@sjcrh/proteinpaint-client 2.84.0 → 2.85.0

package/dist/{2dmaf-REVT2VT3.js → 2dmaf-INIPPZFM.js}

@@ -10,18 +10,19 @@ import {
   newpane3,
   sayerror,
   to_svg
-} from "./chunk-WTVD5AS2.js";
+} from "./chunk-QQESBFZD.js";
 import {
   Menu
 } from "./chunk-7YY2KB6H.js";
 import {
   make_table_2col
 } from "./chunk-2BM5YZ6X.js";
-import "./chunk-5TRXIQ5D.js";
+import "./chunk-VX3F7KVD.js";
 import {
   mclass,
   mclassnonstandard
-} from "./chunk-EHM2BRQX.js";
+} from "./chunk-HWETBYER.js";
+import "./chunk-BU73IBJJ.js";
 import {
   Symbol,
   axisBottom,
@@ -1400,4 +1401,4 @@ export {
   d2mafparseinput,
   d2mafui
 };
-//# sourceMappingURL=2dmaf-REVT2VT3.js.map
+//# sourceMappingURL=2dmaf-INIPPZFM.js.map

package/dist/{2dmaf-REVT2VT3.js.map → 2dmaf-INIPPZFM.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../src/2dmaf.anchors.js", "../src/2dmaf.js"],
   "sourcesContent": ["import { select as d3select } from 'd3-selection'\nimport * as client from './client'\n\nexport default class Anchors {\n\tconstructor(opts) {\n\t\tthis.opts = opts\n\t\tthis.anchorType = opts.anchorType\n\t\tthis.shareheight = opts.shareheight\n\t\tthis.sharewidth = opts.sharewidth\n\t\tconst x = 'x' in opts ? opts.x : 0\n\t\tconst y = 'y' in opts ? opts.y : 0\n\t\tthis.settings = {\n\t\t\tvisible: true,\n\t\t\topacity: 0.3,\n\t\t\tx: x,\n\t\t\ty: y,\n\t\t\txOffset: opts.axiswidth + opts.sp + opts.sample2height,\n\t\t\tyOffset: opts.shareheight,\n\t\t\tcurrX: opts.axiswidth + opts.sp + opts.sample2height + x,\n\t\t\tcurrY: opts.shareheight - y,\n\t\t\tstrokeWidth: 'strokeWidth' in opts ? opts.strokeWidth : 5,\n\t\t\tstroke: 'stroke' in opts ? opts.stroke : 'red',\n\t\t\txarmlen: 'xarmlen' in opts ? opts.xarmlen : 25\n\t\t}\n\t\tthis.addControls(this.anchorType ? null : this.opts.headerdiv)\n\t}\n\n\tsetWrapper(g) {\n\t\tthis.opts.wrapper = g\n\t}\n\n\taddControls(headerdiv = null) {\n\t\tif (headerdiv) {\n\t\t\tconst anchorbtn = headerdiv\n\t\t\t\t.append('button')\n\t\t\t\t.text('Anchors')\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tthis.anchormenu.showunder(event.target)\n\t\t\t\t\tthis.xInput.property('value', (this.settings.x / this.sharewidth).toFixed(2))\n\t\t\t\t\tthis.yInput.property('value', (this.settings.y / this.sharewidth).toFixed(2))\n\t\t\t\t})\n\t\t}\n\n\t\tthis.anchormenu = new client.Menu({ border: 'solid 1px black' })\n\t\tthis.anchormenu.d.style('text-align', 'center')\n\t\tthis.addCoordInput()\n\t\tthis.addColorInput()\n\t\tthis.addOpacityInput()\n\t\tif (!this.anchorType) this.addSubmitBtns()\n\t\telse this.addDeleteBtn()\n\t}\n\n\taddColorInput() {\n\t\tconst div = this.anchormenu.d.append('div')\n\t\tdiv.append('label').html('Color:&nbsp;')\n\t\tthis.strokeInput = div.append('input')\n\t\tthis.strokeInput\n\t\t\t.attr('this.anchorType', 'text')\n\t\t\t.property('value', this.settings.stroke)\n\t\t\t.style('width', '50px')\n\t}\n\n\taddOpacityInput() {\n\t\tconst div = this.anchormenu.d.append('div')\n\t\tdiv.append('label').html('Opacity:&nbsp;')\n\t\tthis.opacityInput = div.append('input')\n\t\tthis.opacityInput\n\t\t\t.attr('this.anchorType', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 1)\n\t\t\t.attr('step', 0.01)\n\t\t\t.property('value', this.settings.opacity)\n\t\t\t.style('width', '50px')\n\t}\n\n\taddSubmitBtns() {\n\t\tif (this.anchorType) return\n\t\tconst div = this.anchormenu.d.append('div')\n\t\tdiv.append('label').html('Add Anchor: ')\n\t\tdiv\n\t\t\t.append('button')\n\t\t\t.html('R')\n\t\t\t.on('click', () => {\n\t\t\t\tnew SyncedAnchors(this.getSettings('r'))\n\t\t\t\tthis.anchormenu.hide()\n\t\t\t})\n\t\tdiv\n\t\t\t.append('button')\n\t\t\t.html('D')\n\t\t\t.on('click', () => {\n\t\t\t\tnew SyncedAnchors(this.getSettings('d'))\n\t\t\t\tthis.anchormenu.hide()\n\t\t\t})\n\t\tdiv\n\t\t\t.append('button')\n\t\t\t.html('X')\n\t\t\t.on('click', () => {\n\t\t\t\tnew SyncedAnchors(this.getSettings('x'))\n\t\t\t\tthis.anchormenu.hide()\n\t\t\t})\n\t\tdiv\n\t\t\t.append('button')\n\t\t\t.html('synced')\n\t\t\t.on('click', () => {\n\t\t\t\tnew SyncedAnchors(this.getSettings('synced'))\n\t\t\t\tthis.anchormenu.hide()\n\t\t\t})\n\t}\n\n\tgetSettings(anchorType) {\n\t\treturn Object.assign({}, this.opts, {\n\t\t\tanchorType: anchorType,\n\t\t\topacity: this.opacityInput.property('value'),\n\t\t\tx: this.xInput.property('value') * this.sharewidth,\n\t\t\ty: this.yInput.property('value') * this.shareheight,\n\t\t\tstroke: this.strokeInput.property('value')\n\t\t})\n\t}\n\n\taddCoordInput() {\n\t\tconst xdiv = this.anchormenu.d.append('div')\n\t\txdiv.append('label').html('X:&nbsp;')\n\t\tthis.xInput = xdiv.append('input')\n\t\tthis.xInput\n\t\t\t.attr('this.anchorType', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 1)\n\t\t\t.attr('step', 0.01)\n\t\t\t.property('value', 0)\n\t\t\t.style('width', '80px')\n\n\t\tconst ydiv = this.anchormenu.d.append('div')\n\t\tydiv.append('label').html('Y:&nbsp;')\n\t\tthis.yInput = ydiv.append('input')\n\t\tthis.yInput\n\t\t\t.attr('this.anchorType', 'number')\n\t\t\t.attr('min', 0)\n\t\t\t.attr('max', 1)\n\t\t\t.attr('step', 0.01)\n\t\t\t.property('value', 0)\n\t\t\t.style('width', '80px')\n\t}\n\n\taddDeleteBtn() {\n\t\tif (!this.anchorType) return\n\t\tconst div = this.anchormenu.d.append('div')\n\t\tdiv\n\t\t\t.append('button')\n\t\t\t.html('Delete')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.g_anchor.remove()\n\t\t\t\tthis.anchormenu.hide()\n\t\t\t})\n\t}\n}\n\nclass SyncedAnchors extends Anchors {\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.render()\n\n\t\tthis.strokeInput.on('change', () => {\n\t\t\tthis.settings.stroke = this.strokeInput.property('value')\n\t\t\tthis.g_anchor.style('stroke', this.settings.stroke)\n\t\t\tthis.anchormenu.hide()\n\t\t})\n\n\t\tthis.opacityInput.on('change', () => {\n\t\t\tthis.settings.opacity = input.property('value')\n\t\t\tthis.g_anchor.style('opacity', this.settings.opacity)\n\t\t\tthis.anchormenu.hide()\n\t\t})\n\n\t\tthis.xInput.on('change', () => {\n\t\t\tthis.settings.x = +this.xInput.property('value') * this.sharewidth\n\t\t\tthis.settings.currX = this.settings.x + this.settings.xOffset\n\t\t\tif (this.d_anchor) {\n\t\t\t\tthis.d_anchor\n\t\t\t\t\t.transition()\n\t\t\t\t\t.duration(1000)\n\t\t\t\t\t.attr('x1', this.settings.currX)\n\t\t\t\t\t.attr('x2', this.settings.currX)\n\t\t\t}\n\t\t\tif (this.x_anchor) {\n\t\t\t\tthis.x_anchor\n\t\t\t\t\t.transition()\n\t\t\t\t\t.duration(1000)\n\t\t\t\t\t.attr('transform', 'translate(' + this.settings.currX + ',' + this.settings.currY + ')')\n\t\t\t}\n\t\t\tthis.anchormenu.hide()\n\t\t})\n\n\t\tthis.yInput.on('change', () => {\n\t\t\tthis.settings.y = +this.yInput.property('value') * this.shareheight\n\t\t\tthis.settings.currY = -this.settings.y + this.settings.yOffset\n\t\t\tif (this.r_anchor) {\n\t\t\t\tthis.r_anchor\n\t\t\t\t\t.transition()\n\t\t\t\t\t.duration(1000)\n\t\t\t\t\t.attr('y1', this.settings.currY)\n\t\t\t\t\t.attr('y2', this.settings.currY)\n\t\t\t}\n\t\t\tif (this.x_anchor) {\n\t\t\t\tthis.x_anchor\n\t\t\t\t\t.transition()\n\t\t\t\t\t.duration(1000)\n\t\t\t\t\t.attr('transform', 'translate(' + this.settings.currX + ',' + this.settings.currY + ')')\n\t\t\t}\n\t\t\tthis.anchormenu.hide()\n\t\t})\n\t}\n\n\trender() {\n\t\tthis.g_anchor = this.opts.wrapper\n\t\t\t.append('g')\n\t\t\t.style('stroke', this.settings.stroke)\n\t\t\t.style('opacity', this.settings.opacity)\n\t\t\t.style('display', this.settings.visible ? '' : 'none')\n\t\t\t.style('stroke-width', this.settings.strokeWidth)\n\t\t\t.on(\n\t\t\t\t'click',\n\t\t\t\tthis.anchorType == 'synced'\n\t\t\t\t\t? null\n\t\t\t\t\t: event => {\n\t\t\t\t\t\t\tthis.anchormenu.showunder(event.target)\n\t\t\t\t\t  }\n\t\t\t)\n\n\t\tthis.renderD()\n\t\tthis.renderR()\n\t\tthis.renderX()\n\t}\n\n\trenderD() {\n\t\tif (!