@sjcrh/proteinpaint-client 2.81.1 → 2.81.2-1

package/dist/{block.tk.bam-SN64QJZA.js → block.tk.bam-63AG2O3T.js}

@@ -1,7 +1,7 @@
 import {
   axisstyle,
   make_radios
-} from "./chunk-AXQGMSEZ.js";
+} from "./chunk-PU7EMWOK.js";
 import "./chunk-7KFEDC2T.js";
 import {
   make_one_checkbox
@@ -10,7 +10,7 @@ import "./chunk-WX2C2ZIZ.js";
 import "./chunk-CVWXP35F.js";
 import "./chunk-OTWQWP6Z.js";
 import "./chunk-6BHKLDWV.js";
-import "./chunk-SWICAWWD.js";
+import "./chunk-TU4H4R2T.js";
 import {
   urlmap_default
 } from "./chunk-OPXTD3S3.js";
@@ -1955,4 +1955,4 @@ function renderGroup(group, tk, block) {
 export {
   loadTk
 };
-//# sourceMappingURL=block.tk.bam-SN64QJZA.js.map
+//# sourceMappingURL=block.tk.bam-63AG2O3T.js.map

package/dist/{block.tk.hicstraw-BLQ4TPWX.js → block.tk.hicstraw-EOEMGOSH.js}

@@ -4,14 +4,14 @@ import {
 } from "./chunk-EW7ND3XZ.js";
 import {
   ColorScale
-} from "./chunk-AXQGMSEZ.js";
+} from "./chunk-PU7EMWOK.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-WX2C2ZIZ.js";
 import "./chunk-CVWXP35F.js";
 import "./chunk-OTWQWP6Z.js";
 import "./chunk-6BHKLDWV.js";
-import "./chunk-SWICAWWD.js";
+import "./chunk-TU4H4R2T.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
@@ -50,7 +50,7 @@ function loadTk(tk, block) {
   block.tkcloakon(tk);
   block.block_setheight();
   Promise.resolve().then(() => {
-    return import("./HicApp-KLMBWHYQ.js").then((p) => {
+    return import("./HicApp-4OAJJINK.js").then((p) => {
       hicstraw = p;
     });
   }).then(() => {
@@ -862,4 +862,4 @@ function textdata_parseraw(tk, block) {
 export {
   loadTk
 };
-//# sourceMappingURL=block.tk.hicstraw-BLQ4TPWX.js.map
+//# sourceMappingURL=block.tk.hicstraw-EOEMGOSH.js.map

package/dist/{block.tk.junction.textmatrixui-CF3BLGOS.js → block.tk.junction.textmatrixui-7S7LZ6PI.js}

@@ -84,7 +84,7 @@ function block_tk_junction_textmatrixui_default(genomes, hostURL, jwt, holder) {
       }
     ];
     first_genetrack_tolist(genomeobj, tracks);
-    import("./block-UXADMA2N.js").then(
+    import("./block-YWY77ICL.js").then(
       (b) => new b.Block({
         hostURL,
         jwt,
@@ -193,4 +193,4 @@ function junction_parsecoord(s, g) {
 export {
   block_tk_junction_textmatrixui_default as default
 };
-//# sourceMappingURL=block.tk.junction.textmatrixui-CF3BLGOS.js.map
+//# sourceMappingURL=block.tk.junction.textmatrixui-7S7LZ6PI.js.map

package/dist/{block.tk.ld-D4Z73BNG.js → block.tk.ld-CPSTDYJR.js}

@@ -1,18 +1,18 @@
 import {
   showLDlegend
-} from "./chunk-S7IXU2TT.js";
+} from "./chunk-ULCFS3DC.js";
 import {
   legend_newrow
 } from "./chunk-H77FJYAH.js";
 import "./chunk-M6GWX3QG.js";
-import "./chunk-AXQGMSEZ.js";
+import "./chunk-PU7EMWOK.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-WX2C2ZIZ.js";
 import "./chunk-CVWXP35F.js";
 import "./chunk-OTWQWP6Z.js";
 import "./chunk-6BHKLDWV.js";
-import "./chunk-SWICAWWD.js";
+import "./chunk-TU4H4R2T.js";
 import "./chunk-IPNHDLML.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
@@ -95,4 +95,4 @@ function makeTk(tk, block) {
 export {
   loadTk
 };
-//# sourceMappingURL=block.tk.ld-D4Z73BNG.js.map
+//# sourceMappingURL=block.tk.ld-CPSTDYJR.js.map

package/dist/{boxplot-MR6KTUUN.js → boxplot-6AG5JKWD.js}

@@ -1,11 +1,11 @@
 import {
   controlsInit
-} from "./chunk-5ZLCRPFR.js";
-import "./chunk-R6DC7BAI.js";
+} from "./chunk-LOV6H3RZ.js";
+import "./chunk-X5ZQI22O.js";
 import "./chunk-U6ZCLI5S.js";
-import "./chunk-2MDPMDCG.js";
+import "./chunk-WA6VYIW4.js";
 import "./chunk-CLHA5AEH.js";
-import "./chunk-AXQGMSEZ.js";
+import "./chunk-PU7EMWOK.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-WX2C2ZIZ.js";
@@ -13,7 +13,7 @@ import "./chunk-CVWXP35F.js";
 import "./chunk-OTWQWP6Z.js";
 import "./chunk-6BHKLDWV.js";
 import "./chunk-EG3MKQQH.js";
-import "./chunk-SWICAWWD.js";
+import "./chunk-TU4H4R2T.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
@@ -284,4 +284,4 @@ var boxplotInit = getCompInit(TdbBoxplot);
 export {
   boxplotInit
 };
-//# sourceMappingURL=boxplot-MR6KTUUN.js.map
+//# sourceMappingURL=boxplot-6AG5JKWD.js.map

package/dist/{brainImaging-I6ZDK532.js → brainImaging-TK2K5UM3.js}

@@ -1,12 +1,12 @@
 import {
   configUiInit
-} from "./chunk-R6DC7BAI.js";
+} from "./chunk-X5ZQI22O.js";
 import {
   topBarInit
 } from "./chunk-U6ZCLI5S.js";
-import "./chunk-2MDPMDCG.js";
+import "./chunk-WA6VYIW4.js";
 import "./chunk-CLHA5AEH.js";
-import "./chunk-AXQGMSEZ.js";
+import "./chunk-PU7EMWOK.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-WX2C2ZIZ.js";
@@ -16,7 +16,7 @@ import "./chunk-6BHKLDWV.js";
 import "./chunk-EG3MKQQH.js";
 import {
   renderTable
-} from "./chunk-SWICAWWD.js";
+} from "./chunk-TU4H4R2T.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
@@ -255,4 +255,4 @@ export {
   getPlotConfig,
   makeChartBtnMenu
 };
-//# sourceMappingURL=brainImaging-I6ZDK532.js.map
+//# sourceMappingURL=brainImaging-TK2K5UM3.js.map

