@sjcrh/proteinpaint-client 2.91.0 → 2.92.0

package/dist/{AppHeader-UOK32X5E.js → AppHeader-ZQKMDQTW.js}

@@ -4,7 +4,7 @@ import {
 } from "./chunk-GLTXSGJ5.js";
 import {
   InputSearch
-} from "./chunk-OHC2VBNI.js";
+} from "./chunk-ZC2JTN3M.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-4WBP22U2.js";
@@ -17,12 +17,12 @@ import "./chunk-VSRNBBZH.js";
 import "./chunk-Z7ZWX5W5.js";
 import "./chunk-NHPZSGTH.js";
 import "./chunk-PBT5AMVE.js";
-import "./chunk-FCUPUFGS.js";
+import "./chunk-Z36HPN3C.js";
 import "./chunk-WTM3GD2X.js";
 import {
   get_tklst
-} from "./chunk-NT57I3IH.js";
-import "./chunk-2XHCEZSM.js";
+} from "./chunk-REZ56N4Q.js";
+import "./chunk-PZTSXGRE.js";
 import "./chunk-MYPTC6HX.js";
 import "./chunk-MKAF2BHB.js";
 import {
@@ -37,7 +37,7 @@ import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
 import {
   block_init_default
-} from "./chunk-CGJTS2OW.js";
+} from "./chunk-DXRDUM7A.js";
 import {
   throwMsgWithFilePathAndFnName
 } from "./chunk-RKJGIOIF.js";
@@ -236,7 +236,7 @@ async function findgene2paint(str, app, genomename, jwt) {
       debugmode: app.debugmode
     };
     first_genetrack_tolist(g, par2.tklst);
-    import("./block-N65B7WJT.js").then((b) => new b.Block(par2)).catch((err) => {
+    import("./block-YQFJGXVO.js").then((b) => new b.Block(par2)).catch((err) => {
       app.error0(err);
     });
     return;
@@ -842,7 +842,7 @@ var AppHeader = class _AppHeader {
         debugmode: app.debugmode
       };
       first_genetrack_tolist(g, par.tklst);
-      import("./block-N65B7WJT.js").then((b) => new b.Block(par));
+      import("./block-YQFJGXVO.js").then((b) => new b.Block(par));
       app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
     });
     return g_browser_btn;
@@ -855,4 +855,4 @@ var AppHeader = class _AppHeader {
 export {
   AppHeader
 };
-//# sourceMappingURL=AppHeader-UOK32X5E.js.map
+//# sourceMappingURL=AppHeader-ZQKMDQTW.js.map

package/dist/{DEanalysis-JPOCDT4F.js → DEanalysis-3HI7SEID.js}

@@ -2,7 +2,7 @@ import "./chunk-Q7EFDAC2.js";
 import {
   axisstyle,
   controlsInit
-} from "./chunk-OHC2VBNI.js";
+} from "./chunk-ZC2JTN3M.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-4WBP22U2.js";
@@ -20,7 +20,7 @@ import {
 import {
   downloadTable,
   renderTable
-} from "./chunk-FCUPUFGS.js";
+} from "./chunk-Z36HPN3C.js";
 import "./chunk-WTM3GD2X.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
@@ -142,7 +142,9 @@ var DEanalysis = class {
         ]
       }
     ];
-    if (output.mid_sample_size_cutoff >= output.sample_size1 && output.mid_sample_size_cutoff < output.sample_size2 && output.sample_size2 < output.high_sample_size_cutoff || output.mid_sample_size_cutoff >= output.sample_size2 && output.mid_sample_size_cutoff < output.sample_size1 && output.sample_size1 < output.high_sample_size_cutoff) {
+    if (JSON.parse(sessionStorage.getItem("optionalFeatures")).run_parametricDE == true || // edgeR (and other parametric methods to be added in the future) option is always shown when serverconfig.features.run_parametricDE is set to true. This has been added so as to make this functionality available only in select few production servers for now.
