call blitzgseas geneset libraries

client/plots/DEanalysis.js

@@ -493,7 +493,7 @@ add:
 				value: sample_size1
 			},
 			{
-				label: self.config.samplelst.groups[1].name + ' sample size (treatment group)',
+				label: self.config.samplelst.groups[1].name + ' sample size (case group)',
 				value: sample_size2
 			}
 		]

client/plots/geneORA.js

@@ -6,6 +6,7 @@ import { getCompInit, copyMerge } from '#rx'
 import { Menu } from '../dom/menu'
 import { newSandboxDiv } from '../dom/sandbox.ts'
 import { select, pointer } from 'd3-selection'
+import { downloadTable } from '../dom/table'
 import { roundValueAuto } from '#shared/roundValue.js'
 
 const hlcolor = '#ffa200'
@@ -114,7 +115,7 @@ class geneORA {
 			})
 		}
 		this.components.controls.on('downloadClick.geneORA', () => {
-			downloadTable(this.table_rows, this.table_cols)
+			downloadTable(this.gene_ora_table_rows, this.gene_ora_table_cols)
 		})
 	}
 	getState(appState) {

client/plots/gsea.js

@@ -7,22 +7,11 @@ import { controlsInit } from './controls'
 import { getCompInit, copyMerge } from '#rx'
 import { Menu } from '../dom/menu'
 import { scaleLog, scaleLinear } from 'd3-scale'
+import { downloadTable } from '../dom/table'
 import { roundValueAuto } from '#shared/roundValue.js'
 
 const tip = new Menu()
 
-// table columns showing analysis results for each gene set
-const gsea_table_cols = [
-	{ label: 'Pathway name' },
-	{ label: 'enrichment score' },
-	{ label: 'normalized enrichment score' },
-	{ label: 'Geneset size' },
-	{ label: 'pvalue' },
-	{ label: 'sidak' },
-	{ label: 'FDR' },
-	{ label: 'Leading edge' }
-]
-
 class gsea {
 	constructor() {
 		this.type = 'gsea'
@@ -53,7 +42,7 @@ class gsea {
 		this.dom.controlsDiv.selectAll('*').remove()
 		const inputs = [
 			{
-				label: 'P-value filter cutoff (linear scale)',
+				label: 'P-value Filter Cutoff (Linear Scale)',
 				type: 'number',
 				chartType: 'gsea',
 				settingsKey: 'pvalue',
@@ -62,18 +51,18 @@ class gsea {
 				max: 1
 			},
 			{
-				label: 'P-value filter type',
+				label: 'P-value Filter Type',
 				type: 'radio',
 				chartType: 'gsea',
 				settingsKey: 'adjusted_original_pvalue',
 				title: 'Toggle between original and adjusted pvalues for volcano plot',
 				options: [
-					{ label: 'adjusted', value: 'adjusted' },
-					{ label: 'original', value: 'original' }
+					{ label: 'Adjusted', value: 'adjusted' },
+					{ label: 'Original', value: 'original' }
 				]
 			},
 			{
-				label: 'Gene set size filter cutoff',
+				label: 'Gene Set Size Filter Cutoff',
 				type: 'number',
 				chartType: 'gsea',
 				settingsKey: 'gene_set_size_cutoff',
@@ -82,7 +71,7 @@ class gsea {
 				max: 20000
 			},
 			{
-				label: 'Filter non-coding genes',
+				label: 'Filter Non-coding Genes',
 				type: 'checkbox',
 				chartType: 'gsea',
 				settingsKey: 'filter_non_coding_genes',
@@ -92,7 +81,7 @@ class gsea {
 		]
 
 		const geneSet = {
-			label: 'Gene set group',
+			label: 'Gene Set Group',
 			type: 'dropdown',
 			chartType: 'gsea',
 			settingsKey: 'pathway',
@@ -104,9 +93,23 @@ class gsea {
 				{ label: 'CC: subset of GO', value: 'CC: subset of GO' },
 				{ label: 'WikiPathways subset of CP', value: 'WikiPathways subset of CP' },
 				{ label: 'REACTOME subset of CP', value: 'REACTOME subset of CP' },
+				/* QUICK FIX
+				geneset name ending in "--blitzgsea" signals to use built-in genesets but not msigdb
+				later a proper fix is to add a radio toggle of Blitzgsea versus MSigDB, and do not use such hardcode
+				*/
 				{ label: 'H: hallmark gene sets', value: 'H: hallmark gene sets' }
 			]
 		}
+
+		// Now blitzgsea geneSets are inside serverconfig flag
+		if (JSON.parse(sessionStorage.getItem('optionalFeatures')).gsea_test == true) {
+			geneSet.options.push(
+				{ label: 'REACTOME (blitzgsea)', value: 'REACTOME--blitzgsea' },
+				{ label: 'KEGG (blitzgsea)', value: 'KEGG--blitzgsea' },
+				{ label: 'WikiPathways (blitzgsea)', value: 'WikiPathways--blitzgsea' }
+			)
+		}
+
 		if (!this.settings.pathway) {
 			geneSet.options.unshift({ label: '-', value: '-' })
 			this.settings.pathway = '-'
@@ -122,7 +125,7 @@ class gsea {
 			})
 		}
 		this.components.controls.on('downloadClick.gsea', () => {
-			downloadTable(this.table_rows, this.table_cols)
+			downloadTable(this.gsea_table_rows, this.gsea_table_cols)
 		})
 	}
 	getState(appState) {
@@ -194,6 +197,7 @@ add:
 
 		// Generating the table
 		self.gsea_table_rows = []
+		Object.keys(output.data).sort((i, j) => Number(i.fdr) - Number(j.fdr)) // Sorting pathways in ascending order of FDR
 		for (const pathway_name of Object.keys(output.data)) {
 			const pathway = output.data[pathway_name]
 			if (
@@ -241,8 +245,19 @@ add:
 
 		self.dom.tableDiv.selectAll('*').remove()
 		const d_gsea = self.dom.tableDiv.append('div')
+		// table columns showing analysis results for each gene set
+		self.gsea_table_cols = [
+			{ label: 'Geneset' },
+			{ label: 'Enrichment Score' },
+			{ label: 'Normalized Enrichment Score' },
+			{ label: 'Geneset Size' },
+			{ label: 'P value' },
+			{ label: 'Sidak' },
+			{ label: 'FDR' },
+			{ label: 'Leading Edge' }
+		]
 		renderTable({
-			columns: gsea_table_cols,
+			columns: self.gsea_table_cols,
 			rows: self.gsea_table_rows,
 			div: d_gsea,
 			showLines: true,