPXP.js"),
-  "../plots/dictionary.js": () => import("./dictionary-EVLEOT72.js"),
-  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-J7ISXY6H.js"),
-  "../plots/geneExpression.js": () => import("./geneExpression-VQPRFNKE.js"),
-  "../plots/geneORA.js": () => import("./geneORA-E3PSS3CI.js"),
-  "../plots/geneset.js": () => import("./geneset-ZX4V3CFB.js"),
-  "../plots/hierCluster.js": () => import("./hierCluster-5JURTKAZ.js"),
-  "../plots/importPlot.js": () => import("./importPlot-3CG6ASNH.js"),
-  "../plots/matrix.js": () => import("./matrix-JC6AJT2N.js"),
-  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-4EERP4KK.js"),
-  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-SMTQOKUY.js"),
-  "../plots/matrix/hierCluster.js": () => import("./hierCluster-BJ5VBPXR.js"),
-  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-PAME7BWU.js"),
-  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-B4L42TBM.js"),
-  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-RH4BOM5F.js"),
-  "../plots/matrix/matrix.config.js": () => import("./matrix.config-6US3AAH7.js"),
-  "../plots/matrix/matrix.data.js": () => import("./matrix.data-FYFXYDA3.js"),
-  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-5FBKGLPS.js"),
-  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-Y7DEG3GS.js"),
-  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-NHWG4WCC.js"),
-  "../plots/matrix/matrix.js": () => import("./matrix-UCHESWVK.js"),
-  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-5DQNT7DD.js"),
-  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-OY7IF6AS.js"),
-  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-GYOXGHPU.js"),
-  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-657TLDAV.js"),
-  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-IMA2ES3T.js"),
-  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-77F36Q5H.js"),
-  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-VR4GULRV.js"),
-  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-KXX7SFX5.js"),
-  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-S6BAFYPR.js"),
-  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-V5NVQGD5.js"),
-  "../plots/matrix/test/matrix.unit.spec.js": () => import("./matrix.unit.spec-R4NMTZYQ.js"),
-  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-BMK6LMBS.js"),
-  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-S7B547V4.js"),
-  "../plots/plot.disco.js": () => import("./plot.disco-K5MMC2GD.js"),
-  "../plots/plot.ssgq.js": () => import("./plot.ssgq-B3OVMZFD.js"),
-  "../plots/singleCellPlot.js": () => import("./singleCellPlot-JJMFJ2KQ.js"),
-  "../plots/stattable.js": () => import("./stattable-XYSC3CYU.js"),
-  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-WAKTGYGP.js"),
-  "../plots/table.js": () => import("./table-GX3VJLPZ.js"),
-  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-S5FE4MMD.js"),
-  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-OWI2C2N5.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-4UHBCXYH.js");
-    case "aggregateMatrix":
-      return await import("./AggregateMatrix-IJE5CM5Y.js");
-    case "animatedBubbleChart":
-      return await import("./animatedBubbleChart-SDBWJELZ.js");
-    case "brainImaging":
-      return await import("./brainImaging-HEWGZZNY.js");
-    case "brainRegions":
-      return await import("./brainRegions-QUGB7YUW.js");
-    case "barchart":
-      return await import("./barchart-RHDKI3NZ.js");
-    case "boxplot":
-      return await import("./BoxPlot-GQYC22KY.js");
-    case "bubbleHeatmap":
-      return await import("./bubbleHeatmap-OZRONGAX.js");
-    case "cellTypeBubbleHeatmap":
-      return await import("./cellTypeBubbleHeatmap-N7NDE325.js");
-    case "correlationVolcano":
-      return await import("./CorrelationVolcano-5CWRWZTI.js");
-    case "cuminc":
-      return await import("./Cuminc-TYHKAPRK.js");
-    case "dataDownload":
-      return await import("./dataDownload-FAWN2WKE.js");
-    case "DEinput":
-      return await import("./DEinput-DU7MF4YY.js");
-    case "dictionary":
-      return await import("./dictionary-EVLEOT72.js");
-    case "differentialAnalysis":
-      return await import("./DifferentialAnalysis-G6FE2MXY.js");
-    case "Disco":
-      return await import("./Disco-B3KGNEAW.js");
-    case "dmr":
-      return await import("./DmrPlot-27NGDMT4.js");
-    case "facet":
-      return await import("./facet-FSOIZJCA.js");
-    case "GeneExpInput":
-      return await import("./GeneExpInput-NDXISF2U.js");
-    case "geneRanking":
-      return await import("./geneRanking-MK3YYINC.js");
-    case "genomeBrowser":
-      return await import("./GB-SXACUA4V.js");
-    case "geomap":
-      return await import("./Geomap-3CNT227W.js");
-    case "grin2":
-      return await import("./grin2-GN3DQNON.js");
-    case "gsea":
-      return await import("./GSEA-EHMBA3TF.js");
-    case "imagePlot":
-      return await import("./imagePlot-4LMIKBVE.js");
-    case "numericDictTermCluster":
-      return await import("./numericDictTermCluster-GLLG6IK2.js");
-    case "profileBarchart2":
-      return await import("./barchart2-CS3E6FOY.js");
-    case "profileForms":
-      return await import("./profileForms-2USYOA34.js");
-    case "profilePlot":
-      return await import("./profilePlot-YGD2CF6P.js");
-    case "profilePolar2":
-      return await import("./polar2-GECELCTG.js");
-    case "profileRadar2":
-      return await import("./radar2-X465RPJX.js");
-    case "profileRadarFacility2":
-      return await import("./radarFacility2-AE7BA62N.js");
-    case "proteinView":
-      return await import("./proteinView-FCPWJLGU.js");
-    case "proteomeAbundance":
-      return await import("./proteomeAbundance-NH3Y4YC7.js");
-    case "proteomeCohortCompare":
-      return await import("./proteomeCohortCompare-TYYUF5A5.js");
-    case "ProteomeInput":
-      return await import("./ProteomeInput-NYPUYVN5.js");
-    case "regression":
-      return await import("./Regression-WDSISHYL.js");
-    case "report":
-      return await import("./report-3Y2OWDF7.js");
-    case "runChart2":
-    //See frequencyChart
-    case "frequencyChart":
-      return await import("./RunChart2-2NPADXUR.js");
-    case "sampleView":
-      return await import("./sampleView-BUMMYRHJ.js");
-    case "sampleScatter":
-      return await import("./scatter-6S5I7OW3.js");
-    case "sc":
-      return await import("./SC-EWDBPHEL.js");
-    case "studyCatalog":
-      return await import("./studyCatalog-Y75LMI62.js");
-    case "cohortSunburst":
-      return await import("./cohortSunburst-WQK2UV25.js");
-    case "summarizeCnvGeneexp":
-      return await import("./summarizeCnvGeneexp-H2NP7VLU.js");
-    case "summarizeGeneexpSurvival":
-      return await import("./summarizeGeneexpSurvival-HTCD3VQQ.js");
-    case "summarizeMutationDiagnosis":
-      return await import("./summarizeMutationDiagnosis-MJGWP7IT.js");
-    case "summarizeMutationSurvival":
-      return await import("./summarizeMutationSurvival-55JW5LA6.js");
-    case "summarizeMutationCnv":
-      return await import("./summarizeMutationCnv-UEGXWK2P.js");
-    case "summaryInput":
-      return await import("./summaryInput-RL2JXRDE.js");
-    case "summary":
-      return await import("./summary-HJO23RGB.js");
-    case "swimmer":
-      return await import("./swimmer-VPKSBV6V.js");
-    case "survival":
-      return await import("./survival-6FLR4YCJ.js");
-    case "table":
-      return await import("./table-GX3VJLPZ.js");
-    case "violin":
-      return await import("./Violin-POGGPCZY.js");
-    case "volcano":
-      return await import("./Volcano-U2B4KEUL.js");
-    case "wsi":
-      return await import("./Wsi-G7OCAJ3R.js");
-    default:
-      if (notFoundMessage) throw notFoundMessage;
-      return await globImport_plots_js(`../plots/${chartType}.js`);
-  }
-}
-
-export {
-  importPlot
-};
-//# sourceMappingURL=chunk-HWNQOADC.js.map

