Merge branch 'master' into topgene_bgzip

CHANGELOG.md

@@ -4,8 +4,15 @@ All notable changes to this project will be documented in this file.
 
 ## Unreleased
 
+Features:
+- GDC cohort-MAF tool: allow to customize output file columns
+- Clicking matrix cell to show similar info table as hovering over the matrix cell.
+- Mds3 track uses simpler radio buttons to toggle between view modes such as lollipop and occurrence
+
 Fixes:
 - Gene exp clustering will display an alert msg to inform user that a map is not doable when there is just one gene
+- display total number of mutations on disco plot
+- Fix oncomatrix error: adding dictionary term from row group menu
 
 
 ## 2.38.1

client/dom/numericAxis.js

@@ -1,5 +1,4 @@
 import { keyupEnter } from '#src/client'
-//import {make_radios} from './radiobuttons.js'
 
 /*
 configure numeric axis

client/dom/radiobutton.js

@@ -17,10 +17,12 @@
 .inputName
 	common Name of <input>, use random number if not given
 */
+
+let nameSuffix = 0
+
 export function make_radios(arg) {
 	const { holder, options, callback, styles } = arg
-	let nameSuffix = 0
-	const inputName = arg.inputName || 'dom-radio-' + nameSuffix++
+	const inputName = arg.inputName || 'pp-dom-radio-' + nameSuffix++
 
 	const divs = holder
 		.selectAll()

client/dom/table2col.js

@@ -1,8 +1,53 @@
+/*
+make a html table of two columns, for showing a list of key-value pairs.
+1st column shows key in gray text, 2nd column shows value in black text, or arbitrary button/svg etc
+as rows are added, as soon as table width exceeds a limit, it auto scrolls
+
+to create new table, do:
+
+	const table = table2col({holder})
+
+when a new row needs to be added, do:
+
+	const [td1,td2] = table.addRow()
+	td1.text('Key')
+	td2.text('Value')
+
+
+arg{}
+	.holder
+	.margin todo
+*/
+export function table2col(arg) {
+	const scrollDiv = arg.holder.append('div').style('max-width', '80vw')
+
+	const table = scrollDiv.append('table').style('margin', '5px 8px').attr('class', 'sja_simpletable')
+	return {
+		scrollDiv,
+		table,
+		addRow: () => {
+			if (table.node().offsetHeight > 500) {
+				scrollDiv
+					.style('height', '450px')
+					.style('resize', 'both')
+					.style('overflow-y', 'scroll')
+					.attr('class', 'sjpp_show_scrollbar')
+			}
+			const tr = table.append('tr')
+			const td1 = tr.append('td').style('padding', '3px').style('color', '#858585')
+			const td2 = tr.append('td')
+			return [td1, td2]
+		}
+	}
+}
+
 /*
 data[ {} ]
 .kvlst[]
 .k
 .v
+
+deprecated, replace with above
 */
 export function make_table_2col(holder, data, overlen) {
 	const color = '#9e9e9e'
@@ -14,44 +59,22 @@ export function make_table_2col(holder, data, overlen) {
 	for (const i of data) {
 		const tr = table.append('tr')
 		if (i.kvlst) {
-			tr.append('td')
-				.attr('rowspan', i.kvlst.length)
-				.style('padding', '3px')
-				.style('color', color)
-				.html(i.k)
-			tr.append('td')
-				.style('padding', '3px')
-				.style('color', color)
-				.html(i.kvlst[0].k)
-			tr.append('td')
-				.style('padding', '3px')
-				.html(i.kvlst[0].v)
+			tr.append('td').attr('rowspan', i.kvlst.length).style('padding', '3px').style('color', color).html(i.k)
+			tr.append('td').style('padding', '3px').style('color', color).html(i.kvlst[0].k)
+			tr.append('td').style('padding', '3px').html(i.kvlst[0].v)
 			for (let j = 1; j < i.kvlst.length; j++) {
 				const tr2 = table.append('tr')
-				tr2
-					.append('td')
-					.style('padding', '3px')
-					.style('color', color)
-					.html(i.kvlst[j].k)
-				tr2
-					.append('td')
-					.style('padding', '3px')
-					.html(i.kvlst[j].v)
+				tr2.append('td').style('padding', '3px').style('color', color).html(i.kvlst[j].k)
+				tr2.append('td').style('padding', '3px').html(i.kvlst[j].v)
 			}
 		} else {
-			tr.append('td')
-				.attr('colspan', 2)
-				.style('padding', '3px')
-				.style('color', color)
-				.html(i.k)
+			tr.append('td').attr('colspan', 2).style('padding', '3px').style('color', color).html(i.k)
 			const td = tr.append('td').style('padding', '3px')
 			if (overlen && i.v.length > overlen) {
 				td.html(i.v.substr(0, overlen - 3) + ' ...&raquo;')
 					.attr('class', 'sja_clbtext')
 					.on('click', () => {
-						td.html(i.v)
-							.classed('sja_clbtext', false)
-							.on('click', null)
+						td.html(i.v).classed('sja_clbtext', false).on('click', null)
 					})
 			} else {
 				td.html(i.v)