['synced', 'd'].includes(this.anchorType)) return\n\t\tthis.d_anchor = this.g_anchor.append('line')\n\t\tconst o = this.opts\n\t\tthis.updateD(o.shareheight + o.sp2, o.shareheight + o.sample1height)\n\t}\n\n\tupdateD(y1, y2) {\n\t\tif (!['synced', 'd'].includes(this.anchorType)) return\n\t\tthis.settings.D = { y1, y2 }\n\t\tthis.d_anchor\n\t\t\t.attr('x1', this.settings.currX)\n\t\t\t.attr('x2', this.settings.currX)\n\t\t\t.attr('y1', y1)\n\t\t\t.attr('y2', y2)\n\t}\n\n\trenderR() {\n\t\tif (!['synced', 'r'].includes(this.anchorType)) return\n\t\tthis.r_anchor = this.g_anchor.append('line')\n\t\tconst o = this.opts\n\t\tthis.updateR(o.axiswidth + o.sp, o.sample2height + o.sp)\n\t}\n\n\tupdateR(x1, x2) {\n\t\tif (!['synced', 'r'].includes(this.anchorType)) return\n\t\tthis.settings.R = { x1, x2 }\n\t\tthis.r_anchor\n\t\t\t.attr('x1', x1)\n\t\t\t.attr('x2', x2)\n\t\t\t.attr('y1', this.settings.currY)\n\t\t\t.attr('y2', this.settings.currY)\n\t}\n\n\trenderX() {\n\t\tif (!['synced', 'x'].includes(this.anchorType)) return\n\t\tthis.x_anchor = this.g_anchor\n\t\t\t.append('g')\n\t\t\t.attr('transform', 'translate(' + this.settings.currX + ',' + this.settings.currY + ')')\n\t\tthis.bindXDrag()\n\n\t\t// create background for better mousemove capture\n\t\tthis.x_anchor\n\t\t\t.append('circle')\n\t\t\t.attr('cx', 0) //this.settings.xarmlen)\n\t\t\t.attr('cy', 0) //this.settings.xarmlen)\n\t\t\t.attr('r', this.settings.xarmlen)\n\t\t\t.style('opacity', 0)\n\n\t\t// make an +\n\t\tthis.x_anchor\n\t\t\t.append('line')\n\t\t\t.attr('x1', -this.settings.xarmlen)\n\t\t\t.attr('x2', this.settings.xarmlen)\n\t\t\t.attr('y1', 0)\n\t\t\t.attr('y2', 0)\n\n\t\tthis.x_anchor\n\t\t\t.append('line')\n\t\t\t.attr('x1', 0)\n\t\t\t.attr('x2', 0)\n\t\t\t.attr('y1', this.settings.xarmlen)\n\t\t\t.attr('y2', -this.settings.xarmlen)\n\t}\n\n\tbindXDrag() {\n\t\tif (!['synced'].includes(this.anchorType)) return\n\t\tthis.x_anchor.on('mousedown', event => {\n\t\t\tconst x = event.clientX\n\t\t\tconst y = event.clientY\n\t\t\tlet _x = this.settings.currX,\n\t\t\t\t_y = this.settings.currY\n\n\t\t\tthis.x_anchor\n\t\t\t\t.on('mousemove', event => {\n\t\t\t\t\t_x = this.settings.currX - x + event.clientX\n\t\t\t\t\t_y = this.settings.currY - y + event.clientY\n\t\t\t\t\tthis.r_anchor.attr('y1', _y).attr('y2', _y)\n\t\t\t\t\tthis.d_anchor.attr('x1', _x).attr('x2', _x)\n\t\t\t\t\tthis.x_anchor.attr('transform', 'translate(' + _x + ',' + _y + ')')\n\t\t\t\t})\n\t\t\t\t.on('mouseup', event => {\n\t\t\t\t\tthis.x_anchor.on('mousemove', null)\n\t\t\t\t\t_x = this.settings.currX - x + event.clientX\n\t\t\t\t\t_y = this.settings.currY - y + event.clientY\n\t\t\t\t\tif (_x == this.settings.currX && _y == this.settings.currY) {\n\t\t\t\t\t\tthis.g_anchor.remove()\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\n\t\t\t\t\tthis.settings.x = _x < this.settings.xOffset ? 0 : _x - this.settings.xOffset\n\t\t\t\t\tthis.settings.y = _y > this.settings.yOffset ? 0 : -(_y - this.settings.yOffset)\n\t\t\t\t\tthis.settings.currX = this.settings.x + this.settings.xOffset\n\t\t\t\t\tthis.settings.currY = -this.settings.y + this.settings.yOffset\n\n\t\t\t\t\tthis.r_anchor\n\t\t\t\t\t\t.transition()\n\t\t\t\t\t\t.duration(100)\n\t\t\t\t\t\t.attr('y1', this.settings.currY)\n\t\t\t\t\t\t.attr('y2', this.settings.currY)\n\t\t\t\t\tthis.d_anchor\n\t\t\t\t\t\t.transition()\n\t\t\t\t\t\t.duration(100)\n\t\t\t\t\t\t.attr('x1', this.settings.currX)\n\t\t\t\t\t\t.attr('x2', this.settings.currX)\n\t\t\t\t\tthis.x_anchor\n\t\t\t\t\t\t.transition()\n\t\t\t\t\t\t.duration(100)\n\t\t\t\t\t\t.attr('transform', 'translate(' + this.settings.currX + ',' + this.settings.currY + ')')\n\t\t\t\t})\n\t\t\t\t.on('mouseleave', () => {\n\t\t\t\t\tthis.x_anchor.on('mousemove', null)\n\t\t\t\t})\n\t\t})\n\t}\n}\n", "import { select as d3select } from 'd3-selection'\nimport * as client from './client'\nimport { scaleLinear } from 'd3-scale'\nimport { axisLeft, axisTop, axisBottom } from 'd3-axis'\nimport { format as d3format } from 'd3-format'\nimport {\n\tsymbol,\n\tsymbolCircle,\n\tsymbolCross,\n\tsymbolDiamond,\n\tsymbolSquare,\n\tsymbolStar,\n\tsymbolTriangle,\n\tsymbolWye\n} from 'd3-shape'\nimport * as common from '#shared/common.js'\nimport Anchors from './2dmaf.anchors'\nimport { renderSandboxFormDiv } from '../dom/sandbox.ts'\n\n/*\ninput file/data is 2dmaf format of 1 pair or multiple pairs\n\nmake a 2dmaf plot for each pair\n\n*/\n\nconst color1 = '#f9766c'\nconst color2 = '#609cff'\nconst colorshare = '#01b937'\nconst symbols = {\n\tcircle: symbolCircle,\n\tcross: symbolCross,\n\tdiamond: symbolDiamond,\n\tsquare: symbolSquare,\n\tstar: symbolStar,\n\ttriangle: symbolTriangle,\n\twye: symbolWye\n}\n// for selecting what tagName to use when appending\n// needed for now until the issue with selection.append([function]) is figured out\nconst symbolFilters = {\n\tpath: d => d.symbol,\n\tcircle: d => !d.symbol\n}\nconst sharedFilters = {\n\tpath: d => d.symbol,\n\tellipse: d => !d.symbol\n}\n\nexport function d2mafui(genomes, holder) {\n\tlet pane, inputdiv, gselect, filediv, saydiv, visualdiv\n\tif (holder !== undefined) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes)\n\telse {\n\t\t;[pane, inputdiv, gselect, filediv, saydiv, visualdiv] = client.newpane3(100, 100, genomes)\n\t\tpane.header.text('2DMAF: mutant allele fraction plot between a pair of samples')\n\t\tpane.body.style('margin', '10px')\n\t}\n\tinputdiv\n\t\t.append('div')\n\t\t.style('margin-top', '20px')\n\t\t.html(\n\t\t\t'<ul>' +\n\t\t\t\t'<li><a href=\"https://docs.google.com/document/d/1anyEDMcW1lTSf8399Li2G9r57V-Fqp2591WvoODY7n4/edit#heading=h.mne2ecmp9m13\" target=_blank>File format</a></li>' +\n\t\t\t\t'<li>To define samples differently than \"Diagnosis/Relapse\", <a href=https://plus.google.com/+XinZhou_s/posts/WqBVvmd3wYR target=_blank>see how</a>.</li>' +\n\t\t\t\t'</ul>'\n\t\t)\n\tinputdiv\n\t\t.append('p')\n\t\t.html('<a href=https://proteinpaint.stjude.org/ppdemo/hg19/2dmaf/2dmaf.txt target=_blank>Example file</a>')\n\tfunction cmt(t, red) {\n\t\tsaydiv.style('color', red ? 'red' : 'black').html(t)\n\t}\n\tconst fileui = () => {\n\t\tfilediv.selectAll('*').remove()\n\t\tconst input = filediv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'file')\n\t\t\t.on('change', event => {\n\t\t\t\tconst file = event.target.files[0]\n\t\t\t\tif (!file) {\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (!file.size) {\n\t\t\t\t\tcmt('Invalid file ' + file.name)\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst reader = new FileReader()\n\t\t\t\treader.onload = event => {\n\t\t\t\t\tconst usegenome = gselect.options[gselect.selectedIndex].innerHTML\n\t\t\t\t\tconst err = parseraw(event.target.result.trim().split(/\\r?