package/dist/chunk-HXRG7XYB.js

@@ -1,54 +0,0 @@
-import {
-  getColors
-} from "./chunk-ZPWBYHNE.js";
-
-// termdb/handlers/junction.customTerm.ts
-var junctionCustomTermSource = "junction";
-function makeJunctionCustomTerm(junctions, eventlabel) {
-  if (!junctions.length) throw new Error("junctions[] is empty");
-  if (!eventlabel) {
-    const term = junctions[0];
-    return {
-      id: `junction:${term.id}`,
-      name: term.name,
-      source: junctionCustomTermSource,
-      tw: {
-        term,
-        q: { mode: "continuous" }
-      }
-    };
-  }
-  const termlst = [...new Map(junctions.map((term) => [term.id, term])).values()];
-  const colorScale = getColors(termlst.length);
-  const termIds = termlst.map((term) => term.id);
-  return {
-    id: `junction-event:${eventlabel}`,
-    name: eventlabel,
-    source: junctionCustomTermSource,
-    eventlabel,
-    tw: {
-      term: {
-        type: "termCollection",
-        isCustom: true,
-        memberType: "numeric",
-        name: eventlabel,
-        termIds,
-        termlst,
-        propsByTermId: Object.fromEntries(termlst.map((term) => [term.id, { color: colorScale(term.id) }])),
-        isleaf: true
-      },
-      q: {
-        mode: "continuous",
-        type: "values",
-        lst: termIds,
-        numerators: termIds
-      }
-    }
-  };
-}
-
-export {
-  junctionCustomTermSource,
-  makeJunctionCustomTerm
-};
-//# sourceMappingURL=chunk-HXRG7XYB.js.map