package/dist/{categorical-2HPTMAKH.js → categorical-FNHJZRSN.js}

@@ -2,11 +2,11 @@ import {
   fillTW,
   getHandler,
   setCategoryMethods
-} from "./chunk-FIIST5SP.js";
+} from "./chunk-UIM2YO7Q.js";
 import "./chunk-AJEQEARY.js";
-import "./chunk-2MDPMDCG.js";
+import "./chunk-WA6VYIW4.js";
 import "./chunk-CLHA5AEH.js";
-import "./chunk-AXQGMSEZ.js";
+import "./chunk-PU7EMWOK.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-WX2C2ZIZ.js";
@@ -14,7 +14,7 @@ import "./chunk-CVWXP35F.js";
 import "./chunk-OTWQWP6Z.js";
 import "./chunk-6BHKLDWV.js";
 import "./chunk-EG3MKQQH.js";
-import "./chunk-SWICAWWD.js";
+import "./chunk-TU4H4R2T.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
@@ -40,4 +40,4 @@ export {
   getHandler,
   setCategoryMethods
 };
-//# sourceMappingURL=categorical-2HPTMAKH.js.map
+//# sourceMappingURL=categorical-FNHJZRSN.js.map

package/dist/{chunk-DQUCI4A5.js → chunk-6SDDZ3OH.js}

@@ -1,6 +1,6 @@
 import {
   loadstudycohort
-} from "./chunk-2NT22HOU.js";
+} from "./chunk-QOK2NF6U.js";
 import {
   corsMessage
 } from "./chunk-6MSAGRRE.js";
@@ -9,7 +9,7 @@ import {
 } from "./chunk-OPXTD3S3.js";
 import {
   block_init_default
-} from "./chunk-RATVZLSH.js";
+} from "./chunk-TJ6VPTKK.js";
 import {
   sayerror
 } from "./chunk-RKJGIOIF.js";
@@ -253,7 +253,7 @@ async function parse(arg) {
     return;
   }
   if (urlp.has("gdcbamslice")) {
-    const _ = await import("./bam-WQL634EI.js");
+    const _ = await import("./bam-TXECENXB.js");
     _.bamsliceui({
       genomes: arg.genomes,
       holder: arg.holder,
@@ -264,7 +264,7 @@ async function parse(arg) {
     return;
   }
   if (urlp.has("gdcmaf")) {
-    const _ = await import("./maf-ZVD4LDZY.js");
+    const _ = await import("./maf-Q5AOJVVF.js");
     _.gdcMAFui({
       holder: arg.holder,
       debugmode: arg.debugmode
@@ -272,7 +272,7 @@ async function parse(arg) {
     return;
   }
   if (urlp.has("gdcsinglecell")) {
-    const _ = await import("./singlecell-ZHT643LZ.js");
+    const _ = await import("./singlecell-JFHP5BY2.js");
     _.gdcSinglecellUi({
       holder: arg.holder,
       debugmode: arg.debugmode
@@ -286,7 +286,7 @@ async function parse(arg) {
       holder: arg.holder,
       state
     };
-    const _ = await import("./app-CNP55RHA.js");
+    const _ = await import("./app-XTZNDE3W.js");
     _.appInit(opts);
     return;
   }
@@ -306,7 +306,7 @@ async function parse(arg) {
     };
     if (!opts.genome)
       throw "invalid genome";
-    const _ = await import("./app-W2ILAHAI.js");
+    const _ = await import("./app-JMNTRCR7.js");
     _.appInit(opts);
     return;
   }
@@ -323,7 +323,7 @@ async function parse(arg) {
     } else if (state?.vocab?.genome) {
       opts.genome = arg.genomes[state.vocab.genome];
     }
-    const _ = await import("./app-W2ILAHAI.js");
+    const _ = await import("./app-JMNTRCR7.js");
     _.appInit(opts);
     return;
   }
@@ -357,7 +357,7 @@ async function parse(arg) {
         genome: arg.genomes[state.vocab.genome]
       };
     }
-    const _ = await import("./app-W2ILAHAI.js");
+    const _ = await import("./app-JMNTRCR7.js");
     _.appInit(opts);
     return;
   }
@@ -399,7 +399,7 @@ async function parse(arg) {
       sessionDaysLeft: res.sessionDaysLeft,
       sessionId: id
     };
-    const _ = await import("./app-W2ILAHAI.js");
+    const _ = await import("./app-JMNTRCR7.js");
     _.appInit(opts);
     return;
   }
@@ -442,7 +442,7 @@ async function parse(arg) {
       enzyme: urlp.get("enzyme"),
       holder: arg.holder
     };
-    const _ = await import("./HicApp-KLMBWHYQ.js");
+    const _ = await import("./HicApp-4OAJJINK.js");
     await _.hicInit(hic);
     return;
   }
@@ -470,7 +470,7 @@ async function parse(arg) {
     const genome = arg.genomes[genomename];
     if (!genome)
       throw "invalid genome: " + genomename;
-    const _ = await import("./mavb-LE4CHOEJ.js");
+    const _ = await import("./mavb-SQ2HK4KA.js");
     _.mavbparseinput(
       {
         genome,
@@ -491,7 +491,7 @@ async function parse(arg) {
     const genome = arg.genomes[genomename];
     if (!genome)
       throw "invalid genome: " + genomename;
-    const _ = await import("./mavb-LE4CHOEJ.js");
+    const _ = await import("./mavb-SQ2HK4KA.js");
     _.mavbparseinput(
       {
         genome,
@@ -532,7 +532,7 @@ async function parse(arg) {
       }
     }
     plot_data.mdssamplescatterplot.genome = genome;
-    const _ = await import("./mds.samplescatterplot-NBMVL75U.js");
+    const _ = await import("./mds.samplescatterplot-WRJNIY2X.js");
     _.init(plot_data.mdssamplescatterplot, arg.holder, false);
     return;
   }
@@ -634,7 +634,7 @@ async function parse(arg) {
     par.tklst = await get_tklst(urlp, genomeobj);
     first_genetrack_tolist(arg.genomes[genomename], par.tklst);
     mayAddBedjfilterbyname(urlp, par.tklst);
-    const b = await import("./block-UXADMA2N.js");
+    const b = await import("./block-YWY77ICL.js");
     new b.Block(par);
     return;
   }
@@ -704,9 +704,9 @@ async function parse(arg) {
     const sample_id = urlp.get("sample");
     if (!sample_id)
       throw "sample_id missing";
-    const vocabApi = (await import("./vocabulary-B256ZDBS.js")).vocabInit({ state: { genome: genomeName, dslabel } });
+    const vocabApi = (await import("./vocabulary-IN52DNA5.js")).vocabInit({ state: { genome: genomeName, dslabel } });
     const termdbConfig = await vocabApi.getTermdbConfig();
-    await (await import("./plot.disco-MVUJXMQ2.js")).default(termdbConfig, dslabel, { sample_id }, arg.holder, genome);
+    await (await import("./plot.disco-ZEDYZUT4.js")).default(termdbConfig, dslabel, { sample_id }, arg.holder, genome);
     return;
   }
   if (urlp.has("study")) {
@@ -1156,4 +1156,4 @@ export {
   parse,
   get_tklst
 };
-//# sourceMappingURL=chunk-DQUCI4A5.js.map
+//# sourceMappingURL=chunk-6SDDZ3OH.js.map