\\n/), genomes[usegenome], file.name, visualdiv)\n\t\t\t\t\tif (err) {\n\t\t\t\t\t\tcmt(err, 1)\n\t\t\t\t\t\tfileui()\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\t// success\n\t\t\t\t\tinputdiv.remove()\n\t\t\t\t\tfilediv.remove()\n\t\t\t\t\tsaydiv.remove()\n\t\t\t\t}\n\t\t\t\treader.onerror = function () {\n\t\t\t\t\tcmt('Error reading file ' + file.name, 1)\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\treader.readAsText(file, 'utf8')\n\t\t\t})\n\n\t\tsetTimeout(() => input.node().focus(), 1100)\n\t}\n\tfileui()\n}\n\nexport function d2mafparseinput(obj, holder) {\n\t/*\n\tobj\n\t.genome\n\t.hostURL\n\t.datasetname\n\t.input TEXt\n\t*/\n\tif (!obj.genome) {\n\t\tclient.sayerror(holder, '.genome missing for 2dmaf')\n\t\treturn\n\t}\n\tif (!obj.input) {\n\t\tclient.sayerror(holder, '.input missing for 2dmaf')\n\t\treturn\n\t}\n\tconst err = parseraw(obj.input.trim().split(/\\r?\\n/), obj.genome, obj.datasetname || 'unnamed dataset', holder)\n\tif (err) {\n\t\tclient.sayerror(holder, '2DMAF data error: ' + err)\n\t}\n}\n\nfunction parseraw(lines, genome, filename, holder) {\n\tconst [headererror, header, headerattrlst] = parseheader(lines[0].trim())\n\tif (headererror) {\n\t\treturn headererror\n\t}\n\n\tconst pairs = {}\n\t// key: pair name, val: {}\n\n\tconst g2mlst = {} // for dataset\n\n\tconst peoplehash = {}\n\n\tconst genehash = {}\n\n\tconst flag = {\n\t\tgood: 0,\n\t\tpurity1set: false,\n\t\tpurity2set: false,\n\t\tpairsetname: {}\n\t}\n\tconst badlines = []\n\n\tconst mclasslabel2key = {}\n\tfor (const k in common.mclass) {\n\t\tmclasslabel2key[common.mclass[k].label.toUpperCase()] = k\n\t}\n\n\tfor (let i = 1; i < lines.length; i++) {\n\t\tif (lines[i] == '') continue\n\t\tif (lines[i][0] == '#') {\n\t\t\tif (lines[i].startsWith('##samplename')) {\n\t\t\t\tconst l = lines[i].trim().split(/[\\s\\t]+/)\n\t\t\t\tif (l.length == 4) {\n\t\t\t\t\tflag.pairsetname[l[1]] = { 1: l[2], 2: l[3] }\n\t\t\t\t} else {\n\t\t\t\t\treturn 'Line ' + (i + 1) + ': invalid samplename line: must be \"##samplename [patient] [sample1] [sample2]\"'\n\t\t\t\t}\n\t\t\t}\n\t\t\tcontinue\n\t\t}\n\t\tconst lst = lines[i].trim().split('\\t')\n\t\tconst m = {}\n\t\tfor (let j = 0; j < header.length; j++) {\n\t\t\tif (lst[j] != undefined && lst[j] != '') {\n\t\t\t\tm[header[j]] = lst[j]\n\t\t\t}\n\t\t}\n\t\tif (!m.sample) {\n\t\t\treturn 'Line ' + (i + 1) + ': missing sample'\n\t\t}\n\t\tif (m.chr) {\n\t\t\tif (m.chr.indexOf('chr') != 0) {\n\t\t\t\tm.chr = 'chr' + m.chr\n\t\t\t}\n\t\t}\n\t\tif (m.chrstart) {\n\t\t\tm.chrstart = Number.parseInt(m.chrstart)\n\t\t\tif (Number.isNaN(m.chrstart)) {\n\t\t\t\treturn 'Line ' + (i + 1) + ': invalid chromosome position'\n\t\t\t}\n\t\t}\n\t\tif (m.Dcnvloh) {\n\t\t\tm.Dcnvlohraw = m.Dcnvloh\n\t\t\tconst s = m.Dcnvloh.toLowerCase()\n\t\t\tif (s == 'yes' || (s != 'diploid' && s != 'haploid')) {\n\t\t\t\tm.Dcnvloh = true\n\t\t\t} else {\n\t\t\t\tm.Dcnvloh = false\n\t\t\t}\n\t\t}\n\t\tif (m.Rcnvloh) {\n\t\t\tm.Rcnvlohraw = m.Rcnvloh\n\t\t\tconst s = m.Rcnvloh.toLowerCase()\n\t\t\tif (s == 'yes' || (s != 'diploid' && s != 'haploid')) {\n\t\t\t\tm.Rcnvloh = true\n\t\t\t} else {\n\t\t\t\tm.Rcnvloh = false\n\t\t\t}\n\t\t}\n\t\t// set\n\t\tif (!m.call_d) {\n\t\t\tbadlines.push([i, 'missing call_d', lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (m.call_d != 'somatic' && m.call_d != 'wildtype') {\n\t\t\tbadlines.push([i, 'call_d is neither somatic nor wildtype', lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (!m.call_r) {\n\t\t\tbadlines.push([i, 'missing call_r', lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (m.call_r != 'somatic' && m.call_r != 'wildtype') {\n\t\t\tbadlines.push([i, 'call_r is neither somatic nor wildtype', lst])\n\t\t\tcontinue\n\t\t}\n\t\tif (m.call_d == 'somatic') {\n\t\t\tif (m.call_r == 'somatic') {\n\t\t\t\tm.set_share = true\n\t\t\t} else {\n\t\t\t\tm.set_1 = true\n\t\t\t}\n\t\t} else {\n\t\t\tif (m.call_r == 'somatic') {\n\t\t\t\tm.set_2 = true\n\t\t\t}\n\t\t}\n\t\t// type\n\t\tif (!m.type) {\n\t\t\tbadlines.push([i, 'missing type', lst])\n\t\t\tcontinue\n\t\t}\n\t\tconst s = m.type.toLowerCase()\n\t\tif (s == 'snv' || s == 'snp' || s == 'mnv' || s == 'complex') {\n\t\t\tm.issnv = true\n\t\t} else if (s == 'indel' || s == 'ins' || s == 'del') {\n\t\t\tm.isindel = true\n\t\t} else {\n\t\t\tbadlines.push([i, 'type must be either SNV or INDEL', lst])\n\t\t\tcontinue\n\t\t}\n\t\t// numbers\n\n\t\t// required: MinD.D TinD.D\n\t\tlet key = 'MinD.D'\n\t\tlet a = Number.parseInt(m[key])\n\t\tif (Number.isNaN(a) || a < 0) {\n\t\t\tbadlines.push([i, 'invalid ' + key + ' value', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm[key] = a\n\n\t\tkey = 'TinD.D'\n\t\ta = Number.parseInt(m[key])\n\t\tif (Number.isNaN(a) || a < 0) {\n\t\t\tbadlines.push([i, 'invalid ' + key + ' value', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm[key] = a\n\n\t\tif (m['TinD.D'] < m['MinD.D']) {\n\t\t\tbadlines.push([i, 'TinD.D value lower than MinD.D', lst])\n\t\t\tcontinue\n\t\t}\n\n\t\t// optional\n\t\tkey = 'MinN.D'\n\t\tif (key in m) {\n\t\t\ta = Number.parseInt(m[key])\n\t\t\tif (Number.isNaN(a) || a < 0) {\n\t\t\t\tdelete m[key]\n\t\t\t} else {\n\t\t\t\tm[key] = a\n\t\t\t}\n\t\t}\n\t\tkey = 'TinN.D'\n\t\tif (key in m) {\n\t\t\ta = Number.parseInt(m[key])\n\t\t\tif (Number.isNaN(a) || a < 0) {\n\t\t\t\tdelete m[key]\n\t\t\t} else {\n\t\t\t\tm[key] = a\n\t\t\t}\n\t\t}\n\n\t\t// required: MinD.R, TinD.R\n\t\tkey = 'MinD.R'\n\t\ta = Number.parseInt(m[key])\n\t\tif (Number.isNaN(a) || a < 0) {\n\t\t\tbadlines.push([i, 'invalid ' + key + ' value', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm[key] = a\n\t\tkey = 'TinD.R'\n\t\ta = Number.parseInt(m[key])\n\t\tif (Number.isNaN(a) || a < 0) {\n\t\t\tbadlines.push([i, 'invalid ' + key + ' value', lst])\n\t\t\tcontinue\n\t\t}\n\t\tm[key] = a\n\n\t\tif (m['TinD.R'] < m['MinD.R']) {\n\t\t\tbadlines.push([i, 'TinD.R value lower than MinD.R', lst])\n\t\t\tcontinue\n\t\t}\n\n\t\t// optional\n\t\tkey = 'MinN.R'\n\t\tif (key in m) {\n\t\t\ta = Number.parseInt(m[key])\n\t\t\tif (Number.isNaN(a) || a < 0) {\n\t\t\t\tdelete m[key]\n\t\t\t} else {\n\t\t\t\tm[key] = a\n\t\t\t}\n\t\t}\n\t\tkey = 'TinN.R'\n\t\tif (key in m) {\n\t\t\ta = Number.parseInt(m[key])\n\t\t\tif (Number.isNaN(a) || a < 0) {\n\t\t\t\tdelete m[key]\n\t\t\t} else {\n\t\t\t\tm[key] = a\n\t\t\t}\n\t\t}\n\n\t\tif (m.symbol) {\n\t\t\tif (!symbols[m.symbol]) {\n\t\t\t\tbadlines.push([i, \"Invalid symbol value='\" + m.symbol + \"'\", lst])\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\n\t\tif (m.class) {\n\t\t\tconst s = m.class.toUpperCase()\n\t\t\tif (s in mclasslabel2key) {\n\t\t\t\tm.class = mclasslabel2key[s]\n\t\t\t} else {\n\t\t\t\tbadlines.push([i, 'invalid mutation class ' + m.class, lst])\n\t\t\t\tcontinue\n\t\t\t}\n\t\t}\n\t\t// style\n\t\tm.style = {\n\t\t\tfill: m.issnv ? 