+    output.mid_sample_size_cutoff >= output.sample_size1 && // Invoked only when one sample size is low than the mid_sample_size_cutoff and the other one is higher but the higher sample size is lower than the high cutoff so that the DE computation does not take a lot of time on the server
+    output.mid_sample_size_cutoff < output.sample_size2 && output.sample_size2 < output.high_sample_size_cutoff || output.mid_sample_size_cutoff >= output.sample_size2 && output.mid_sample_size_cutoff < output.sample_size1 && output.sample_size1 < output.high_sample_size_cutoff) {
       inputs.push({
         label: "Method",
         type: "radio",
@@ -154,8 +156,6 @@ var DEanalysis = class {
           { label: "wilcoxon", value: "wilcoxon" }
         ]
       });
-      this.settings.method = output.method;
-      this.state.config = output.method;
     }
     if (this.app.opts.genome.termdbs) {
       inputs.push({
@@ -408,11 +408,11 @@ async function render_volcano(self, output) {
         value: num_significant_genes + num_non_significant_genes
       },
       {
-        label: self.config.state.groups[0].name + " sample size",
+        label: self.config.state.groups[0].name + " sample size (control group)",
         value: sample_size1
       },
       {
-        label: self.config.state.groups[1].name + " sample size",
+        label: self.config.state.groups[1].name + " sample size (treatment group)",
         value: sample_size2
       }
     ];
@@ -555,12 +555,12 @@ async function getPlotConfig(opts, app) {
       settings: {
         DEanalysis: {
           pvalue: 0.05,
-          foldchange: 2,
+          foldchange: 0,
           min_count: 10,
           min_total_count: 15,
           pvaluetable: false,
           adjusted_original_pvalue: "adjusted",
-          method: void 0,
+          method: "wilcoxon",
           gene_ora: void 0,
           gsea: void 0
         }
@@ -644,4 +644,4 @@ export {
   makeChartBtnMenu,
   openHiercluster
 };
-//# sourceMappingURL=DEanalysis-JPOCDT4F.js.map
+//# sourceMappingURL=DEanalysis-3HI7SEID.js.map

package/dist/DEanalysis-3HI7SEID.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/DEanalysis.js"],
+  "sourcesContent": ["import { axisstyle } from '#dom/axisstyle'\nimport { table2col } from '#dom/table2col'\nimport { Menu } from '../dom/menu'\nimport { renderTable } from '../dom/table'\nimport * as d3axis from 'd3-axis'\nimport { controlsInit } from './controls'\nimport { select as d3select } from 'd3-selection'\nimport { getCompInit, copyMerge } from '#rx'\nimport { dofetch3 } from '#common/dofetch'\nimport { scaleLog, scaleLinear } from 'd3-scale'\nimport { d3lasso } from '../common/lasso'\nimport { downloadTable } from '../dom/table'\nimport { roundValueAuto } from '#shared/roundValue.js'\n\n/*\n\nopts{}\n\tsamplelst{}\n\t\tgroups[]\n\nthis{}\n\tapp{}\n\t\tvocabApi\n*/\n\nconst hlcolor = '#ffa200'\nconst tip = new Menu()\nclass DEanalysis {\n\tconstructor() {\n\t\tthis.type = 'DEanalysis'\n\t}\n\tasync init(opts) {\n\t\tconst config = opts.plots.find(p => p.id === this.id)\n\t\tconst controlsDiv = this.opts.holder.append('div').style('display', 'inline-block')\n\t\tconst mainDiv = this.opts.holder.append('div').style('display', 'inline-block').style('margin-left', '50px')\n\t\tconst holder = mainDiv.append('div').style('display', 'inline-block')\n\t\tconst detailsDiv = mainDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin-top', '50px')\n\n\t\tconst tableDiv = this.opts.holder.append('div').style('margin-left', '50px')\n\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\theader: this.opts.header,\n\t\t\tcontrolsDiv,\n\t\t\tdetailsDiv,\n\t\t\ttableDiv\n\t\t}\n\t}\n\n\tasync setControls(output) {\n\t\tthis.dom.controlsDiv.selectAll('*').remove()\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\tlabel: 'Minimum read count',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'min_count',\n\t\t\t\ttitle: 'Relative cpm cutoff for filtering a gene compared to all samples and genes in dataset',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 10000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Minimum total read count',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'min_total_count',\n\t\t\t\ttitle: 'Minimum total read count required for each sample',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 10000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'P-value significance (linear scale)',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'pvalue',\n\t\t\t\ttitle: 'P-value significance',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 1\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Fold change (log scale)',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'foldchange',\n\t\t\t\ttitle: 'Fold change',\n\t\t\t\tmin: -10,\n\t\t\t\tmax: 10\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'P-value table',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'pvaluetable',\n\t\t\t\ttitle: 'Display table showing original and adjusted pvalues for all significant genes',\n\t\t\t\tboxLabel: ''\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'P-value',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'adjusted_original_pvalue',\n\t\t\t\ttitle: 'Toggle between original and adjusted pvalues for volcano plot',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'adjusted', value: 'adjusted' },\n\t\t\t\t\t{ label: 'original', value: 'original' }\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\n\t\tif (\n\t\t\tJSON.parse(sessionStorage.getItem('optionalFeatures')).run_parametricDE == true || // edgeR (and other parametric methods to be added in the future) option is always shown when serverconfig.features.run_parametricDE is set to true. This has been added so as to make this functionality available only in select few production servers for now.\n\t\t\t(output.mid_sample_size_cutoff >= output.sample_size1 && // Invoked only when one sample size is low than the mid_sample_size_cutoff and the other one is higher but the higher sample size is lower than the high cutoff so that the DE computation does not take a lot of time on the server\n\t\t\t\toutput.mid_sample_size_cutoff < output.sample_size2 &&\n\t\t\t\toutput.sample_size2 < output.high_sample_size_cutoff) ||\n\t\t\t(output.mid_sample_size_cutoff >= output.sample_size2 &&\n\t\t\t\toutput.mid_sample_size_cutoff < output.sample_size1 &&\n\t\t\t\toutput.sample_size1 < output.high_sample_size_cutoff)\n\t\t) {\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Method',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'method',\n\t\t\t\ttitle: 'Toggle between edgeR and wilcoxon test',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'edgeR', value: 'edgeR' },\n\t\t\t\t\t{ label: 'wilcoxon', value: 'wilcoxon' }\n\t\t\t\t]\n\t\t\t})\n\t\t}\n\n\t\t//if (\n\t\t//\t(output.mid_sample_size_cutoff >= output.sample_size1 &&\n\t\t//\t\toutput.mid_sample_size_cutoff < output.sample_size2 &&\n\t\t//\t\toutput.sample_size2 < output.high_sample_size_cutoff) ||\n\t\t//\t(output.mid_sample_size_cutoff >= output.sample_size2 &&\n\t\t//\t\toutput.mid_sample_size_cutoff < output.sample_size1 &&\n\t\t//\t\toutput.sample_size1 < output.high_sample_size_cutoff)\n\t\t//) {\n\t\t//\t// Invoked only when one sample size is low than the mid_sample_size_cutoff and the other one is higher but the higher sample size is lower than the high cutoff so that the DE computation does not take a lot of time on the server\n\t\t//\tinputs.push({\n\t\t//\t\tlabel: 'Method',\n\t\t//\t\ttype: 'radio',\n\t\t//\t\tchartType: 'DEanalysis',\n\t\t//\t\tsettingsKey: 'method',\n\t\t//\t\ttitle: 'Toggle between edgeR and wilcoxon test',\n\t\t//\t\toptions: [\n\t\t//\t\t\t{ label: 'edgeR', value: 'edgeR' },\n\t\t//\t\t\t{ label: 'wilcoxon', value: 'wilcoxon' }\n\t\t//\t\t]\n\t\t//\t})\n\t\t//\tthis.settings.method = output.method\n\t\t//\tthis.state.config = output.method\n\t\t//}\n\n\t\tif (this.app.opts.genome.termdbs) {\n\t\t\t// Check if genome build contains termdbs, only then enable gene ora\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Gene set overrepresentation analysis',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'gene_ora',\n\t\t\t\ttitle: 'Toggle between analyzing upregulated, downregulated or both genes',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'upregulated', value: 'upregulated' },\n\t\t\t\t\t{ label: 'downregulated', value: 'downregulated' },\n\t\t\t\t\t{ label: 'both', value: 'both' }\n\t\t\t\t]\n\t\t\t})\n\t\t}\n\n\t\tif (this.app.opts.genome.termdbs && !this.settings.gsea) {\n\t\t\t// Check if genome build contains termdbs, only then enable gene ora\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Gene set enrichment analysis',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'gsea',\n\t\t\t\ttitle: 'Gene set enrichment analysis',\n\t\t\t\toptions: [{ label: 'Submit', value: 'Submit' }]\n\t\t\t})\n\t\t}\n\n\t\tif (this.settings.pvaluetable == true) {\n\t\t\t// This currently does not work as hierarchial clustering code needs to be changed\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Hierarchial Clustering',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'hierCluster',\n\t\t\t\ttitle: 'Toggle between various methods for selecting genes for hierarchial clustering',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Top 