package/dist/{chunk-UQTS4237.js → chunk-6ZPY2IJH.js}

@@ -5,7 +5,7 @@ import {
   isUsableTerm,
   showTvsMenu,
   vocabInit
-} from "./chunk-WIDWN7RE.js";
+} from "./chunk-NB3LAVWW.js";
 import {
   Tabs
 } from "./chunk-7KFEDC2T.js";
@@ -550,7 +550,7 @@ var storeInit = getInitFxn(TdbStore);
 
 // import("./handlers/**/*.ts") in termdb/TermTypeSearch.ts
 var globImport_handlers_ts = __glob({
-  "./handlers/geneExpression.ts": () => import("./geneExpression-T5SD35B5.js"),
+  "./handlers/geneExpression.ts": () => import("./geneExpression-SXIB22D2.js"),
   "./handlers/geneVariant.ts": () => import("./geneVariant-R5PQQR4R.js"),
   "./handlers/snp.ts": () => import("./snp-YPBPSLIE.js"),
   "./handlers/snplocus.ts": () => import("./snplocus-DSM7T52C.js"),
@@ -1298,4 +1298,4 @@ var appInit = getAppInit(TdbApp);
 export {
   appInit
 };
-//# sourceMappingURL=chunk-UQTS4237.js.map
+//# sourceMappingURL=chunk-6ZPY2IJH.js.map

package/dist/{chunk-5XHFFUAI.js → chunk-BLLHQUKP.js}

@@ -1,6 +1,6 @@
 import {
   renderTable
-} from "./chunk-SWICAWWD.js";
+} from "./chunk-TU4H4R2T.js";
 import {
   __export
 } from "./chunk-F3OQE4AZ.js";
@@ -256,10 +256,20 @@ function showTable4selectedRows(clickedRowNames, rowType) {
     (c) => this.hierClusterData.byTermId[c]?.gencodeId ? [{ value: c, url: `${templates.gene.base}${this.hierClusterData.byTermId[c].gencodeId}` }] : [{ value: c }]
   ) : clickedRowNames.map((c) => [{ value: c }]);
   const columns = [{ label: rowType }];
+  const div = this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px");
+  const buttonDiv = div.append("div").style("padding", "5px");
+  const copyButton = buttonDiv.append("button").text(`Copy ${rowType}`).attr("class", ".sja_menu_div button").style("margin-top", "2px").style("padding", "5px").on("click", () => {
+    const geneNames = rows.map((row) => row[0].value).join("\n");
+    navigator.clipboard.writeText(geneNames).then(() => {
+      alert(`${rowType} copied to clipboard`);
+    }).catch((err) => {
+      console.error("Failed to copy: ", err);
+    });
+  });
   renderTable({
     rows,
     columns,
-    div: this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px"),
+    div: div.append("div"),
     showLines: true,
     maxHeight: "35vh",
     resize: true
@@ -422,4 +432,4 @@ export {
   setClusteringBtn,
   hierCluster_interactivity_exports
 };
-//# sourceMappingURL=chunk-5XHFFUAI.js.map
+//# sourceMappingURL=chunk-BLLHQUKP.js.map