'white' : 'black',\n\t\t\tfillhl: m.class ? common.mclass[m.class].color : '#ccc',\n\t\t\tstroke: m.chr == 'chrX' ? 'black' : m.issnv ? 'black' : 'none',\n\t\t\tstrokehl: m.class ? common.mclass[m.class].color : 'black',\n\t\t\tfillopacity: m.issnv ? 0 : 0.2,\n\t\t\tstrokeopacity: 0.2\n\t\t}\n\n\t\tif (m['TinD.D'] > 0) {\n\t\t\tm.maf1 = m['MinD.D'] / m['TinD.D']\n\t\t}\n\t\tif (m['TinD.R'] > 0) {\n\t\t\tm.maf2 = m['MinD.R'] / m['TinD.R']\n\t\t}\n\n\t\t// good mutation\n\n\t\tpeoplehash[m.sample] = 1\n\t\tif (m.gene) {\n\t\t\tgenehash[m.gene] = 1\n\t\t}\n\t\tif (!(m.sample in pairs)) {\n\t\t\tpairs[m.sample] = {\n\t\t\t\tname: m.sample,\n\t\t\t\tshown: false,\n\t\t\t\theader: header,\n\t\t\t\tmlst: []\n\t\t\t}\n\t\t}\n\n\t\tconst v = pairs[m.sample]\n\t\tv.mlst.push(m)\n\n\t\t// tumor purity may be present in every line, need to be consistant across entire sample\n\t\tif (m.purity1) {\n\t\t\tlet p = Number.parseFloat(m.purity1)\n\t\t\tif (Number.isNaN(p)) {\n\t\t\t\tbadlines.push([i, 'diagnosis tumor purity should be a number'])\n\t\t\t\tp = 0\n\t\t\t} else {\n\t\t\t\tif (p > 1) {\n\t\t\t\t\tp /= 100\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (p > 0) {\n\t\t\t\t// valid purity\n\t\t\t\tif (v.purity1 == undefined) {\n\t\t\t\t\tv.purity1 = p\n\t\t\t\t\tflag.purity1set = true\n\t\t\t\t} else if (v.purity1 != p) {\n\t\t\t\t\tbadlines.push([\n\t\t\t\t\t\ti,\n\t\t\t\t\t\t'diagnosis tumor purity value ' + p + ' is different from existing value ' + v.purity1 + ' in ' + m.sample,\n\t\t\t\t\t\tlst\n\t\t\t\t\t])\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (m.purity2) {\n\t\t\tlet p = Number.parseFloat(m.purity2)\n\t\t\tif (Number.isNaN(p)) {\n\t\t\t\tbadlines.push([i, 'relapse tumor purity should be a number'])\n\t\t\t\tp = 0\n\t\t\t} else {\n\t\t\t\tif (p > 1) {\n\t\t\t\t\tp /= 100\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (p > 0) {\n\t\t\t\t// valid purity\n\t\t\t\tif (v.purity2 == undefined) {\n\t\t\t\t\tv.purity2 = p\n\t\t\t\t\tflag.purity2set = true\n\t\t\t\t} else if (v.purity2 != p) {\n\t\t\t\t\tbadlines.push([\n\t\t\t\t\t\ti,\n\t\t\t\t\t\t'relapse tumor purity value ' + p + ' is different from existing value ' + v.purity2 + ' in ' + m.sample,\n\t\t\t\t\t\tlst\n\t\t\t\t\t])\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tflag.good++\n\n\t\t/*\n\t\tif(m.gene) {\n\t\t\t// bulkdata register\n\t\t\tvar _gn=m.gene.toUpperCase()\n\t\t\tif(!(_gn in g2mlst)) {\n\t\t\t\tg2mlst[_gn]=[]\n\t\t\t}\n\t\t\tif(m.call_d=='somatic') {\n\t\t\t\tvar m2={}\n\t\t\t\tfor(var k in m) {\n\t\t\t\t\tm2[k]=m[k]\n\t\t\t\t}\n\t\t\t\tm2.sample=m.sample+'.D'\n\t\t\t\tm2.origin='S'\n\t\t\t\tm2.dt=sja.dtsnvindel\n\t\t\t\tm2.maf_diagnosis={v1:m['MinD.D'],v2:m['TinD.D'],f:m.maf1}\n\t\t\t\tif('MinN.D' in m) {\n\t\t\t\t\tm2.maf_diagnosis_normal={v1:m['MinN.D'],v2:m['TinN.D'],f:m['MinN.D']/m['TinN.D']}\n\t\t\t\t}\n\t\t\t\tg2mlst[_gn].push(m2)\n\t\t\t}\n\t\t\tif(m.call_r=='somatic') {\n\t\t\t\tvar m2={}\n\t\t\t\tfor(var k in m) {\n\t\t\t\t\tm2[k]=m[k]\n\t\t\t\t}\n\t\t\t\tm2.sample=m.sample+'.R'\n\t\t\t\tm2.origin='R'\n\t\t\t\tm2.dt=sja.dtsnvindel\n\t\t\t\tm2.maf_relapse={v1:m['MinD.R'],v2:m['TinD.R'],f:m.maf2}\n\t\t\t\tif('MinN.D' in m) {\n\t\t\t\t\tm2.maf_relapse_normal={v1:m['MinN.D'],v2:m['TinN.D'],f:m['MinN.D']/m['TinN.D']}\n\t\t\t\t}\n\t\t\t\tg2mlst[_gn].push(m2)\n\t\t\t}\n\t\t}\n\t\t*/\n\t}\n\t// done iterating\n\tif (badlines.length > 0) {\n\t\tclient.bulk_badline(header, badlines)\n\t}\n\tif (flag.good == 0) {\n\t\treturn 'No valid data.'\n\t}\n\n\t// good data ready\n\tholder.append('p').text('File: ' + filename)\n\n\t/*\n\tno dataset\n\n\t// register in dataset\n\tvar dsname=thisfile.name;\n\tif(dsname in sja.datasets) {\n\t\t// name already used\n\t\tdsname='user: '+dsname;\n\t\tif(dsname in sja.datasets) {\n\t\t\tvar j=1;\n\t\t\tvar n2=dsname+' '+j;\n\t\t\twhile(n2 in sja.datasets) {\n\t\t\t\tj++;\n\t\t\t\tn2=dsname+' '+j;\n\t\t\t}\n\t\t}\n\t}\n\n\tvar s=gselect[0][0]\n\tvar usegenome=s.options[s.selectedIndex].innerHTML\n\tvar hassample=header.indexOf('sample')!=-1\n\tsja.datasets[dsname]={\n\t\tgenome:usegenome,\n\t\tshortlabel:dsname,\n\t\tbulkdata:g2mlst,\n\t\theader:header,\n\t\tmbygmcoord:true,\n\t\tsample_attributes:hparse.atlst,\n\t\thassample:hassample\n\t\t}\n\t*/\n\n\t// people and gene total number\n\tlet peopletotal = 0\n\tfor (const n in peoplehash) peopletotal++\n\tlet genetotal = 0\n\tfor (const n in genehash) genetotal++\n\n\tconst boxh = 16\n\tconst table = holder.append('table')\n\n\tconst tr = table.append('tr')\n\tconst td = tr.append('td').attr('valign', 'top')\n\ttd.append('div').html(\n\t\t'<div style=\"display:inline-block;width:' +\n\t\t\tboxh +\n\t\t\t'px;height:' +\n\t\t\tboxh +\n\t\t\t'px;background-color:' +\n\t\t\tcolor1 +\n\t\t\t'\"></div> Diagnosis only ' +\n\t\t\t'<div style=\"display:inline-block;width:' +\n\t\t\tboxh +\n\t\t\t'px;height:' +\n\t\t\tboxh +\n\t\t\t'px;background-color:' +\n\t\t\tcolorshare +\n\t\t\t'\"></div> Shared ' +\n\t\t\t'<div style=\"display:inline-block;width:' +\n\t\t\tboxh +\n\t\t\t'px;height:' +\n\t\t\tboxh +\n\t\t\t'px;background-color:' +\n\t\t\tcolor2 +\n\t\t\t'\"></div> Relapse only'\n\t)\n\tconst peopleholder = td\n\t\t.append('div')\n\t\t.style('margin-top', '10px')\n\t\t.style('height', '200px')\n\t\t.style('width', '300px')\n\t\t.style('padding', '5px')\n\t\t.style('overflow-y', 'scroll')\n\t\t.style('resize', 'both')\n\t\t.style('border', 'solid 1px #ccc')\n\n\tconst geneholder = td\n\t\t.append('div')\n\t\t.style('margin-top', '10px')\n\t\t.style('height', '200px')\n\t\t.style('width', '300px')\n\t\t.style('padding', '5px')\n\t\t.style('overflow-y', 'scroll')\n\t\t.style('resize', 'both')\n\t\t.style('border', 'solid 1px #ccc')\n\n\tconst showholder = tr.append('td').style('vertical-align', 'top')\n\n\tfor (const n in pairs) {\n\t\tconst ss = flag.pairsetname[n]\n\t\tif (ss) {\n\t\t\tpairs[n].setname = ss\n\t\t} else {\n\t\t\tpairs[n].setname = { 1: 'Diagnosis', 2: 'Relapse' }\n\t\t}\n\t}\n\n\tconst odata = {\n\t\tgenome: genome,\n\t\t//dsname:dsname,\n\t\tpairs: pairs,\n\t\tcolor1: color1,\n\t\tcolor2: color2,\n\t\tcolorshare: colorshare,\n\t\trowh: boxh,\n\t\tpeoplewidth: 150,\n\t\tgenewidth: 150,\n\t\tshowholder: showholder,\n\t\t//peoplelimit:Math.min(20,peopletotal),\n\t\tgenelimit: Math.min(20, genetotal),\n\t\tpurity1set: flag.purity1set,\n\t\tpurity2set: flag.purity2set\n\t}\n\n\td2maf_peopletable(odata, peopleholder)\n\n\t//d2maf_genetable(odata)\n}\n\nfunction parseheader(line) {\n\tconst lower = line.toLowerCase().split('\\t')\n\tconst header = line.split('\\t')\n\tif (header.length <= 1) {\n\t\treturn ['invalid file header']\n\t}\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = lower.indexOf(i)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\n\tlet i = htry('person', 'sample', 'samplename', 'patient')\n\tif (i == -1) return ['sample missing from header']\n\theader[i] = 'sample'\n\n\ti = htry('type')\n\tif (i == -1) return ['type missing from header']\n\theader[i] = 'type'\n\n\ti = htry('mind.d1_g1', 'mind.d', 'mind')\n\tif (i == -1) return ['MinD.D missing from header']\n\theader[i] = 'MinD.D'\n\n\ti = htry('tind.d1_g1', 'tind.d', 'tind')\n\tif (i == -1) return ['TinD.D missing from