100 genes', value: 'top100' },\n\t\t\t\t\t{ label: 'Top 100 upregulated', value: 'top100up' },\n\t\t\t\t\t{ label: 'Top 100 downregulated', value: 'top100down' }\n\t\t\t\t]\n\t\t\t})\n\t\t\tthis.settings.hierCluster = 'top100'\n\t\t}\n\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controlsDiv,\n\t\t\t\tinputs: inputs\n\t\t\t})\n\t\t}\n\t\tthis.components.controls.on('downloadClick.DEanalysis', () => {\n\t\t\tdownloadTable(this.table_rows, this.table_cols)\n\t\t})\n\t}\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn {\n\t\t\tconfig\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = JSON.parse(JSON.stringify(this.state.config))\n\t\tthis.settings = this.config.settings.DEanalysis\n\t\tif (this.dom.detailsDiv) {\n\t\t\tthis.dom.detailsDiv.selectAll('*').remove()\n\t\t}\n\t\tif (this.dom.holder) {\n\t\t\tthis.dom.holder.selectAll('*').remove()\n\t\t}\n\t\tconst wait = this.dom.detailsDiv.append('div').text('Loading...')\n\t\tconst output = await runDEanalysis(this) // \"this.config\" was changed from \"this.state.config\". Hope this does not create any problems.\n\t\twait.remove()\n\t\toutput.mid_sample_size_cutoff = 8 // mid sample size cutoff for method toggle to appear\n\t\toutput.high_sample_size_cutoff = 30 // high sample size cutoff for method toggle to not appear, so that very high sample-size groups are not analyzed by edgeR. The exact cutoff value will need to be determined with more examples.\n\t\tawait this.setControls(output)\n\t\tthis.dom.header.html(\n\t\t\tthis.config.state.groups[0].name +\n\t\t\t\t' vs ' +\n\t\t\t\tthis.config.state.groups[1].name +\n\t\t\t\t' <span style=\"font-size:.8em;opacity:.7\">DIFFERENTIAL GENE EXPRESSION</span>'\n\t\t)\n\t\trender_volcano(this, output)\n\t}\n}\n\nasync function render_volcano(self, output) {\n\t/*\nm {}\n- gene\n- logfoldchange\n- averagevalue\n- pvalue\n\nadd:\n- vo_circle\n\t*/\n\n\t// Delete previous holder, if present\n\tconst sample_size1 = output.sample_size1\n\tconst sample_size2 = output.sample_size2\n\tconst mavb = output.data\n\tconst holder = self.dom.holder\n\tholder.selectAll('*').remove()\n\tself.dom.detailsDiv.selectAll('*').remove()\n\tself.dom.tableDiv.selectAll('*').remove()\n\tlet minlogfc = 0,\n\t\tmaxlogfc = 0,\n\t\tminlogpv = 0,\n\t\tmaxlogpv = 0\n\tfor (const d of mavb) {\n\t\tminlogfc = Math.min(minlogfc, d.fold_change)\n\t\tmaxlogfc = Math.max(maxlogfc, d.fold_change)\n\t\tif (d.adjusted_p_value == 0) {\n\t\t\tcontinue\n\t\t} else {\n\t\t\tminlogpv = Math.min(minlogpv, d.adjusted_p_value)\n\t\t\tmaxlogpv = Math.max(maxlogpv, d.adjusted_p_value)\n\t\t}\n\t}\n\n\tlet yaxisw,\n\t\txaxish,\n\t\twidth,\n\t\theight,\n\t\txpad,\n\t\typad,\n\t\ttoppad = 50,\n\t\trightpad = 50,\n\t\tradius\n\n\tconst svg = holder.append('svg')\n\tconst yaxisg = svg.append('g')\n\tconst xaxisg = svg.append('g')\n\tconst xlab = svg.append('text').text('log2(fold change)').attr('fill', 'black').attr('text-anchor', 'middle')\n\tconst ylab = svg.append('text').text('-log10(adjusted P value)').attr('fill', 'black').attr('text-anchor', 'middle')\n\n\tmavb.vo_dotarea = svg.append('g')\n\n\tconst box = mavb.vo_dotarea\n\t\t.append('rect')\n\t\t.attr('stroke', '#ededed')\n\t\t.attr('fill', 'none')\n\t\t.attr('shape-rendering', 'crispEdges')\n\tconst xscale = scaleLinear().domain([minlogfc, maxlogfc])\n\tconst yscale = scaleLinear().domain([minlogpv, maxlogpv])\n\tlet radiusscale\n\tconst dotg = mavb.vo_dotarea\n\t\t.selectAll()\n\t\t.data(mavb)\n\t\t.enter()\n\t\t.append('g')\n\t\t.each(function (d) {\n\t\t\td.vo_g = this\n\t\t})\n\tconst fold_change_cutoff = self.settings.foldchange\n\t//console.log(\"self.settings:\",self.settings)\n\t//self.config.settings.DEanalysis.min_count = self.settings.min_count\n\t//self.config.settings.DEanalysis.min_total_count = self.settings.min_total_count\n\tif (self.settings.pvalue == 0) throw 'p-value significance cannot be zero'\n\tconst p_value_cutoff = -Math.log10(self.settings.pvalue)\n\tconst p_value_adjusted_original = self.settings.adjusted_original_pvalue\n\tlet num_significant_genes = 0\n\tlet num_non_significant_genes = 0\n\tself.table_rows = []\n\tconst circle = dotg\n\t\t.append('circle')\n\t\t.attr('stroke', d => {\n\t\t\tlet color\n\t\t\tconst value3 = roundValueAuto(d.fold_change)\n\t\t\tconst value4 = roundValueAuto(Math.pow(10, -d.original_p_value))\n\t\t\tconst value5 = roundValueAuto(Math.pow(10, -d.adjusted_p_value))\n\t\t\tif (\n\t\t\t\tp_value_adjusted_original == 'adjusted' &&\n\t\t\t\td.adjusted_p_value > p_value_cutoff &&\n\t\t\t\tMath.abs(d.fold_change) > fold_change_cutoff\n\t\t\t) {\n\t\t\t\tcolor = 'red'\n\t\t\t\tnum_significant_genes += 