package/dist/chunk-J5KCTRJC.js

@@ -1,80 +0,0 @@
-import {
-  addGeneSearchbox,
-  getGEunit,
-  getSampleTypeLabelByTerms,
-  getSelectedSampleTypes,
-  getSelectedSampleTypesByTerms,
-  renderSampleTypeSelect,
-  renderSampleTypesByTermsSelect,
-  table2col
-} from "./chunk-NNDKYTUV.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  TermTypes
-} from "./chunk-ZPWBYHNE.js";
-
-// termdb/handlers/geneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    this.dom = {};
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    this.dom.sampleTypeDiv = holder.append("div");
-    this.mayRenderSampleTypeSelect();
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch)
-    });
-    holder.select(".sja_genesearchinput").style("margin", "0px");
-  }
-  mayRenderSampleTypeSelect() {
-    this.dom.sampleTypeDiv.selectAll("*").remove();
-    this.querySampleTypes = this.app.vocabApi.termdbConfig?.queries.geneExpression.sampleTypes;
-    this.querySampleTypesByTerms = this.app.vocabApi.termdbConfig?.queries.geneExpression.sampleTypesByTerms;
-    if (Array.isArray(this.querySampleTypes) && this.querySampleTypes.length >= 2 || this.querySampleTypesByTerms) {
-      const table = table2col({ holder: this.dom.sampleTypeDiv, margin: "0px 0px 15px 0px" });
-      const [td1, td2] = table.addRow();
-      td1.text("Sample Type");
-      td2.style("padding-left", "10px");
-      if (this.querySampleTypesByTerms) {
-        this.sampleTypeSelect = renderSampleTypesByTermsSelect(
-          td2,
-          this.querySampleTypesByTerms,
-          this.app.vocabApi.termdbConfig
-        );
-      } else {
-        this.sampleTypeSelect = renderSampleTypeSelect(td2, this.querySampleTypes, this.app.vocabApi.termdbConfig);
-      }
-    }
-  }
-  async selectGene(geneSearch) {
-    const gene = geneSearch?.geneSymbol;
-    if (!gene) throw new Error("No gene selected");
-    const sampleTypes = this.querySampleTypesByTerms ? getSelectedSampleTypesByTerms(this.sampleTypeSelect, this.querySampleTypesByTerms) : getSelectedSampleTypes(this.sampleTypeSelect) || this.querySampleTypes;
-    if (this.sampleTypeSelect && !sampleTypes?.length) {
-      return;
-    }
-    const unit = getGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    const term = { gene, name, type: TermTypes.GENE_EXPRESSION, sampleTypes };
-    if (this.querySampleTypesByTerms) {
-      const sampleTypeLabel = getSampleTypeLabelByTerms(this.sampleTypeSelect);
-      if (sampleTypeLabel) {
-        term.sampleTypeLabel = sampleTypeLabel;
-        term.name += ` (${sampleTypeLabel})`;
-      }
-    }
-    this.callback(term);
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-J5KCTRJC.js.map

package/dist/chunk-JMFVXWDX.js

@@ -1,59 +0,0 @@
-import {
-  plotColor
-} from "./chunk-ZPWBYHNE.js";
-
-// plots/scatter/settings/defaults.ts
-function getDefaultScatterSettings(opts = {}) {
-  const overrides = opts?.overrides || {};
-  const defaults = {
-    size: 0.8,
-    minShapeSize: 0.5,
-    maxShapeSize: 4,
-    scaleDotOrder: "Ascending",
-    refSize: 0.8,
-    svgw: 600,
-    svgh: 600,
-    svgd: 600,
-    axisTitleFontSize: 16,
-    showAxes: true,
-    showRef: true,
-    opacity: 0.6,
-    defaultColor: plotColor,
-    regression: "None",
-    fov: 50,
-    threeSize: 5e-3,
-    threeFOV: 70,
-    maxSvgSamplesCutoff: 2e4,
-    // if a cohort is larger than this, switch from svg to webgl/canvas rendering
-    //ColorScale settings
-    colorScaleMode: "auto",
-    colorScalePercentile: 95,
-    colorScaleMinFixed: null,
-    colorScaleMaxFixed: null,
-    noExpColor: "#F5F5F5",
-    // light gray, for dots with no gene expression value
-    expColor: "#ff000d",
-    // default color for the maximum gene expression value
-    //3D Plot settings
-    showContour: false,
-    colorContours: false,
-    contourBandwidth: 30,
-    contourThresholds: 10,
-    duration: 500,
-    useGlobalMinMax: true,
-    saveZoomTransform: false,
-    // Axis scale settings
-    minXScale: null,
-    maxXScale: null,
-    minYScale: null,
-    maxYScale: null,
-    itemLabel: opts?.singleCellPlot ? "Cell" : "Sample",
-    maxTooltipRows: 5
-  };
-  return Object.assign(defaults, overrides);
-}
-
-export {
-  getDefaultScatterSettings
-};
-//# sourceMappingURL=chunk-JMFVXWDX.js.map