package/dist/{chunk-5XHFFUAI.js.map → chunk-BLLHQUKP.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../plots/matrix/hierCluster.interactivity.js", "../../shared/utils/src/clustering.js"],
-  "sourcesContent": ["import { renderTable } from '#dom'\nimport { clusterMethodLst, distanceMethodLst } from '#shared/clustering.js'\n\n// Given a clusterId, return all its children clusterIds\nexport function getAllChildrenClusterIds(clickedClusterId, left) {\n\tconst mergedClusters = left\n\t\t? this.hierClusterData.clustering.row.mergedClusters\n\t\t: this.hierClusterData.clustering.col.mergedClusters\n\tconst children = mergedClusters.get(clickedClusterId).childrenClusters || []\n\tlet allChildren = [...children]\n\tfor (const child of children) {\n\t\tallChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left))\n\t}\n\treturn allChildren\n}\n\nexport function addSelectedSamplesOptions(clickedSampleNames, event) {\n\tconst l = this.settings.matrix.controlLabels\n\tconst ss = this.opts.allow2selectSamples\n\tconst optionArr = [\n\t\t{\n\t\t\tlabel: 'Zoom in',\n\t\t\tcallback: () => {\n\t\t\t\tthis.triggerZoomBranch(this, clickedSampleNames)\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: `List ${clickedSampleNames.length} ${l.samples}`,\n\t\t\tcallback: () => this.showTable4selectedSamples(clickedSampleNames)\n\t\t}\n\t]\n\n\t// when allow2selectSamples presents\n\tif (ss) {\n\t\toptionArr.push({\n\t\t\tlabel: ss.buttonText || `Select ${l.samples}`,\n\t\t\tcallback: async () => {\n\t\t\t\tss.callback({\n\t\t\t\t\tsamples: clickedSampleNames.map(c => {\n\t\t\t\t\t\treturn { 'cases.case_id': c }\n\t\t\t\t\t}),\n\t\t\t\t\tsource: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t} else {\n\t\tif (this.state.nav && this.state.nav.header_mode !== 'hidden') {\n\t\t\tconst samples = clickedSampleNames.map(c => this.sampleOrder.find(s => s.row.sample == c).row)\n\t\t\tfor (const s of samples) {\n\t\t\t\tif (!s.sampleId) s.sampleId = s.sample\n\t\t\t}\n\t\t\toptionArr.push({\n\t\t\t\tlabel: 'Add to a group',\n\t\t\t\tcallback: async () => {\n\t\t\t\t\tconst group = {\n\t\t\t\t\t\tname: 'Group',\n\t\t\t\t\t\titems: samples\n\t\t\t\t\t}\n\t\t\t\t\tthis.addGroup(group)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tthis.mouseout()\n\tthis.dom.tip.hide()\n\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\tthis.dom.dendroClickMenu.d\n\t\t.selectAll('div')\n\t\t.data(optionArr)\n\t\t.enter()\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('border-radius', '0px')\n\t\t.html(d => d.label)\n\t\t.attr('data-testid', d => `hierCluster_dendro_menu_${d.label.split(' ')[0]}`)\n\t\t.on('click', event => {\n\t\t\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\t\t\tevent.target.__data__.callback()\n\t\t})\n\tthis.dom.dendroClickMenu.show(event.clientX, event.clientY)\n}\n\nexport function addSelectedRowsOptions(clickedRowNames, event) {\n\t// TODO to support other hierCluster types\n\tconst rowType =\n\t\tthis.config.dataType == 'geneExpression'\n\t\t\t? 'genes'\n\t\t\t: this.config.dataType == 'metaboliteIntensity'\n\t\t\t? 'metabolites'\n\t\t\t: 'items'\n\n\tconst optionArr = [\n\t\t{\n\t\t\tlabel: `List ${clickedRowNames.length} ${rowType}`,\n\t\t\tcallback: () => this.showTable4selectedRows(clickedRowNames, rowType)\n\t\t}\n\t]\n\n\tif (this.app.opts.genome.termdbs) {\n\t\t// Check if genome build contains termdbs, only then enable gene ora\n\t\toptionArr.push({\n\t\t\tlabel: `Gene set overrepresentation analysis`,\n\t\t\tdisabled: clickedRowNames.length < 15 || clickedRowNames.length > 500,\n\t\t\tcallback: () => {\n\t\t\t\tif (clickedRowNames.length < 15 || clickedRowNames.length > 500) return\n\t\t\t\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\t\t\t\tconst sample_genes = clickedRowNames\n\t\t\t\tconst geneORAparams = {\n\t\t\t\t\tsample_genes: sample_genes.toString(),\n\t\t\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome\n\t\t\t\t}\n\t\t\t\tconst config = {\n\t\t\t\t\tchartType: 'geneORA',\n\t\t\t\t\tgeneORAparams: geneORAparams\n\t\t\t\t}\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\tthis.mouseout()\n\tthis.dom.tip.hide()\n\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\tthis.dom.dendroClickMenu.d\n\t\t.selectAll('div')\n\t\t.data(optionArr)\n\t\t.enter()\n\t\t.append('div')\n\t\t.attr('class', d => (d.disabled ? 'sja_menuoption_not_interactive' : 'sja_menuoption'))\n\t\t.style('opacity', d => (d.disabled ? 0.5 : 1))\n\t\t.style('border-radius', '0px')\n\t\t.html(d =>\n\t\t\td.disabled\n\t\t\t\t? `${d.label} <span style=\"font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;\">Only available when 15 - 500 genes selected</span>`\n\t\t\t\t: d.label\n\t\t)\n\t\t.attr('data-testid', d => `hierCluster_dendro_menu_${d.label.split(' ')[0]}`)\n\t\t.on('click', event => {\n\t\t\tif (event.target.__data__?.callback) event.target.__data__.callback()\n\t\t})\n\tthis.dom.dendroClickMenu.show(event.clientX, event.clientY)\n}\n\n// zoom in matrix to the selected dendrogram branch\nexport function triggerZoomBranch(self, clickedSampleNames) {\n\tif (self.zoomArea) {\n\t\tself.zoomArea.remove()\n\t\tdelete self.zoomArea\n\t}\n\tconst c = {\n\t\tstartCell: self.serieses[0].cells.find(d => d.sample == clickedSampleNames[0]),\n\t\tendCell: self.serieses[0].cells.find(d => d.sample == clickedSampleNames[clickedSampleNames.length - 1])\n\t}\n\n\tconst s = self.settings.matrix\n\tconst d = self.dimensions\n\tconst start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell\n\tconst zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2)\n\tconst centerCell = self.sampleOrder[zoomIndex] // || self.getImgCell(event)\n\tconst colw = self.computedSettings.colw || self.settings.matrix.colw\n\tconst maxZoomLevel = s.colwMax / colw\n\tconst minZoomLevel = s.colwMin / colw\n\tconst tentativeZoomLevel = Math.max(\n\t\t1,\n\t\t((s.zoomLevel * d.mainw) / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw)) * 0.7\n\t)\n\tconst zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel))\n\t//const zoomCenter = centerCell.totalIndex * d.dx + (centerCell.grpIndex - 1) * s.colgspace + d.seriesXoffset\n\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: {\n\t\t\tsettings: {\n\t\t\t\tmatrix: {\n\t\t\t\t\tzoomLevel,\n\t\t\t\t\tzoomCenterPct: 0.5,\n\t\t\t\t\t//zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,\n\t\t\t\t\tzoomIndex,\n\t\t\t\t\tzoomGrpIndex: centerCell.grpIndex\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t})\n\tself.resetInteractions()\n}\n\n// show the list of clicked samples as a table\nexport function showTable4selectedSamples(clickedSampleNames) {\n\tconst templates = this.state.termdbConfig.urlTemplates\n\tconst rows = templates?.sample\n\t\t? clickedSampleNames.map(c => [\n\t\t\t\t{ value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }\n\t\t  ])\n\t\t: clickedSampleNames.map(c => [{ value: this.hierClusterData.bySampleId[c].label }])\n\n\tconst columns = [{ label: this.settings.matrix.controlLabels.Sample }]\n\n\trenderTable({\n\t\trows,\n\t\tcolumns,\n\t\tdiv: this.dom.dendroClickMenu.clear().d.append('div').style('margin', '10px'),\n\t\tshowLines: true,\n\t\tmaxHeight: '35vh',\n\t\tresize: true\n\t})\n}\n\n// show the list of clicked samples as a table\nexport function showTable4selectedRows(clickedRowNames, rowType) {\n\tconst templates = this.state.termdbConfig.urlTemplates\n\n\tconst rows =\n\t\ttemplates?.gene && this.config.dataType == 'geneExpression' && this.hierClusterData.byTermId\n\t\t\t? clickedRowNames.map(c =>\n\t\t\t\t\tthis.hierClusterData.byTermId[c]?.gencodeId\n\t\t\t\t\t\t? [{ value: c, url: `${templates.gene.base}${this.hierClusterData.byTermId[c].gencodeId}` }]\n\t\t\t\t\t\t: [{ value: c }]\n\t\t\t  )\n\t\t\t: clickedRowNames.map(c => [{ value: c }])\n\n\tconst columns = [{ label: rowType }]\n\n\trenderTable({\n\t\trows,\n\t\tcolumns,\n\t\tdiv: this.dom.dendroClickMenu.clear().d.append('div').style('margin', '10px'),\n\t\tshowLines: true,\n\t\tmaxHeight: '35vh',\n\t\tresize: true\n\t})\n}\n\n// add the clicked samples into a group\nexport async function addGroup(group) {\n\tgroup.plotId = this.id\n\tawait this.app.vocabApi.addGroup(group)\n\tthis.dom.tip.hide()\n}\n\n// upon clicking, find the corresponding clicked clusterId from this.hierClusterData.clustering.col.mergedClusters\nexport function getClusterFromTopDendrogram(event) {\n\t// Need imgBox to find the position of event relative to dendrogram\n\tif (event.target.tagName == 'image') this.imgBox = event.target.getBoundingClientRect()\n\telse return\n\n\tconst y = event.clientY - this.imgBox.y - event.target.clientTop\n\tconst xMin = this.dimensions.xMin\n\tconst x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin\n\n\tfor (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {\n\t\tconst { x1, y1, x2, y2, clusterY } = cluster.clusterPosition\n\t\tif (\n\t\t\t(x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5) ||\n\t\t\t(clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5) ||\n\t\t\t(clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5)\n\t\t) {\n\t\t\treturn clusterId\n\t\t}\n\t}\n}\n\n// upon clicking, find the corresponding clicked clusterId from this.hierClusterData.clustering.row.mergedClusters\nexport function getClusterFromLeftDendrogram(event) {\n\t// Need imgBox to find the position of event relative to dendrogram\n\tif (event.target.tagName == 'image') this.imgBox = event.target.getBoundingClientRect()\n\telse return\n\n\tconst y = event.clientY - this.imgBox.y - event.target.clientTop\n\tconst xMin = this.dimensions.xMin\n\tconst x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin\n\n\tfor (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {\n\t\tconst { x1, y1, x2, y2, clusterX } = cluster.clusterPosition\n\t\tif (\n\t\t\t(y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5) ||\n\t\t\t(clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5) ||\n\t\t\t(clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5)\n\t\t) {\n\t\t\treturn clusterId\n\t\t}\n\t}\n}\n\nexport function setClusteringBtn(holder, callback) {\n\tconst cl = this.config.settings.matrix.controlLabels\n\tconst ClusterLabel = `Cluster ${cl.Samples}`\n\tholder\n\t\t.append('button')\n\t\t//.property('disabled', d => d.disabled)\n\t\t.datum({\n\t\t\tlabel: `Clustering`,\n\t\t\trows: [\n\t\t\t\t{\n\t\t\t\t\tlabel: ClusterLabel,\n\t\t\t\t\ttitle: `Option to enable ${cl.samples} clustering, instead of enable ${cl.samples} sorting.`,\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'clusterSamples',\n\t\t\t\t\tboxLabel: `Cluster ${cl.samples} (Disable ${cl.samples} sorting)`,\n\t\t\t\t\tcallback: checked => {\n\t\t\t\t\t\tif (!checked) {\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.yDendrogramHeight = 0\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.clusterSamples = false\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.config.divideBy = null\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.yDendrogramHeight = 200\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.clusterSamples = true\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\tconfig: this.config\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Clustering Method`,\n\t\t\t\t\ttitle: `Sets which clustering method to use`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'clusterMethod',\n\t\t\t\t\toptions: clusterMethodLst\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Distance Method`,\n\t\t\t\t\ttitle: `Sets which distance method to use for clustering`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'distanceMethod',\n\t\t\t\t\toptions: distanceMethodLst\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Column Dendrogram Height`,\n\t\t\t\t\ttitle: `The maximum height to render the column dendrogram`,\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'yDendrogramHeight',\n\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\treturn plot.settings.hierCluster.clusterSamples ? 'table-row' : 'none'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Row Dendrogram Width`,\n\t\t\t\t\ttitle: `The maximum width to render the row dendrogram`,\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'xDendrogramHeight'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `z-score Cap`,\n\t\t\t\t\ttitle: `Cap the z-score scale to not exceed this absolute value`,\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'zScoreCap'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Color Scheme`,\n\t\t\t\t\ttitle: `Sets which color scheme to use`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'colorScale',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Blue-White-Red',\n\t\t\t\t\t\t\tvalue: 'blueWhiteRed',\n\t\t\t\t\t\t\ttitle: `color scheme Blue-White-Red`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Green-Black-Red',\n\t\t\t\t\t\t\tvalue: 'greenBlackRed',\n\t\t\t\t\t\t\ttitle: `color scheme Green-Black-Red`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Blue-Yellow-Red',\n\t\t\t\t\t\t\tvalue: 'blueYellowRed',\n\t\t\t\t\t\t\ttitle: `color scheme Blue-Yellow-Red`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Green-White-Red',\n\t\t\t\t\t\t\tvalue: 'greenWhiteRed',\n\t\t\t\t\t\t\ttitle: `color scheme Green-White-Red`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Blue-Black-Yellow',\n\t\t\t\t\t\t\tvalue: 'blueBlackYellow',\n\t\t\t\t\t\t\ttitle: `color scheme Blue-Black-Yellow`\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t\t.html(d => d.label)\n\t\t.style('margin', '2px 0')\n\t\t.on('click', callback)\n}\n", "export const clusterMethodLst = [\n\t{\n\t\tlabel: 'Average',\n\t\tvalue: 'average',\n\t\ttitle: `Cluster by average value`\n\t},\n\t{\n\t\tlabel: `Complete`,\n\t\tvalue: 'complete',\n\t\ttitle: `Use the complete clustering method`\n\t},\n\t{\n\t\tlabel: `Single`,\n\t\tvalue: 'single',\n\t\ttitle: `Use the single clustering method`\n\t},\n\t{\n\t\tlabel: `Ward.D`,\n\t\tvalue: 'ward.D',\n\t\ttitle: `Use the ward.D clustering method`\n\t},\n\t{\n\t\tlabel: `Ward.D2`,\n\t\tvalue: 'ward.D2',\n\t\ttitle: `Use the ward.D2 clustering method`\n\t},\n\t{\n\t\tlabel: `Mcquitty`,\n\t\tvalue: 'mcquitty',\n\t\ttitle: `Use the Mcquity clustering method`\n\t}\n\t/* These methods are currently disabled because the dendrogram lines tend to cross one another.\n\t{\n\t\tlabel: `Centroid`,\n\t\tvalue: 'centroid',\n\t\ttitle: `Use the centroid clustering method`\n\t},\n    \t{\n\t\tlabel: `Median`,\n\t\tvalue: 'median',\n\t\ttitle: `Use the median clustering method`\n\t}\n        */\n]\nexport const distanceMethodLst = [\n\t{\n\t\tlabel: 'Euclidean',\n\t\tvalue: 'euclidean',\n\t\ttitle: `Calculate distance using euclidean method`\n\t},\n\t{\n\t\tlabel: 'Maximum',\n\t\tvalue: 'maximum',\n\t\ttitle: `Maximum distance between two components of x and y`\n\t},\n\t{\n\t\tlabel: 'Manhattan',\n\t\tvalue: 'manhattan',\n\t\ttitle: `Calculate distance using the absolute distance between the two vectors`\n\t},\n\t{\n\t\tlabel: 'Canberra',\n\t\tvalue: 'canberra',\n\t\ttitle: `Calculate distance using Canberra method`\n\t}\n]\n"],