1\n\n\t\t\t\tself.table_rows.push([\n\t\t\t\t\t{ value: d.gene_name },\n\t\t\t\t\t{ value: d.gene_symbol },\n\t\t\t\t\t{ value: value3 },\n\t\t\t\t\t{ value: value4 },\n\t\t\t\t\t{ value: value5 }\n\t\t\t\t])\n\t\t\t} else if (\n\t\t\t\tp_value_adjusted_original == 'original' &&\n\t\t\t\td.original_p_value > p_value_cutoff &&\n\t\t\t\tMath.abs(d.fold_change) > fold_change_cutoff\n\t\t\t) {\n\t\t\t\tcolor = 'red'\n\t\t\t\tnum_significant_genes += 1\n\t\t\t\tself.table_rows.push([\n\t\t\t\t\t{ value: d.gene_name },\n\t\t\t\t\t{ value: d.gene_symbol },\n\t\t\t\t\t{ value: value3 },\n\t\t\t\t\t{ value: value4 },\n\t\t\t\t\t{ value: value5 }\n\t\t\t\t])\n\t\t\t} else {\n\t\t\t\tcolor = 'black'\n\t\t\t\tnum_non_significant_genes += 1\n\t\t\t}\n\t\t\treturn color\n\t\t})\n\t\t.attr('stroke-opacity', 0.2)\n\t\t.attr('stroke-width', 1)\n\t\t.attr('fill', hlcolor)\n\t\t.attr('fill-opacity', 0)\n\t\t.each(function (d) {\n\t\t\td.vo_circle = this\n\t\t})\n\t\t.on('mouseover', circlemouseover)\n\t\t.on('mouseout', circlemouseout)\n\t//.on('click', (event, d) => {\n\t//\tcircleclick(d, mavb, event.clientX, event.clientY)\n\t//})\n\tself.table_rows.sort((a, b) => a[2].value - b[2].value).reverse() // Sorting genes in descending order of fold change\n\t//console.log(\n\t//\t'Percentage of significant genes:',\n\t//\t(num_significant_genes * 100) / (num_significant_genes + num_non_significant_genes)\n\t//)\n\n\tconst logfc0line = mavb.vo_dotarea.append('line').attr('stroke', '#ccc').attr('shape-rendering', 'crispEdges')\n\n\tfunction resize(w, h) {\n\t\twidth = w\n\t\theight = h\n\t\tyaxisw = Math.max(50, width / 8)\n\t\txaxish = Math.max(50, height / 8)\n\n\t\tradius = Math.max(width, height) / 80\n\t\tconst maxradius = radius * 3\n\t\tif (radiusscale) radiusscale.range([radius, maxradius])\n\t\tcircle.each(d => {\n\t\t\td.vo_radius = radiusscale ? radiusscale(Math.abs(d.tvalue)) : radius\n\t\t})\n\n\t\txpad = Math.max(maxradius, width / 50)\n\t\typad = Math.max(maxradius, height / 50)\n\t\tyaxisg.attr('transform', 'translate(' + yaxisw + ',' + toppad + ')')\n\t\txaxisg.attr('transform', 'translate(' + (yaxisw + xpad) + ',' + (toppad + height + ypad) + ')')\n\t\txlab.attr('x', yaxisw + xpad + width / 2).attr('y', toppad + height + ypad + xaxish - 5)\n\t\tylab.attr('transform', 'translate(15,' + (toppad + height / 2) + ') rotate(-90)')\n\t\tmavb.vo_dotarea.attr('transform', 'translate(' + (yaxisw + xpad) + ',' + toppad + ')')\n\t\tbox.attr('width', width).attr('height', height)\n\t\txscale.range([0, width])\n\t\tyscale.range([height, 0])\n\t\tdotg.attr('transform', d => {\n\t\t\treturn 'translate(' + xscale(d.fold_change) + ',' + yscale(d.adjusted_p_value) + ')'\n\t\t})\n\t\tcircle.attr('r', d => {\n\t\t\treturn d.vo_radius\n\t\t})\n\t\tlogfc0line.attr('x1', xscale(0)).attr('x2', xscale(0)).attr('y2', height)\n\n\t\tsvg.attr('width', yaxisw + xpad + width + rightpad).attr('height', toppad + height + ypad + xaxish)\n\t\taxisstyle({\n\t\t\taxis: yaxisg.call(d3axis.axisLeft().scale(yscale)),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t\taxisstyle({\n\t\t\taxis: xaxisg.call(d3axis.axisBottom().scale(xscale)),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t}\n\tresize(400, 400)\n\n\tif (mavb[0].adjusted_p_value != undefined) {\n\t\t// enable pvalue switching between adjusted and unadjusted\n\t\tconst row = holder.append('div').style('margin', '20px')\n\t\tminlogpv = 0\n\t\tmaxlogpv = 0\n\t\tlet text_string\n\t\tfor (const d of mavb) {\n\t\t\tlet pv\n\t\t\tif (p_value_adjusted_original == 'adjusted') {\n\t\t\t\tpv = d.adjusted_p_value\n\t\t\t} else {\n\t\t\t\tpv = d.original_p_value\n\t\t\t}\n\t\t\tif (pv == 0) continue\n\t\t\tminlogpv = Math.min(minlogpv, pv)\n\t\t\tmaxlogpv = Math.max(maxlogpv, pv)\n\t\t}\n\t\tyscale.domain([minlogpv, maxlogpv])\n\t\taxisstyle({\n\t\t\taxis: yaxisg.call(d3axis.axisLeft().scale(yscale)),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t\tdotg.attr('transform', d => {\n\t\t\tlet pv\n\t\t\tif (p_value_adjusted_original == 'adjusted') {\n\t\t\t\tpv = d.adjusted_p_value\n\t\t\t} else {\n\t\t\t\tpv = d.original_p_value\n\t\t\t}\n\t\t\treturn 'translate(' + xscale(d.fold_change) + ',' + yscale(pv) + ')'\n\t\t})\n\t\tif (p_value_adjusted_original == 'adjusted') {\n\t\t\ttext_string = '-log10(adjusted P value)'\n\t\t} else {\n\t\t\ttext_string = '-log10(original P value)'\n\t\t}\n\t\tylab.text(text_string)\n\t\tconst table_stats = table2col({ holder: self.dom.detailsDiv })\n\t\tconst addStats = [\n\t\t\t{\n\t\t\t\tlabel: 'Percentage of significant genes',\n\t\t\t\tvalue: roundValueAuto((num_significant_genes * 100) / (num_significant_genes + num_non_significant_genes))\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Number