header']\n\theader[i] = 'TinD.D'\n\n\ti = htry('mind.r1_g1', 'mind.r', 'minr')\n\tif (i == -1) return ['MinD.R missing from header']\n\theader[i] = 'MinD.R'\n\n\ti = htry('tind.r1_g1', 'tind.r', 'tinr')\n\tif (i == -1) return ['TinD.R missing from header']\n\theader[i] = 'TinD.R'\n\n\ti = htry('call_d1_g1', 'call_d')\n\tif (i == -1) return ['call_d missing from header']\n\theader[i] = 'call_d'\n\n\ti = htry('call_r1_g1', 'call_r')\n\tif (i == -1) return ['call_r missing from header']\n\theader[i] = 'call_r'\n\n\ti = htry('genename', 'gene')\n\tif (i == -1) return ['gene missing from header']\n\theader[i] = 'gene'\n\n\ti = htry('amino_acid_change', 'annovar_sj_aachange', 'aachange', 'protein_change')\n\tif (i == -1) return ['amino_acid_change missing from header']\n\theader[i] = 'mname'\n\n\ti = htry('class', 'mclass', 'variant_class', 'variant_classification', 'annovar_sj_class')\n\tif (i == -1) return ['variant_class missing from header']\n\theader[i] = 'class'\n\n\ti = htry('chromosome', 'chr')\n\tif (i == -1) return ['chromosome missing from header']\n\theader[i] = 'chr'\n\n\ti = htry('start', 'start_position', 'wu_hg19_pos', 'chr_position')\n\tif (i == -1) return ['start missing from header']\n\theader[i] = 'chrstart'\n\n\t// optional\n\ti = htry('minn.d1_g1', 'minn.d')\n\tif (i != -1) header[i] = 'MinN.D'\n\ti = htry('tinn.d1_g1', 'tinn.d')\n\tif (i != -1) header[i] = 'TinN.D'\n\ti = htry('minn.r1_g1', 'minn.r')\n\tif (i != -1) header[i] = 'MinN.R'\n\ti = htry('tinn.r1_g1', 'tinn.r')\n\tif (i != -1) header[i] = 'TinN.R'\n\n\ti = htry('mrna_accession', 'refseq_mrna_id', 'annovar_sj_filter_isoform', 'refseq')\n\tif (i != -1) header[i] = 'isoform'\n\ti = htry('primary_purity', 'purity_d')\n\tif (i != -1) header[i] = 'purity1'\n\ti = htry('relapse_purity', 'purity_r')\n\tif (i != -1) header[i] = 'purity2'\n\ti = htry('tag_d_cnvloh', 'cnvloh_d')\n\tif (i != -1) header[i] = 'Dcnvloh'\n\ti = htry('tag_r_cnvloh', 'cnvloh_r')\n\tif (i != -1) header[i] = 'Rcnvloh'\n\n\tconst atlst = []\n\tfor (const j of header) {\n\t\tswitch (j) {\n\t\t\tcase 'Dcnvloh':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'D. CNV/LOH',\n\t\t\t\t\tget: m => m.Dcnvlohraw\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'Rcnvloh':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'R. CNV/LOH',\n\t\t\t\t\tget: m => m.Rcnvlohraw\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'type':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'Type',\n\t\t\t\t\tget: m => m.type\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'chr':\n\t\t\t\tbreak\n\t\t\tcase 'chrstart':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'Genome Loc.',\n\t\t\t\t\tget: m => m.chr + ':' + (m.chrstart + 1)\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'class':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'Class',\n\t\t\t\t\tget: m => {\n\t\t\t\t\t\tif (m.class == common.mclassnonstandard) {\n\t\t\t\t\t\t\treturn m.originalclasslabel ? m.originalclasslabel : common.mclass[m.class].label\n\t\t\t\t\t\t}\n\t\t\t\t\t\treturn common.mclass[m.class].label\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'mname':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'Mutation',\n\t\t\t\t\tget: m => {\n\t\t\t\t\t\tlet s = m.mname\n\t\t\t\t\t\tif (!s) s = m.cdna_change\n\t\t\t\t\t\treturn s\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'MinD.D':\n\t\t\t\tatlst.push({\n\t\t\t\t\tismaf: true,\n\t\t\t\t\twidth: 60,\n\t\t\t\t\theight: 14,\n\t\t\t\t\treadcountcredible: 30,\n\t\t\t\t\tget: m => m.maf_diagnosis,\n\t\t\t\t\tlabel: 'D. tumor MAF',\n\t\t\t\t\tfill: '#F7483B',\n\t\t\t\t\tfillbg: '#FCBAB6'\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'TinD.D':\n\t\t\t\tbreak\n\t\t\tcase 'MinD.R':\n\t\t\t\tatlst.push({\n\t\t\t\t\tismaf: true,\n\t\t\t\t\twidth: 60,\n\t\t\t\t\theight: 14,\n\t\t\t\t\treadcountcredible: 30,\n\t\t\t\t\tget: m => m.maf_relapse,\n\t\t\t\t\tlabel: 'R. tumor MAF',\n\t\t\t\t\tfill: '#146EFF',\n\t\t\t\t\tfillbg: '#B6D5FC'\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'TinD.R':\n\t\t\t\tbreak\n\t\t\tcase 'MinN.D':\n\t\t\t\tatlst.push({\n\t\t\t\t\tismaf: true,\n\t\t\t\t\twidth: 60,\n\t\t\t\t\theight: 14,\n\t\t\t\t\treadcountcredible: 30,\n\t\t\t\t\tget: m => m.maf_diagnosis_normal,\n\t\t\t\t\tlabel: 'D. normal MAF',\n\t\t\t\t\tfill: '#F7483B',\n\t\t\t\t\tfillbg: '#FCBAB6'\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'TinN.D':\n\t\t\t\tbreak\n\t\t\tcase 'MinN.R':\n\t\t\t\tatlst.push({\n\t\t\t\t\tismaf: true,\n\t\t\t\t\twidth: 60,\n\t\t\t\t\theight: 14,\n\t\t\t\t\treadcountcredible: 30,\n\t\t\t\t\tget: m => m.maf_relapse_normal,\n\t\t\t\t\tlabel: 'R. normal MAF',\n\t\t\t\t\tfill: '#146EFF',\n\t\t\t\t\tfillbg: '#B6D5FC'\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'TinN.R':\n\t\t\t\tbreak\n\t\t\tcase 'call_d':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'D. call',\n\t\t\t\t\tget: m => m.call_d\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'call_r':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'R. call',\n\t\t\t\t\tget: m => m.call_r\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'purity1':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'D. purity',\n\t\t\t\t\tget: m => m.purity1\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tcase 'purity2':\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: 'R. purity',\n\t\t\t\t\tget: m => m.purity2\n\t\t\t\t})\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tatlst.push({\n\t\t\t\t\tlabel: j,\n\t\t\t\t\tget: m => m[j]\n\t\t\t\t})\n\t\t}\n\t}\n\treturn [null, header, atlst]\n}\n\nfunction d2maf_render(showholder, pdata) {\n\tconst tooltip = new client.Menu({ border: 'solid 1px black' })\n\n\tconst set_1 = []\n\tconst set_2 = []\n\tconst set_share = []\n\tconst mlst = pdata.mlst\n\tconst person = mlst[0].sample\n\tconst symbolgen = symbol()\n\n\tlet maxtotal = 0\n\tlet bysymbol = {}\n\tconst mclasses = {}\n\tfor (const m of mlst) {\n\t\tif (m['TinD.D'] > 0) {\n\t\t\tmaxtotal = Math.max(maxtotal, m['TinD.D'])\n\t\t}\n\t\tif (m['TinD.R'] > 0) {\n\t\t\tmaxtotal = Math.max(maxtotal, m['TinD.R'])\n\t\t}\n\t\tif (m.set_share) {\n\t\t\tset_share.push(m)\n\t\t} else if (m.set_1) {\n\t\t\tset_1.push(m)\n\t\t} else if (m.set_2) {\n\t\t\tset_2.push(m)\n\t\t}\n\t\tif (!