-  "mappings": 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+  "sourcesContent": ["import { renderTable } from '#dom'\nimport { clusterMethodLst, distanceMethodLst } from '#shared/clustering.js'\n\n// Given a clusterId, return all its children clusterIds\nexport function getAllChildrenClusterIds(clickedClusterId, left) {\n\tconst mergedClusters = left\n\t\t? this.hierClusterData.clustering.row.mergedClusters\n\t\t: this.hierClusterData.clustering.col.mergedClusters\n\tconst children = mergedClusters.get(clickedClusterId).childrenClusters || []\n\tlet allChildren = [...children]\n\tfor (const child of children) {\n\t\tallChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left))\n\t}\n\treturn allChildren\n}\n\nexport function addSelectedSamplesOptions(clickedSampleNames, event) {\n\tconst l = this.settings.matrix.controlLabels\n\tconst ss = this.opts.allow2selectSamples\n\tconst optionArr = [\n\t\t{\n\t\t\tlabel: 'Zoom in',\n\t\t\tcallback: () => {\n\t\t\t\tthis.triggerZoomBranch(this, clickedSampleNames)\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: `List ${clickedSampleNames.length} ${l.samples}`,\n\t\t\tcallback: () => this.showTable4selectedSamples(clickedSampleNames)\n\t\t}\n\t]\n\n\t// when allow2selectSamples presents\n\tif (ss) {\n\t\toptionArr.push({\n\t\t\tlabel: ss.buttonText || `Select ${l.samples}`,\n\t\t\tcallback: async () => {\n\t\t\t\tss.callback({\n\t\t\t\t\tsamples: clickedSampleNames.map(c => {\n\t\t\t\t\t\treturn { 'cases.case_id': c }\n\t\t\t\t\t}),\n\t\t\t\t\tsource: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t} else {\n\t\tif (this.state.nav && this.state.nav.header_mode !== 'hidden') {\n\t\t\tconst samples = clickedSampleNames.map(c => this.sampleOrder.find(s => s.row.sample == c).row)\n\t\t\tfor (const s of samples) {\n\t\t\t\tif (!s.sampleId) s.sampleId = s.sample\n\t\t\t}\n\t\t\toptionArr.push({\n\t\t\t\tlabel: 'Add to a group',\n\t\t\t\tcallback: async () => {\n\t\t\t\t\tconst group = {\n\t\t\t\t\t\tname: 'Group',\n\t\t\t\t\t\titems: samples\n\t\t\t\t\t}\n\t\t\t\t\tthis.addGroup(group)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tthis.mouseout()\n\tthis.dom.tip.hide()\n\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\tthis.dom.dendroClickMenu.d\n\t\t.selectAll('div')\n\t\t.data(optionArr)\n\t\t.enter()\n\t\t.append('div')\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('border-radius', '0px')\n\t\t.html(d => d.label)\n\t\t.attr('data-testid', d => `hierCluster_dendro_menu_${d.label.split(' ')[0]}`)\n\t\t.on('click', event => {\n\t\t\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\t\t\tevent.target.__data__.callback()\n\t\t})\n\tthis.dom.dendroClickMenu.show(event.clientX, event.clientY)\n}\n\nexport function addSelectedRowsOptions(clickedRowNames, event) {\n\t// TODO to support other hierCluster types\n\tconst rowType =\n\t\tthis.config.dataType == 'geneExpression'\n\t\t\t? 'genes'\n\t\t\t: this.config.dataType == 'metaboliteIntensity'\n\t\t\t? 'metabolites'\n\t\t\t: 'items'\n\n\tconst optionArr = [\n\t\t{\n\t\t\tlabel: `List ${clickedRowNames.length} ${rowType}`,\n\t\t\tcallback: () => this.showTable4selectedRows(clickedRowNames, rowType)\n\t\t}\n\t]\n\n\tif (this.app.opts.genome.termdbs) {\n\t\t// Check if genome build contains termdbs, only then enable gene ora\n\t\toptionArr.push({\n\t\t\tlabel: `Gene set overrepresentation analysis`,\n\t\t\tdisabled: clickedRowNames.length < 15 || clickedRowNames.length > 500,\n\t\t\tcallback: () => {\n\t\t\t\tif (clickedRowNames.length < 15 || clickedRowNames.length > 500) return\n\t\t\t\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\t\t\t\tconst sample_genes = clickedRowNames\n\t\t\t\tconst geneORAparams = {\n\t\t\t\t\tsample_genes: sample_genes.toString(),\n\t\t\t\t\tgenome: this.app.vocabApi.opts.state.vocab.genome\n\t\t\t\t}\n\t\t\t\tconst config = {\n\t\t\t\t\tchartType: 'geneORA',\n\t\t\t\t\tgeneORAparams: geneORAparams\n\t\t\t\t}\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\tthis.mouseout()\n\tthis.dom.tip.hide()\n\tthis.dom.dendroClickMenu.d.selectAll('*').remove()\n\tthis.dom.dendroClickMenu.d\n\t\t.selectAll('div')\n\t\t.data(optionArr)\n\t\t.enter()\n\t\t.append('div')\n\t\t.attr('class', d => (d.disabled ? 'sja_menuoption_not_interactive' : 'sja_menuoption'))\n\t\t.style('opacity', d => (d.disabled ? 0.5 : 1))\n\t\t.style('border-radius', '0px')\n\t\t.html(d =>\n\t\t\td.disabled\n\t\t\t\t? `${d.label} <span style=\"font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;\">Only available when 15 - 500 genes selected</span>`\n\t\t\t\t: d.label\n\t\t)\n\t\t.attr('data-testid', d => `hierCluster_dendro_menu_${d.label.split(' ')[0]}`)\n\t\t.on('click', event => {\n\t\t\tif (event.target.__data__?.callback) event.target.__data__.callback()\n\t\t})\n\tthis.dom.dendroClickMenu.show(event.clientX, event.clientY)\n}\n\n// zoom in matrix to the selected dendrogram branch\nexport function triggerZoomBranch(self, clickedSampleNames) {\n\tif (self.zoomArea) {\n\t\tself.zoomArea.remove()\n\t\tdelete self.zoomArea\n\t}\n\tconst c = {\n\t\tstartCell: self.serieses[0].cells.find(d => d.sample == clickedSampleNames[0]),\n\t\tendCell: self.serieses[0].cells.find(d => d.sample == clickedSampleNames[clickedSampleNames.length - 1])\n\t}\n\n\tconst s = self.settings.matrix\n\tconst d = self.dimensions\n\tconst start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell\n\tconst zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2)\n\tconst centerCell = self.sampleOrder[zoomIndex] // || self.getImgCell(event)\n\tconst colw = self.computedSettings.colw || self.settings.matrix.colw\n\tconst maxZoomLevel = s.colwMax / colw\n\tconst minZoomLevel = s.colwMin / colw\n\tconst tentativeZoomLevel = Math.max(\n\t\t1,\n\t\t((s.zoomLevel * d.mainw) / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw)) * 0.7\n\t)\n\tconst zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel))\n\t//const zoomCenter = centerCell.totalIndex * d.dx + (centerCell.grpIndex - 1) * s.colgspace + d.seriesXoffset\n\n\tself.app.dispatch({\n\t\ttype: 'plot_edit',\n\t\tid: self.id,\n\t\tconfig: {\n\t\t\tsettings: {\n\t\t\t\tmatrix: {\n\t\t\t\t\tzoomLevel,\n\t\t\t\t\tzoomCenterPct: 0.5,\n\t\t\t\t\t//zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,\n\t\t\t\t\tzoomIndex,\n\t\t\t\t\tzoomGrpIndex: centerCell.grpIndex\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t})\n\tself.resetInteractions()\n}\n\n// show the list of clicked samples as a table\nexport function showTable4selectedSamples(clickedSampleNames) {\n\tconst templates = this.state.termdbConfig.urlTemplates\n\tconst rows = templates?.sample\n\t\t? clickedSampleNames.map(c => [\n\t\t\t\t{ value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }\n\t\t  ])\n\t\t: clickedSampleNames.map(c => [{ value: this.hierClusterData.bySampleId[c].label }])\n\n\tconst columns = [{ label: this.settings.matrix.controlLabels.Sample }]\n\n\trenderTable({\n\t\trows,\n\t\tcolumns,\n\t\tdiv: this.dom.dendroClickMenu.clear().d.append('div').style('margin', '10px'),\n\t\tshowLines: true,\n\t\tmaxHeight: '35vh',\n\t\tresize: true\n\t})\n}\n\n// show the list of clicked samples as a table\nexport function showTable4selectedRows(clickedRowNames, rowType) {\n\tconst templates = this.state.termdbConfig.urlTemplates\n\n\tconst rows =\n\t\ttemplates?.gene && this.config.dataType == 'geneExpression' && this.hierClusterData.byTermId\n\t\t\t? clickedRowNames.map(c =>\n\t\t\t\t\tthis.hierClusterData.byTermId[c]?.gencodeId\n\t\t\t\t\t\t? [{ value: c, url: `${templates.gene.base}${this.hierClusterData.byTermId[c].gencodeId}` }]\n\t\t\t\t\t\t: [{ value: c }]\n\t\t\t  )\n\t\t\t: clickedRowNames.map(c => [{ value: c }])\n\n\tconst columns = [{ label: rowType }]\n\n\tconst div = this.dom.dendroClickMenu.clear().d.append('div').style('margin', '10px')\n\n\t// Create a button to copy names in the table\n\tconst buttonDiv = div.append('div').style('padding', '5px')\n\tconst copyButton = buttonDiv\n\t\t.append('button')\n\t\t.text(`Copy ${rowType}`)\n\t\t.attr('class', '.sja_menu_div