of significant genes',\n\t\t\t\tvalue: num_significant_genes\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Number of total genes',\n\t\t\t\tvalue: num_significant_genes + num_non_significant_genes\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: self.config.state.groups[0].name + ' sample size (control group)',\n\t\t\t\tvalue: sample_size1\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: self.config.state.groups[1].name + ' sample size (treatment group)',\n\t\t\t\tvalue: sample_size2\n\t\t\t}\n\t\t]\n\n\t\tfor (const dataRow of addStats) {\n\t\t\tconst [td1, td2] = table_stats.addRow()\n\t\t\ttd1.text(dataRow.label)\n\t\t\ttd2.style('text-align', 'end').text(dataRow.value)\n\t\t}\n\n\t\tself.table_cols = [\n\t\t\t{ label: 'Gene Name' },\n\t\t\t{ label: 'Gene Symbol' },\n\t\t\t{ label: 'log2 Fold change' },\n\t\t\t{ label: 'Original p-value (linear scale)' },\n\t\t\t{ label: 'Adjusted p-value (linear scale)' }\n\t\t]\n\t\tif (self.settings.pvaluetable == true) {\n\t\t\tconst d = self.dom.tableDiv.append('div').html(`<br>DE analysis results`)\n\t\t\trenderTable({\n\t\t\t\tcolumns: self.table_cols,\n\t\t\t\trows: self.table_rows,\n\t\t\t\tdiv: d,\n\t\t\t\tshowLines: true,\n\t\t\t\tmaxHeight: '150vh',\n\t\t\t\tresize: true\n\t\t\t})\n\t\t} else {\n\t\t\tself.dom.tableDiv.selectAll('*').remove()\n\t\t}\n\n\t\tif (self.settings.gene_ora && self.app.opts.genome.termdbs) {\n\t\t\t// Currently backend only uses msigdb, but in future may use other databases in genome.termdbs{}. In ui will need to generate a <select> to choose one key of termdbs{}.\n\t\t\t//console.log('Run gene ora:', self.settings.gene_ora)\n\t\t\t//console.log('output.data:', output.data)\n\t\t\tconst sample_genes = []\n\t\t\tconst background_genes = []\n\t\t\t//console.log('self:', self)\n\t\t\t//console.log('fold_change_cutoff:', fold_change_cutoff)\n\n\t\t\t// Need to handle those genes which do not have a name\n\t\t\tif (self.settings.gene_ora == 'upregulated') {\n\t\t\t\tfor (const gene of output.data) {\n\t\t\t\t\tif (gene.gene_symbol.length > 0) {\n\t\t\t\t\t\t// Do not include blank rows\n\t\t\t\t\t\tif (fold_change_cutoff < Math.abs(gene.fold_change) && gene.fold_change > 0) {\n\t\t\t\t\t\t\tsample_genes.push(gene.gene_symbol)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tbackground_genes.push(gene.gene_symbol)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else if (self.settings.gene_ora == 'downregulated') {\n\t\t\t\tfor (const gene of output.data) {\n\t\t\t\t\tif (gene.gene_symbol.length > 0) {\n\t\t\t\t\t\t// Do not include blank rows\n\t\t\t\t\t\tif (fold_change_cutoff < Math.abs(gene.fold_change) && gene.fold_change < 0) {\n\t\t\t\t\t\t\tsample_genes.push(gene.gene_symbol)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tbackground_genes.push(gene.gene_symbol)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else if (self.settings.gene_ora == 'both') {\n\t\t\t\tfor (const gene of output.data) {\n\t\t\t\t\tif (gene.gene_symbol.length > 0) {\n\t\t\t\t\t\t// Do not include blank rows\n\t\t\t\t\t\tif (fold_change_cutoff < Math.abs(gene.fold_change)) {\n\t\t\t\t\t\t\tsample_genes.push(gene.gene_symbol)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tbackground_genes.push(gene.gene_symbol)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconsole.log('Unrecognized option')\n\t\t\t}\n\n\t\t\tconst geneORAparams = {\n\t\t\t\tsample_genes: sample_genes.toString(),\n\t\t\t\tbackground_genes: background_genes.toString(),\n\t\t\t\tgenome: self.app.vocabApi.opts.state.vocab.genome,\n\t\t\t\tora_request_type: self.settings.gene_ora,\n\t\t\t\tnum_samples_genes: sample_genes.length,\n\t\t\t\tnum_background_genes: background_genes.length\n\t\t\t}\n\n\t\t\t// Check if a previous requests has already been made with the same parameters\n\t\t\tconst previous_geneORA = self.app.getState().plots.find(x => x.chartType == 'geneORA')\n\n\t\t\tif (previous_geneORA) {\n\t\t\t\tif (\n\t\t\t\t\tprevious_geneORA.geneORAparams.ora_request_type == self.settings.gene_ora &&\n\t\t\t\t\tprevious_geneORA.geneORAparams.num_samples_genes == sample_genes.length &&\n\t\t\t\t\tprevious_geneORA.geneORAparams.num_background_genes == background_genes.length\n\t\t\t\t) {\n\t\t\t\t\t// The check for number of background genes and sample genes have been added so that the same gene ORA request type (upregulated/downregulated/both) is not triggerred, but if any other DE parameter is changed (min_count etc.) then a new gene ORA request of the same type can be made.