(m.class in mclasses)) {\n\t\t\tmclasses[m.class] = 0\n\t\t}\n\t\tif (m.symbol) {\n\t\t\tif (!bysymbol[m.symbol]) {\n\t\t\t\tbysymbol[m.symbol] = { numlines: 0, label: m.symbollabel, hidden: false }\n\t\t\t}\n\t\t\tbysymbol[m.symbol].numlines++\n\t\t}\n\t\tmclasses[m.class]++\n\t}\n\n\tconst a = Math.min(window.innerWidth, window.innerHeight)\n\n\tconst axiswidth = 50,\n\t\tsharewidth = a * 0.5,\n\t\tshareheight = a * 0.5,\n\t\tsample1height = shareheight / 2,\n\t\tsample2height = sharewidth / 2,\n\t\tsp = axiswidth / 3,\n\t\tsp2 = sample1height / 5,\n\t\tlabelfontsize = Math.min(20, (12 * a) / 500),\n\t\tradius = a / 40,\n\t\tindelboxw = radius * 0.7,\n\t\tr_cnvloh = 3\n\n\tconst radiusscale = scaleLinear()\n\t\t.domain([0, maxtotal])\n\t\t.range([radius / 2, radius])\n\tconst radiustoarea = d => Math.PI * Math.pow(radiusscale(d), 2)\n\n\tfor (const m of mlst) {\n\t\t// for creating dot label upon pushing button\n\t\tm.radius = Math.max(m['TinD.D'] ? radiusscale(m['TinD.D']) : 0, m['TinD.R'] ? radiusscale(m['TinD.R']) : 0)\n\t}\n\n\t// holder\n\tconst outtable = showholder.append('table')\n\tconst tr = outtable.append('tr')\n\tconst tdgraph = tr.append('td').style('vertical-align', 'top')\n\tconst tdgenetable = tr.append('td').style('vertical-align', 'top')\n\ttdgenetable\n\t\t.append('div')\n\t\t.style('margin', '10px')\n\t\t.text('Name: ' + person)\n\n\t// controls\n\tconst headerdiv = tdgraph.append('div')\n\n\theaderdiv\n\t\t.append('button')\n\t\t.text('Hide')\n\t\t.on('click', () => {\n\t\t\tpdata.shown = false\n\t\t\tif (pdata.handle) {\n\t\t\t\tpdata.handle.attr('font-weight', 'normal')\n\t\t\t}\n\t\t\touttable.remove()\n\t\t})\n\n\tconst anchors = new Anchors({ axiswidth, sp, sp2, sample1height, sample2height, shareheight, sharewidth, headerdiv })\n\n\theaderdiv\n\t\t.append('button')\n\t\t.text('Screenshot')\n\t\t.on('click', () => {\n\t\t\tclient.to_svg(svg.node(), '2dmaf_' + pdata.name)\n\t\t})\n\n\t{\n\t\t// mclass filter\n\t\tconst mcselect = headerdiv.append('select').on('change', event => {\n\t\t\tconst v = event.target.options[event.target.selectedIndex].value\n\t\t\tif (v == 'all') {\n\t\t\t\tselect_share.transition().attr('transform', d => d.posstring + ' scale(1)')\n\t\t\t\tselect_set1.transition().attr('transform', d => d.posstring + ' scale(1)')\n\t\t\t\tselect_set2.transition().attr('transform', d => d.posstring + ' scale(1)')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tselect_share.transition().attr('transform', d => d.posstring + ' scale(' + (d.class == v ? 1 : 0) + ')')\n\t\t\tselect_set1.transition().attr('transform', d => d.posstring + ' scale(' + (d.class == v ? 1 : 0) + ')')\n\t\t\tselect_set2.transition().attr('transform', d => d.posstring + ' scale(' + (d.class == v ? 1 : 0) + ')')\n\t\t})\n\t\tmcselect.append('option').text('Show all mutation classes').property('value', 'all')\n\t\tconst lst = []\n\t\tfor (const c in mclasses) {\n\t\t\tlst.push([c, mclasses[c]])\n\t\t}\n\t\tlst.sort((a, b) => b[1] - a[1])\n\t\tfor (const i of lst) {\n\t\t\tmcselect\n\t\t\t\t.append('option')\n\t\t\t\t.text((i[0] in common.mclass ? common.mclass[i[0]].label : i[0]) + ' (' + i[1] + ')')\n\t\t\t\t.property('value', i[0])\n\t\t}\n\t}\n\n\t/*\nif(pdata.purity1!=undefined) {\n\theaderdiv.append('span').html('&nbsp;Diagnosis expected MAF&nbsp;')\n\tconst select=headerdiv.append('select')\n\tselect.append('option').text('off').property('value','off')\n\tselect.append('option').text('diploid').property('value','diploid')\n\tselect.append('option').text('1-copy loss').property('value','loss')\n\tselect.append('option').text('copy-neutral LOH').property('value','cnloh')\n\tselect.on('change',(event)=>{\n\t\tconst v=event.target.options[event.target.selectedIndex].value\n\t\tif(v=='off') {\n\t\t\temafline_1.transition().duration(1000).attr('fill-opacity',0)\n\t\t\treturn\n\t\t}\n\t\tlet x\n\t\tif(v=='diploid') {\n\t\t\tx=pdata.purity1/2\n\t\t} else if(v=='loss') {\n\t\t\tx=pdata.purity1/(2-pdata.purity1)\n\t\t} else {\n\t\t\tx=pdata.purity1\n\t\t}\n\t\temafline_1.transition().duration(1000)\n\t\t\t.attr('fill-opacity',1)\n\t\t\t.attr('x',x*sharewidth)\n\t})\n}\nif(pdata.purity2!=undefined) {\n\theaderdiv.append($('<span>').html('&nbsp;Relapse expected MAF&nbsp;'))\n\t.append($('<select>')\n\t\t.append($('<option>').text('off').attr('value','off'))\n\t\t.append($('<option>').text('diploid').attr('value','diploid'))\n\t\t.append($('<option>').text('1-copy loss').attr('value','loss'))\n\t\t.append($('<option>').text('copy-neutral LOH').attr('value','cnloh'))\n\t\t.on('change',function(e){\n\t\t\tvar v=e.target.options[e.target.selectedIndex].value\n\t\t\tif(v=='off') {\n\t\t\t\temafline_2.transition().duration(1000).attr('fill-opacity',0)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tvar x\n\t\t\tif(v=='diploid') {\n\t\t\t\tx=pdata.purity2/2\n\t\t\t} else if(v=='loss') {\n\t\t\t\tx=pdata.purity2/(2-pdata.purity2)\n\t\t\t} else {\n\t\t\t\tx=pdata.purity2\n\t\t\t}\n\t\t\temafline_2.transition().duration(1000)\n\t\t\t\t.attr('fill-opacity',1)\n\t\t\t\t.attr('y',(1-x)*shareheight)\n\t\t})\n\t)\n}\n*/\n\n\tconst svg = tdgraph\n\t\t.append('svg')\n\t\t.attr('width', axiswidth + sp + sample2height + sharewidth + sp * 2)\n\t\t.attr('height', axiswidth + sp + sample1height + shareheight + sp * 2)\n\tconst g = svg.append('g').attr('transform', 'translate(' + sp + ',' + sp + ')')\n\n\tanchors.setWrapper(g.append('g'))\n\n\t// axis 1 (horizontal)\n\tconst scale1 = scaleLinear().domain([0, 1]).range([0, sharewidth])\n\tconst scalediv1 = g\n\t\t.append('g')\n\t\t.attr('transform', 'translate(' + (axiswidth + sp + sample2height) + ',' + (shareheight + sample1height + sp) + ')')\n\t\t.call(axisBottom().scale(scale1).tickSize(5))\n\tclient.axisstyle({ axis: scalediv1, showline: true, fontsize: labelfontsize * 0.8 })\n\n\t// axis 1 label\n\tconst c = set_1.length + set_share.length\n\tscalediv1\n\t\t.append('text')\n\t\t.text(pdata.setname[1] + ', n=' + c + (pdata.purity1 ? ', purity=' + pdata.purity1 : ''))\n\t\t.attr('x', sharewidth / 2)\n\t\t.attr('y', axiswidth - 4)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', labelfontsize)\n\n\t// axis 2 (vertical)\n\tconst scale2 = scaleLinear().domain([0, 1]).range([shareheight, 0])\n\tconst scalediv2 = g\n\t\t.append('g')\n\t\t.attr('transform', 'translate(' + axiswidth + ',0)')\n\t\t.call(axisLeft().scale(scale2).tickSize(5))\n\tclient.axisstyle({ axis: scalediv2, showline: true, fontsize: labelfontsize * 0.8 })\n\n\t// axis 2 label\n\tconst c2 = set_2.length + set_share.length\n\tscalediv2\n\t\t.append('text')\n\t\t.text(pdata.setname[2] + ', n=' + c2 + (pdata.purity2 ? ', purity=' + pdata.purity2 : ''))\n\t\t.attr('transform', 'translate(' + (labelfontsize - axiswidth - 10) + ',' + shareheight / 2 + ') rotate(-90)')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('font-size', labelfontsize)\n\n\t// border\n\tg.append('path')\n\t\t.attr(\n\t\t\t'd',\n\t\t\t'M' +\n\t\t\t\t(axiswidth + sp) +\n\t\t\t\t',0' +\n\t\t\t\t'h' +\n\t\t\t\t(sample2height + sharewidth) +\n\t\t\t\t'v' +\n\t\t\t\t(shareheight + sample1height) +\n\t\t\t\t'h-' +\n\t\t\t\tsharewidth +\n\t\t\t\t'v-' +\n\t\t\t\t(sample1height + shareheight) +\n\t\t\t\t'M' +\n\t\t\t\t(axiswidth + sp) +\n\t\t\t\t',0' +\n\t\t\t\t'v' +\n\t\t\t\tshareheight +\n\t\t\t\t'h' +\n\t\t\t\t(sample2height + sharewidth) +\n\t\t\t\t'M' +\n\t\t\t\t(axiswidth + sp + sample2height) +\n\t\t\t\t',' +\n\t\t\t\tshareheight +\n\t\t\t\t'l' +\n\t\t\t\tsharewidth +\n\t\t\t\t',-' +\n\t\t\t\tshareheight\n\t\t)\n\t\t.attr('fill', 'none')\n\t\t.attr('stroke', 'black')\n\t\t.attr('shape-rendering', 'crispEdges')\n\t\t.attr('stroke-dasharray', '5,5')\n\n\t// set share\n\tconst select_share = g\n\t\t.append('g')\n\t\t.attr('transform', 'translate(' + (axiswidth + sp + sample2height) + ',0)')\n\t\t.selectAll()\n\t\t.data(set_share)\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('transform', d => {\n\t\t\td.posstring = 'translate(' + scale1(d.maf1) + ',' + scale2(d.maf2) + ')'\n\t\t\treturn d.posstring\n\t\t})\n\n\t// set share - cnv loh\n\tselect_share\n\t\t.filter(d => d.Dcnvloh)\n\t\t.append('circle')\n\t\t.attr('cy', d => {\n\t\t\treturn d.issnv ? radiusscale(d['TinD.R']) : indelboxw / 2\n\t\t})\n\t\t.attr('fill', '#858585')\n\t\t.attr('r', r_cnvloh)\n\tselect_share\n\t\t.filter(d => d.Rcnvloh)\n\t\t.append('circle')\n\t\t.attr('cx', d => {\n\t\t\treturn d.issnv ? -radiusscale(d['TinD.D']) : -indelboxw / 2\n\t\t})\n\t\t.attr('fill', '#858585')\n\t\t.attr('r', r_cnvloh)\n\n\t// set share - snv\n\tlet snv = select_share\n\t//.filter(function(d){return d.issnv})\n\n\t// not sure why this documented option to supply a function to append is not working\n\t// snv.append(function(d){return document.createElement(1 || d.symbol ? 