button')\n\t\t.style('margin-top', '2px')\n\t\t.style('padding', '5px')\n\t\t.on('click', () => {\n\t\t\tconst geneNames = rows.map(row => row[0].value).join('\\n')\n\t\t\tnavigator.clipboard\n\t\t\t\t.writeText(geneNames)\n\t\t\t\t.then(() => {\n\t\t\t\t\talert(`${rowType} copied to clipboard`)\n\t\t\t\t})\n\t\t\t\t.catch(err => {\n\t\t\t\t\tconsole.error('Failed to copy: ', err)\n\t\t\t\t})\n\t\t})\n\trenderTable({\n\t\trows,\n\t\tcolumns,\n\t\tdiv: div.append('div'),\n\t\tshowLines: true,\n\t\tmaxHeight: '35vh',\n\t\tresize: true\n\t})\n}\n\n// add the clicked samples into a group\nexport async function addGroup(group) {\n\tgroup.plotId = this.id\n\tawait this.app.vocabApi.addGroup(group)\n\tthis.dom.tip.hide()\n}\n\n// upon clicking, find the corresponding clicked clusterId from this.hierClusterData.clustering.col.mergedClusters\nexport function getClusterFromTopDendrogram(event) {\n\t// Need imgBox to find the position of event relative to dendrogram\n\tif (event.target.tagName == 'image') this.imgBox = event.target.getBoundingClientRect()\n\telse return\n\n\tconst y = event.clientY - this.imgBox.y - event.target.clientTop\n\tconst xMin = this.dimensions.xMin\n\tconst x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin\n\n\tfor (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {\n\t\tconst { x1, y1, x2, y2, clusterY } = cluster.clusterPosition\n\t\tif (\n\t\t\t(x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5) ||\n\t\t\t(clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5) ||\n\t\t\t(clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5)\n\t\t) {\n\t\t\treturn clusterId\n\t\t}\n\t}\n}\n\n// upon clicking, find the corresponding clicked clusterId from this.hierClusterData.clustering.row.mergedClusters\nexport function getClusterFromLeftDendrogram(event) {\n\t// Need imgBox to find the position of event relative to dendrogram\n\tif (event.target.tagName == 'image') this.imgBox = event.target.getBoundingClientRect()\n\telse return\n\n\tconst y = event.clientY - this.imgBox.y - event.target.clientTop\n\tconst xMin = this.dimensions.xMin\n\tconst x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin\n\n\tfor (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {\n\t\tconst { x1, y1, x2, y2, clusterX } = cluster.clusterPosition\n\t\tif (\n\t\t\t(y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5) ||\n\t\t\t(clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5) ||\n\t\t\t(clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5)\n\t\t) {\n\t\t\treturn clusterId\n\t\t}\n\t}\n}\n\nexport function setClusteringBtn(holder, callback) {\n\tconst cl = this.config.settings.matrix.controlLabels\n\tconst ClusterLabel = `Cluster ${cl.Samples}`\n\tholder\n\t\t.append('button')\n\t\t//.property('disabled', d => d.disabled)\n\t\t.datum({\n\t\t\tlabel: `Clustering`,\n\t\t\trows: [\n\t\t\t\t{\n\t\t\t\t\tlabel: ClusterLabel,\n\t\t\t\t\ttitle: `Option to enable ${cl.samples} clustering, instead of enable ${cl.samples} sorting.`,\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'clusterSamples',\n\t\t\t\t\tboxLabel: `Cluster ${cl.samples} (Disable ${cl.samples} sorting)`,\n\t\t\t\t\tcallback: checked => {\n\t\t\t\t\t\tif (!checked) {\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.yDendrogramHeight = 0\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.clusterSamples = false\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.config.divideBy = null\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.yDendrogramHeight = 200\n\t\t\t\t\t\t\tthis.config.settings.hierCluster.clusterSamples = true\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: this.id,\n\t\t\t\t\t\t\tconfig: this.config\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Clustering Method`,\n\t\t\t\t\ttitle: `Sets which clustering method to use`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'clusterMethod',\n\t\t\t\t\toptions: clusterMethodLst\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Distance Method`,\n\t\t\t\t\ttitle: `Sets which distance method to use for clustering`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'distanceMethod',\n\t\t\t\t\toptions: distanceMethodLst\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Column Dendrogram Height`,\n\t\t\t\t\ttitle: `The maximum height to render the column dendrogram`,\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'yDendrogramHeight',\n\t\t\t\t\tgetDisplayStyle(plot) {\n\t\t\t\t\t\treturn plot.settings.hierCluster.clusterSamples ? 'table-row' : 'none'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Row Dendrogram Width`,\n\t\t\t\t\ttitle: `The maximum width to render the row dendrogram`,\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'xDendrogramHeight'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `z-score Cap`,\n\t\t\t\t\ttitle: `Cap the z-score scale to not exceed this absolute value`,\n\t\t\t\t\ttype: 'number',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'zScoreCap'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tlabel: `Color Scheme`,\n\t\t\t\t\ttitle: `Sets which color scheme to use`,\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tsettingsKey: 'colorScale',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Blue-White-Red',\n\t\t\t\t\t\t\tvalue: 'blueWhiteRed',\n\t\t\t\t\t\t\ttitle: `color scheme Blue-White-Red`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Green-Black-Red',\n\t\t\t\t\t\t\tvalue: 'greenBlackRed',\n\t\t\t\t\t\t\ttitle: `color scheme Green-Black-Red`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Blue-Yellow-Red',\n\t\t\t\t\t\t\tvalue: 'blueYellowRed',\n\t\t\t\t\t\t\ttitle: `color scheme Blue-Yellow-Red`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Green-White-Red',\n\t\t\t\t\t\t\tvalue: 'greenWhiteRed',\n\t\t\t\t\t\t\ttitle: `color scheme Green-White-Red`\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Blue-Black-Yellow',\n\t\t\t\t\t\t\tvalue: 'blueBlackYellow',\n\t\t\t\t\t\t\ttitle: `color scheme Blue-Black-Yellow`\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t]\n\t\t})\n\t\t.html(d => d.label)\n\t\t.style('margin', '2px 0')\n\t\t.on('click', callback)\n}\n", "export const clusterMethodLst = [\n\t{\n\t\tlabel: 'Average',\n\t\tvalue: 'average',\n\t\ttitle: `Cluster by average value`\n\t},\n\t{\n\t\tlabel: `Complete`,\n\t\tvalue: 'complete',\n\t\ttitle: `Use the complete clustering method`\n\t},\n\t{\n\t\tlabel: `Single`,\n\t\tvalue: 'single',\n\t\ttitle: `Use the single clustering method`\n\t},\n\t{\n\t\tlabel: `Ward.D`,\n\t\tvalue: 'ward.D',\n\t\ttitle: `Use the ward.D clustering method`\n\t},\n\t{\n\t\tlabel: `Ward.D2`,\n\t\tvalue: 'ward.D2',\n\t\ttitle: `Use the ward.D2 clustering method`\n\t},\n\t{\n\t\tlabel: `Mcquitty`,\n\t\tvalue: 'mcquitty',\n\t\ttitle: `Use the Mcquity clustering method`\n\t}\n\t/* These methods are currently disabled because the dendrogram lines tend to cross one another.\n\t{\n\t\tlabel: `Centroid`,\n\t\tvalue: 'centroid',\n\t\ttitle: `Use the centroid clustering method`\n\t},\n    \t{\n\t\tlabel: `Median`,\n\t\tvalue: 'median',\n\t\ttitle: `Use the median clustering method`\n\t}\n        */\n]\nexport const distanceMethodLst = [\n\t{\n\t\tlabel: 'Euclidean',\n\t\tvalue: 'euclidean',\n\t\ttitle: `Calculate distance using euclidean method`\n\t},\n\t{\n\t\tlabel: 'Maximum',\n\t\tvalue: 'maximum',\n\t\ttitle: `Maximum distance between two components of x and y`\n\t},\n\t{\n\t\tlabel: 'Manhattan',\n\t\tvalue: 'manhattan',\n\t\ttitle: `Calculate distance using the absolute distance between the two vectors`\n\t},\n\t{\n\t\tlabel: 'Canberra',\n\t\tvalue: 'canberra',\n\t\ttitle: `Calculate distance using Canberra method`\n\t}\n]\n"],
+  "mappings": 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 }