\n\t\t\t\t\t//alert(self.settings.gene_ora + \"geneORA already open\")\n\t\t\t\t} else {\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchartType: 'geneORA',\n\t\t\t\t\t\tgeneORAparams: geneORAparams\n\t\t\t\t\t}\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t} else {\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\tself.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\n\t\tif (self.settings.gsea && self.app.opts.genome.termdbs) {\n\t\t\t// Currently backend only uses msigdb, but in future may use other databases in genome.termdbs{}. In ui will need to generate a <select> to choose one key of termdbs{}.\n\t\t\t//self.settings.gsea = false\n\t\t\tconst input_genes = output.data.map(i => i.gene_symbol)\n\t\t\tconst gsea_params = {\n\t\t\t\tgenes: input_genes,\n\t\t\t\tfold_change: output.data.map(i => i.fold_change),\n\t\t\t\tgenome: self.app.vocabApi.opts.state.vocab.genome,\n\t\t\t\tgenes_length: input_genes.length\n\t\t\t}\n\t\t\t//console.log(\"gsea_params:\",gsea_params)\n\t\t\t// Check if a previous requests has already been made with the same parameters\n\t\t\tconst previous_gsea = self.app.getState().plots.find(x => x.chartType == 'gsea')\n\t\t\tif (previous_gsea) {\n\t\t\t\tif (previous_gsea.gsea_params.genes_length == input_genes.length) {\n\t\t\t\t\t// GSEA window already open for these parameters\n\t\t\t\t} else {\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\tchartType: 'gsea',\n\t\t\t\t\t\tgsea_params: gsea_params\n\t\t\t\t\t}\n\t\t\t\t\tself.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconst config = {\n\t\t\t\t\tchartType: 'gsea',\n\t\t\t\t\tgsea_params: gsea_params\n\t\t\t\t}\n\t\t\t\tself.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\t//console.log('this.app.getState:', self.app.getState())\n\t}\n\treturn svg\n}\n\nexport async function getPlotConfig(opts, app) {\n\ttry {\n\t\tif (opts.samplelst.groups.length != 2) throw 'opts.samplelst.groups[].length!=2'\n\t\tif (opts.samplelst.groups[0].values?.length < 1) throw 'group 1 not having >1 samples'\n\t\tif (opts.samplelst.groups[1].values?.length < 1) throw 'group 2 not having >1 samples'\n\t\tconst config = {\n\t\t\t//idea for fixing nav button\n\t\t\t//samplelst: { groups: app.opts.state.groups}\n\t\t\tsettings: {\n\t\t\t\tDEanalysis: {\n\t\t\t\t\tpvalue: 0.05,\n\t\t\t\t\tfoldchange: 0,\n\t\t\t\t\tmin_count: 10,\n\t\t\t\t\tmin_total_count: 15,\n\t\t\t\t\tpvaluetable: false,\n\t\t\t\t\tadjusted_original_pvalue: 'adjusted',\n\t\t\t\t\tmethod: 'wilcoxon',\n\t\t\t\t\tgene_ora: undefined,\n\t\t\t\t\tgsea: undefined\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn copyMerge(config, opts)\n\t} catch (e) {\n\t\tthrow `${e} [DEanalysis getPlotConfig()]`\n\t}\n}\n\nexport const DEanalysisInit = getCompInit(DEanalysis)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = DEanalysisInit\n\nexport function makeChartBtnMenu(holder, chartsInstance) {\n\t/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n        termdbConfig is accessible at chartsInstance.state.termdbConfig{}\n        mass option is accessible at chartsInstance.app.opts{}\n\t*/\n\t// to fill in menu, create options in \"holder\"\n\t// to hide menu, call chartsInstance.dom.tip.hide()\n\t// upon clicking an option, generate plot:\n\tchartsInstance.prepPlot({\n\t\tconfig: {\n\t\t\tchartType: 'DEanalysis'\n\t\t}\n\t})\n}\n\nfunction circlemouseover(event, d) {\n\ttip.clear().show(event.clientX, event.clientY)\n\tconst lst = [\n\t\t{ k: 'gene_name', v: d.gene_name },\n\t\t{ k: 'gene_symbol', v: d.gene_symbol },\n\t\t{ k: 'log fold change', v: roundValueAuto(d.fold_change) },\n\t\t{ k: 'log original p-value', v: roundValueAuto(d.original_p_value) },\n\t\t{ k: 'log adjusted p-value', v: roundValueAuto(d.adjusted_p_value) }\n\t]\n\tconst table = table2col({ holder: tip.d })\n\tfor (const item of lst) {\n\t\tconst [td1, td2] = table.addRow()\n\t\ttd1.text(item.k)\n\t\ttd2.text(item.v)\n\t}\n\n\tif (!d.ma_label) {\n\t\td3select(d.ma_circle).attr('fill-opacity', 0.9)\n\t\td3select(d.vo_circle).attr('fill-opacity', 0.9)\n\t}\n}\n\nfunction circlemouseout(event, d) {\n\ttip.hide()\n\tif (!d.ma_label) {\n\t\td3select(d.ma_circle).attr('fill-opacity', 0)\n\t\td3select(d.vo_circle).attr('fill-opacity', 0)\n\t}\n}\n\nexport async function openHiercluster(term, samplelstTW, app, id, newId) {\n\t// barchart config.term{} name is confusing, as it is actually a termsetting object, not t    erm\n\t// thus convert the given term into a termwrapper\n\t// tw.q can be missing and will be filled in with default setting\n\tconst tw = term.term ? term : { term }\n\n\tlet config = {\n\t\tchartType: 'hierCluster',\n\t\tgenes: ['barchart', xxx]\n\t}\n\tif (id) config.insertBefore = id\n\tif (newId) config.id = newId()\n\tawait app.dispatch({\n\t\ttype: 'plot_create',\n\t\tconfig\n\t})\n}\n\nasync function runDEanalysis(self) {\n\tconst output = await dofetch3('DEanalysis', {\n\t\tbody: {\n\t\t\tgenome: self.app.vocabApi.vocab.genome,\n\t\t\tdslabel: self.app.vocabApi.vocab.dslabel,\n\t\t\tsamplelst: self.config.samplelst,\n\t\t\tmin_count: self.settings.min_count,\n\t\t\tmin_total_count: self.settings.min_total_count,\n\t\t\tmethod: self.settings.method\n\t\t}\n\t})\n\tif (output.error) console.log('server side error:', output.error)\n\treturn output\n}\n"],