client/mass/app.js

@@ -126,7 +126,7 @@ class MassApp {
 		const newPlots = {}
 		let sandbox
 		for (const plot of this.state.plots) {
-			if (!(plot.id in this.components.plots)) {
+			if (this.components.plots && !(plot.id in this.components.plots)) {
 				sandbox = newSandboxDiv(this.dom.plotDiv, {
 					close: () => {
 						this.api.dispatch({

client/mass/test/barchart.integration.spec.js

@@ -8,10 +8,13 @@ const vocabData = require('../../termdb/test/vocabData')
 const hideCategory = require('../../plots/barchart.events.js').hideCategory
 
 /*
+TODO cover all combinations
+
 Tests:
-	single barchart, categorical bars
-	single chart, with overlay
-	multiple charts
+	term1=categorical
+	term1=categorical, term2=defaultbins
+	term0=defaultbins, term1=categorical
+	term1=geneVariant
 	series visibility - q.hiddenValue
 	series visibility - numeric
 	series visibility - condition
@@ -55,7 +58,7 @@ tape('\n', function (test) {
 	test.end()
 })
 
-tape('single barchart, categorical bars', function (test) {
+tape('term1=categorical', function (test) {
 	test.timeoutAfter(3000)
 
 	runpp({
@@ -101,26 +104,16 @@ tape('single barchart, categorical bars', function (test) {
 	}
 })
 
-tape('single chart, with overlay', function (test) {
+tape('term1=categorical, term2=defaultbins', function (test) {
 	test.timeoutAfter(5000)
 	test.plan(4)
-	const termfilter = { filter: [] }
 	runpp({
 		state: {
-			termfilter,
 			plots: [
 				{
 					chartType: 'barchart',
 					term: { id: 'diaggrp' },
-					term2: { id: 'agedx' },
-					settings: {
-						controls: {
-							term2: { id: 'agedx', term: termjson['agedx'] }
-						},
-						barchart: {
-							overlay: 'tree'
-						}
-					}
+					term2: { id: 'agedx' }
 				}
 			]
 		},
@@ -217,23 +210,15 @@ tape('single chart, with overlay', function (test) {
 	}
 })
 
-tape('multiple charts', function (test) {
+tape('term0=defaultbins, term1=categorical', function (test) {
 	test.timeoutAfter(3000)
 	runpp({
 		state: {
 			plots: [
 				{
 					chartType: 'barchart',
 					term: { id: 'diaggrp' },
-					term0: { id: 'agedx' },
-					settings: {
-						barchart: {
-							divideBy: 'tree'
-						},
-						controls: {
-							term0: { id: 'agedx', term: termjson['agedx'] }
-						}
-					}
+					term0: { id: 'agedx' }
 				}
 			]
 		},
@@ -254,6 +239,34 @@ tape('multiple charts', function (test) {
 	}
 })
 
+tape('term1=geneVariant', function (test) {
+	test.timeoutAfter(3000)
+	runpp({
+		state: {
+			plots: [
+				{
+					chartType: 'summary', // cannot use 'barchart', breaks
+					term: { term: { type: 'geneVariant', name: 'TP53' } }
+				}
+			]
+		},
+		barchart: {
+			callbacks: {
+				'postRender.test': testNumCharts
+			}
+		}
+	})
+
+	let barDiv
+	function testNumCharts(barchart) {
+		barDiv = barchart.Inner.dom.barDiv
+		const numCharts = barDiv.selectAll('.pp-sbar-div').size()
+		test.true(numCharts > 2, 'should have more than 2 charts by TP53')
+		if (test._ok) barchart.Inner.app.destroy()
+		test.end()
+	}
+})
+
 tape('series visibility - q.hiddenValues', function (test) {
 	test.timeoutAfter(5000)
 	test.plan(2)