package/dist/{chunk-XMQWL2ZA.js → chunk-CGRLJLI3.js}

@@ -1,7 +1,7 @@
 import {
   fillTermWrapper,
   termsettingInit
-} from "./chunk-2MDPMDCG.js";
+} from "./chunk-WA6VYIW4.js";
 import {
   isNumericTerm
 } from "./chunk-OTWQWP6Z.js";
@@ -355,4 +355,4 @@ function sleep(ms) {
 export {
   setRenderers
 };
-//# sourceMappingURL=chunk-XMQWL2ZA.js.map
+//# sourceMappingURL=chunk-CGRLJLI3.js.map

package/dist/{chunk-5JGU6PEQ.js → chunk-CLX5YITI.js}

@@ -1,9 +1,9 @@
 import {
   getPlotConfig
-} from "./chunk-FBNO7NSG.js";
+} from "./chunk-YMJEVHPD.js";
 import {
   fillTermWrapper
-} from "./chunk-2MDPMDCG.js";
+} from "./chunk-WA6VYIW4.js";
 import {
   TermTypes
 } from "./chunk-OTWQWP6Z.js";
@@ -80,4 +80,4 @@ async function getPlotConfig2(opts = {}, app) {
 export {
   getPlotConfig2 as getPlotConfig
 };
-//# sourceMappingURL=chunk-5JGU6PEQ.js.map
+//# sourceMappingURL=chunk-CLX5YITI.js.map