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+  "names": []
+}

package/dist/{Disco-ZYPMYP2E.js → Disco-VSLMH7IW.js}

@@ -1,7 +1,7 @@
 import {
   configUiInit,
   svgLegend
-} from "./chunk-OHC2VBNI.js";
+} from "./chunk-ZC2JTN3M.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-4WBP22U2.js";
@@ -16,7 +16,7 @@ import "./chunk-VSRNBBZH.js";
 import "./chunk-Z7ZWX5W5.js";
 import "./chunk-NHPZSGTH.js";
 import "./chunk-PBT5AMVE.js";
-import "./chunk-FCUPUFGS.js";
+import "./chunk-Z36HPN3C.js";
 import "./chunk-WTM3GD2X.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
@@ -224,7 +224,7 @@ var DiscoInteractions = class {
           }
         ]
       };
-      const _ = await import("./block.init-BQCHC3WP.js");
+      const _ = await import("./block.init-5F26S4V6.js");
       await _.default(arg);
     };
   }
@@ -2482,4 +2482,4 @@ export {
   discoInit,
   getPlotConfig
 };
-//# sourceMappingURL=Disco-ZYPMYP2E.js.map
+//# sourceMappingURL=Disco-VSLMH7IW.js.map

package/dist/{Disco.UI-G3GAHU6Q.js → Disco.UI-4PHNVJKL.js}

@@ -1,6 +1,6 @@
 import {
   launch
-} from "./chunk-JBYJMF2E.js";
+} from "./chunk-QEHA27EP.js";
 import {
   makeBtn,
   makeFileUpload,
@@ -9,11 +9,11 @@ import {
   makeResetBtn,
   makeTextAreaInput
 } from "./chunk-CVRLSPB3.js";
-import "./chunk-VKP2QBZV.js";
-import "./chunk-ZROHWTSW.js";
+import "./chunk-UWXKF5GA.js";
+import "./chunk-O6XO5GFR.js";
 import "./chunk-5MDPW4SY.js";
 import "./chunk-NEKINX6F.js";
-import "./chunk-OHC2VBNI.js";
+import "./chunk-ZC2JTN3M.js";
 import {
   Tabs
 } from "./chunk-7KFEDC2T.js";
@@ -28,7 +28,7 @@ import "./chunk-VSRNBBZH.js";
 import "./chunk-Z7ZWX5W5.js";
 import "./chunk-NHPZSGTH.js";
 import "./chunk-PBT5AMVE.js";
-import "./chunk-FCUPUFGS.js";
+import "./chunk-Z36HPN3C.js";
 import "./chunk-WTM3GD2X.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
@@ -250,4 +250,4 @@ function backButton(holder, genomes) {
 export {
   init_discoplotUI
 };
-//# sourceMappingURL=Disco.UI-G3GAHU6Q.js.map
+//# sourceMappingURL=Disco.UI-4PHNVJKL.js.map

package/dist/{DragControls-XN4IHBGY.js → DragControls-UVVSECD2.js}

@@ -5,7 +5,7 @@ import {
   Raycaster,
   Vector2,
   Vector3
-} from "./chunk-DZTTAFY6.js";
+} from "./chunk-YNH7AQH7.js";
 import "./chunk-F3OQE4AZ.js";
 
 // ../node_modules/three/examples/jsm/controls/DragControls.js
@@ -128,4 +128,4 @@ var DragControls = class extends EventDispatcher {
 export {
   DragControls
 };
-//# sourceMappingURL=DragControls-XN4IHBGY.js.map
+//# sourceMappingURL=DragControls-UVVSECD2.js.map

package/dist/{HicApp-NSUVNIPD.js → HicApp-TB6CQVOL.js}

@@ -1,12 +1,12 @@
 import {
   blocklazyload
-} from "./chunk-64A6MQVL.js";
+} from "./chunk-M7UM6ZD4.js";
 import {
   hicParseFile
 } from "./chunk-VIEDCIGF.js";
 import {
   ColorScale
-} from "./chunk-OHC2VBNI.js";
+} from "./chunk-ZC2JTN3M.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-4WBP22U2.js";
@@ -19,7 +19,7 @@ import "./chunk-VSRNBBZH.js";
 import "./chunk-Z7ZWX5W5.js";
 import "./chunk-NHPZSGTH.js";
 import "./chunk-PBT5AMVE.js";
-import "./chunk-FCUPUFGS.js";
+import "./chunk-Z36HPN3C.js";
 import "./chunk-WTM3GD2X.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
@@ -1775,7 +1775,7 @@ var InfoBar = class {
     this.colorScale = new ColorScale({
       barheight: 20,
       barwidth: 100,
-      data: [this.parent("min"), this.parent("max")],
+      domain: [this.parent("min"), this.parent("max")],
       fontSize: 12,
       height: 40,
       width: 150,
@@ -1807,10 +1807,10 @@ var InfoBar = class {
       const max = this.parent("max");
       if (min < 0) {
         this.colorScale.colors = ["blue", "white", "red"];
-        this.colorScale.data = [min, 0, max];
+        this.colorScale.domain = [min, 0, max];
       } else {
         this.colorScale.colors = ["white", "red"];
-        this.colorScale.data = [0, max];
+        this.colorScale.domain = [0, max];
       }
       this.colorScale.markedValue = min;
       this.colorScale.updateScale();
@@ -2282,4 +2282,4 @@ var hicInit = getAppInit(HicApp);
 export {
   hicInit
 };
-//# sourceMappingURL=HicApp-NSUVNIPD.js.map
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