'path' : 'circle')})\n\t// ... do this instead for now\n\tfor (const tagName in sharedFilters) {\n\t\tsnv\n\t\t\t.filter(sharedFilters[tagName])\n\t\t\t.append(tagName)\n\t\t\t.attr('rx', d => (d.symbol ? null : radiusscale(d['TinD.D'])))\n\t\t\t.attr('ry', d => (d.symbol ? null : radiusscale(d['TinD.R'])))\n\t\t\t.attr('d', d =>\n\t\t\t\t!d.symbol\n\t\t\t\t\t? null\n\t\t\t\t\t: symbolgen.type(symbols[d.symbol]).size(radiustoarea(d['TinD.D']) + radiustoarea(d['TinD.R']) / 2)()\n\t\t\t)\n\t\t\t.attr('fill', d => d.style.fill)\n\t\t\t.attr('fill-opacity', d => d.style.fillopacity)\n\t\t\t.attr('stroke', d => d.style.stroke)\n\t\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t\t.attr('stroke-dasharray', d => (d.chr == 'chrX' ? '5,5' : 'none'))\n\t\t\t.on('mouseover', (event, d) => d2maf_dotmover(event, d, tooltip))\n\t\t\t.on('mouseout', (event, d) => d2maf_dotmout(event, d, tooltip))\n\t\t\t.on('click', (event, d) => d2maf_minfo(event, pdata.header, d))\n\t}\n\tsnv\n\t\t.append('line')\n\t\t.attr('stroke', d => d.style.stroke)\n\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t.attr('x1', -3)\n\t\t.attr('y1', -3)\n\t\t.attr('x2', 3)\n\t\t.attr('y2', 3)\n\tsnv\n\t\t.append('line')\n\t\t.attr('stroke', d => d.style.stroke)\n\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t.attr('x1', -3)\n\t\t.attr('y1', 3)\n\t\t.attr('x2', 3)\n\t\t.attr('y2', -3)\n\t/*\n// set share - indel\nselect_share\n\t.filter(function(d){return d.isindel})\n\t.append('rect')\n\t.attr('fill',function(d){return d.style.fill})\n\t.attr('fill-opacity',function(d){return d.style.fillopacity})\n\t.attr('stroke',function(d){return d.chr=='chrX' ? '#858585' : 'none'})\n\t.attr('stroke-dasharray',function(d){return d.chr=='chrX' ? '5,5' : 'none'})\n\t.attr({\n\t\tx:-indelboxw/2,\n\t\ty:-indelboxw/2,\n\t\twidth:indelboxw,\n\t\theight:indelboxw,\n\t\t'shape-rendering':'crispEdges'\n\t\t})\n\t.on('mouseover',function(event,d){ sja.f.crypt_2dmaf_dotmover(d,this) })\n\t.on('mouseout',function(event,d){ sja.f.crypt_2dmaf_dotmout(d,this) })\n\t.on('click',function(event,d){ sja.f.crypt_2dmaf_minfo(pdata.header,d) })\n\t*/\n\n\t// set 1 - total coverage axis\n\tconst set1totalscale = scaleLinear()\n\t\t.domain([0, maxtotal])\n\t\t.range([sample1height - sp2, 0])\n\tconst g_set1 = g\n\t\t.append('g')\n\t\t.attr('transform', 'translate(' + (axiswidth + sp + sample2height) + ',' + (shareheight + sp2) + ')')\n\tconst emaflinecolor = '#FFBEAD'\n\tconst emafline_1 = g_set1\n\t\t.append('rect')\n\t\t.attr('fill', emaflinecolor)\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('x', 0)\n\t\t.attr('width', 3)\n\t\t.attr('height', sample1height - sp2)\n\tclient.axisstyle({\n\t\taxis: g_set1.call(axisLeft().scale(set1totalscale).tickValues([0, maxtotal])),\n\t\tshowline: true,\n\t\tfontsize: labelfontsize * 0.8\n\t})\n\tg_set1\n\t\t.append('g')\n\t\t.attr('transform', 'translate(-' + labelfontsize / 2 + ',' + (sample1height - sp2) / 2 + ')')\n\t\t.append('text')\n\t\t.text('D total')\n\t\t.attr('font-size', labelfontsize * 0.8)\n\t\t.attr('font-family', client.font)\n\t\t.attr('fill', 'black')\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('dominant-baseline', 'middle')\n\t\t.attr('transform', 'rotate(-90)')\n\n\t// set 1\n\tconst select_set1 = g_set1\n\t\t.selectAll()\n\t\t.data(set_1)\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('transform', d => {\n\t\t\td.posstring = 'translate(' + scale1(d.maf1) + ',' + set1totalscale(d['TinD.D']) + ')'\n\t\t\treturn d.posstring\n\t\t})\n\n\t// set 1 - cnv loh\n\tselect_set1\n\t\t.filter(d => d.Dcnvloh)\n\t\t.append('circle')\n\t\t.attr('cy', d => {\n\t\t\treturn d.issnv ? radiusscale(d['TinD.R']) : indelboxw / 2\n\t\t})\n\t\t.attr('fill', '#858585')\n\t\t.attr('r', r_cnvloh)\n\tselect_set1\n\t\t.filter(d => d.Rcnvloh)\n\t\t.append('circle')\n\t\t.attr('cx', d => (d.issnv ? -radiusscale(d['TinD.D']) : -indelboxw / 2))\n\t\t.attr('fill', '#858585')\n\t\t.attr('r', r_cnvloh)\n\n\t// set 1 - snv\n\tsnv = select_set1\n\t// not sure why this documented option to supply a function to append is not working\n\t// snv.append(function(d){return document.createElement(1 || d.symbol ? 'path' : 'circle')})\n\t// ... do this instead for now\n\tfor (const tagName in symbolFilters) {\n\t\tsnv\n\t\t\t.filter(symbolFilters[tagName])\n\t\t\t.append(tagName)\n\t\t\t.attr('class', d => (d.symbol ? 'twodmaf-' + d.symbol : null))\n\t\t\t.attr('r', d => (d.symbol ? null : radiusscale(d['TinD.R'])))\n\t\t\t.attr('d', d => (!d.symbol ? null : symbolgen.type(symbols[d.symbol]).size(radiustoarea(d['TinD.R']))()))\n\t\t\t.attr('fill', d => d.style.fill)\n\t\t\t.attr('fill-opacity', d => d.style.fillopacity)\n\t\t\t.attr('stroke', d => d.style.stroke)\n\t\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t\t.attr('stroke-dasharray', d => (d.chr == 'chrX' ? '5,5' : 'none'))\n\t\t\t.on('mouseover', (event, d) => d2maf_dotmover(event, d, tooltip))\n\t\t\t.on('mouseout', (event, d) => d2maf_dotmout(event, d, tooltip))\n\t\t\t.on('click', (event, d) => d2maf_minfo(event, pdata.header, d))\n\t}\n\tsnv\n\t\t.append('line')\n\t\t.attr('stroke', d => d.style.stroke)\n\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t.attr('x1', -3)\n\t\t.attr('y1', -3)\n\t\t.attr('x2', 3)\n\t\t.attr('y2', 3)\n\tsnv\n\t\t.append('line')\n\t\t.attr('stroke', d => d.style.stroke)\n\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t.attr('x1', -3)\n\t\t.attr('y1', 3)\n\t\t.attr('x2', 3)\n\t\t.attr('y2', -3)\n\t/*\n// set 1 - indel\nselect_set1\n\t.filter(function(d){return d.isindel})\n\t.append('rect')\n\t.attr('fill',function(d){return d.style.fill})\n\t.attr('fill-opacity',function(d){return d.style.fillopacity})\n\t.attr('stroke',function(d){return d.chr=='chrX' ? '#858585' : 'none'})\n\t.attr('stroke-dasharray',function(d){return d.chr=='chrX' ? '5,5' : 'none'})\n\t.attr({\n\t\tx:-indelboxw/2,\n\t\ty:-indelboxw/2,\n\t\twidth:indelboxw,\n\t\theight:indelboxw,\n\t\t'shape-rendering':'crispEdges'\n\t\t})\n\t.on('mouseover',function(event,d){ sja.f.crypt_2dmaf_dotmover(d,this) })\n\t.on('mouseout',function(event,d){ sja.f.crypt_2dmaf_dotmout(d,this) })\n\t.on('click',function(event,d){ sja.f.crypt_2dmaf_minfo(pdata.header,d) })\n\t*/\n\n\t// set 2 - total coverage axis\n\tconst set2totalscale = scaleLinear()\n\t\t.domain([0, maxtotal])\n\t\t.range([0, sample2height - sp2])\n\tconst g_set2 = g.append('g').attr('transform', 'translate(' + (axiswidth + sp) + ',0)')\n\tconst emafline_2 = g_set2\n\t\t.append('rect')\n\t\t.attr('fill', emaflinecolor)\n\t\t.attr('fill-opacity', 0)\n\t\t.attr('y', shareheight)\n\t\t.attr('width', sample2height - sp2)\n\t\t.attr('height', 3)\n\tconst g_set2_axis = g_set2\n\t\t.append('g')\n\t\t.attr('transform', 'translate(0,' + shareheight + ')')\n\t\t.call(axisBottom().scale(set2totalscale).tickValues([0, maxtotal]))\n\tclient.axisstyle({\n\t\taxis: g_set2_axis,\n\t\tshowline: true,\n\t\tfontsize: labelfontsize * 0.8\n\t})\n\tg_set2\n\t\t.append('text')\n\t\t.text('R total')\n\t\t.attr('font-size', labelfontsize * 0.8)\n\t\t.attr('font-family', client.font)\n\t\t.attr('fill', 'black')\n\t\t.attr('x', (sample2height - sp2) / 2)\n\t\t.attr('y', shareheight + labelfontsize)\n\t\t.attr('text-anchor', 'middle')\n\t// set 2\n\tconst select_set2 = g_set2\n\t\t.selectAll()\n\t\t.data(set_2)\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('transform', d => {\n\t\t\td.posstring = 'translate(' + set2totalscale(d['TinD.R']) + ',' + scale2(d.maf2) + ')'\n\t\t\treturn d.posstring\n\t\t})\n\n\t// set 2 - cnv loh\n\tselect_set2\n\t\t.filter(d => d.Dcnvloh)\n\t\t.append('circle')\n\t\t.attr('cy', d => (d.issnv ? radiusscale(d['TinD.R']) : indelboxw / 2))\n\t\t.attr('fill', '#858585')\n\t\t.attr('r', r_cnvloh)\n\tselect_set2\n\t\t.filter(d => d.Rcnvloh)\n\t\t.append('circle')\n\t\t.attr('cx', d => (d.issnv ? -radiusscale(d['TinD.D']) : -indelboxw / 2))\n\t\t.attr('fill', '#858585')\n\t\t.attr('r', r_cnvloh)\n\n\t// set 2 - snv\n\tsnv = select_set2\n\t//.filter(function(d){return d.issnv});\n\n\t// not sure why this documented option to supply a function to append is not working\n\t// snv.append(function(d){return document.createElement(1 || d.symbol ? 'path' : 'circle')})\n\t// ... do this instead for now\n\tfor (const tagName in symbolFilters) {\n\t\tsnv\n\t\t\t.filter(symbolFilters[tagName])\n\t\t\t.append(tagName)\n\t\t\t.attr('class', d => (d.symbol ? 'twodmaf-' + d.symbol : null))\n\t\t\t.attr('r', d => (d.symbol ? null : radiusscale(d['TinD.D'])))\n\t\t\t.attr('d', d => (!d.symbol ? null : symbolgen.type(symbols[d.symbol]).size(radiustoarea(d['TinD.R']))()))\n\t\t\t.attr('fill', d => d.style.fill)\n\t\t\t.attr('fill-opacity', d => d.style.fillopacity)\n\t\t\t.attr('stroke', d => d.style.stroke)\n\t\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t\t.attr('stroke-dasharray', d => (d.chr == 'chrX' ? '5,5' : 'none'))\n\t\t\t.on('mouseover', (event, d) => d2maf_dotmover(event, d, tooltip))\n\t\t\t.on('mouseout', (event, d) => d2maf_dotmout(event, d, tooltip))\n\t\t\t.on('click', (event, d) => d2maf_minfo(event, pdata.header, d))\n\t}\n\tsnv\n\t\t.append('line')\n\t\t.attr('stroke', d => d.style.stroke)\n\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t.attr('x1', -3)\n\t\t.attr('y1', -3)\n\t\t.attr('x2', 3)\n\t\t.attr('y2', 3)\n\tsnv\n\t\t.append('line')\n\t\t.attr('stroke', d => d.style.stroke)\n\t\t.attr('stroke-opacity', d => d.style.strokeopacity)\n\t\t.attr('x1', -3)\n\t\t.attr('y1', 3)\n\t\t.attr('x2', 3)\n\t\t.attr('y2', -3)\n\t/*\n// set 2 - indel\nselect_set2\n\t.filter(function(d){return d.isindel})\n\t.append('rect')\n\t.attr('fill',function(d){return d.style.fill})\n\t.attr('fill-opacity',function(d){return d.style.fillopacity})\n\t.attr('stroke',function(d){return d.chr=='chrX' ? '#858585' : 'none'})\n\t.attr('stroke-dasharray',function(d){return d.chr=='chrX' ? '5,5' : 'none'})\n\t.attr({\n\t\tx:-indelboxw/2,\n\t\ty:-indelboxw/2,\n\t\twidth:indelboxw,\n\t\theight:indelboxw,\n\t\t'shape-rendering':'crispEdges'\n\t\t})\n\t.on('mouseover',function(d){ sja.f.crypt_2dmaf_dotmover(d,this) })\n\t.on('mouseout',function(d){ sja.f.crypt_2dmaf_dotmout(d,this) })\n\t.on('click',function(d){ sja.f.crypt_2dmaf_minfo(pdata.header,d) })\n\t*/\n\n\t// legend - person name\n\tconst leng = g.append('g').attr('transform', 'translate(0,' + (shareheight + sp2) + ')')\n\tlet y = labelfontsize\n\tleng.append('text').text(person).attr('font-size', labelfontsize).attr('y', y)\n\t// legend - snv text\n\tconst r1 = radiusscale(20),\n\t\tr2 = radiusscale(maxtotal)\n\ty += labelfontsize + r2\n\tlet x\n\tleng\n\t\t.append('text')\n\t\t.text('SNV coverage')\n\t\t.attr('y', y)\n\t\t.attr('dominant-baseline', 'middle')\n\t\t.each(function () {\n\t\t\tx = this.getBBox().width\n\t\t})\n\n\t// legend - snv ball 1\n\tx += r1 + 10\n\tleng.append('circle').attr('cx', x).attr('cy', y).attr('r', r1).attr('stroke', 'black').attr('fill', 'none')\n\tleng\n\t\t.append('text')\n\t\t.text(20)\n\t\t.attr('x', x)\n\t\t.attr('y', y)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('dominant-baseline', 'middle')\n\tx += r1 + r2 + 10\n\n\t// legend - snv ball 2\n\tleng.append('circle').attr('cx', x).attr('cy', y).attr('r', r2).attr('stroke', 'black').attr('fill', 'none')\n\tleng\n\t\t.append('text')\n\t\t.text(maxtotal)\n\t\t.attr('x', x)\n\t\t.attr('y', y)\n\t\t.attr('text-anchor', 'middle')\n\t\t.attr('dominant-baseline', 'middle')\n\n\t// legend - indel\n\ty += r2 + 10\n\tleng\n\t\t.append('text')\n\t\t.text('Indel')\n\t\t.attr('y', y)\n\t\t.attr('dominant-baseline', 'middle')\n\t\t.each(function () {\n\t\t\tx = this.getBBox().width\n\t\t})\n\tleng\n\t\t.append('circle')\n\t\t.attr('cx', x + 10 + indelboxw / 2)\n\t\t.attr('cy', y)\n\t\t.attr('r', indelboxw / 2)\n\t\t.attr('fill', 'black')\n\t\t.attr('fill-opacity', 0.3)\n\ty += 30\n\n\t// legend - chrx\n\tleng\n\t\t.append('text')\n\t\t.text('chrX')\n\t\t.attr('y', y)\n\t\t.attr('dominant-baseline', 'middle')\n\t\t.each(function () {\n\t\t\tx = this.getBBox().width\n\t\t})\n\tx += r1 + 10\n\tleng\n\t\t.append('circle')\n\t\t.attr('cx', x)\n\t\t.attr('cy', y)\n\t\t.attr('r', 10)\n\t\t.attr('stroke', 'black')\n\t\t.attr('stroke-dasharray', '5,5')\n\t\t.attr('fill', 'none')\n\ty += 30\n\n\t// legend - cnv/loh in d\n\tleng\n\t\t.append('text')\n\t\t.text('D. CNV/LOH')\n\t\t.attr('y', y)\n\t\t.attr('dominant-baseline', 'middle')\n\t\t.each(function () {\n\t\t\tx = this.getBBox().width\n\t\t})\n\tx += r1 + 10\n\tleng.append('circle').attr('cx', x).attr('cy', y).attr('r', 10).attr('stroke', 'black').attr('fill', 'none')\n\tleng\n\t\t.append('circle')\n\t\t.attr('cx', x)\n\t\t.attr('cy', y + 10)\n\t\t.attr('r', r_cnvloh)\n\t\t.attr('fill', 'black')\n\ty += 30\n\n\t// legend - cnv/loh in r\n\tleng\n\t\t.append('text')\n\t\t.text('R. CNV/LOH')\n\t\t.attr('y', y)\n\t\t.attr('dominant-baseline', 'central')\n\t\t.each(function () {\n\t\t\tx = this.getBBox().width\n\t\t})\n\tx += r1 + 10\n\tleng.append('circle').attr('cx', x).attr('cy', y).attr('r', 10).attr('stroke', 'black').attr('fill', 'none')\n\tleng\n\t\t.append('circle')\n\t\t.attr('cx', x - 10)\n\t\t.attr('cy', y)\n\t\t.attr('r', r_cnvloh)\n\t\t.attr('fill', 'black')\n\ty += 30\n\n\tif (pdata.purity1 != undefined || pdata.purity2 != undefined) {\n\t\t// emaf\n\t\tleng\n\t\t\t.append('text')\n\t\t\t.text('Expected MAF')\n\t\t\t.attr('y', y)\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t.each(function () {\n\t\t\t\tx = this.getBBox().width\n\t\t\t})\n\t\tx += 10\n\t\tleng.append('rect').attr('fill', emaflinecolor).attr('x', x).attr('y', y).attr('width', 40).attr('height', 3)\n\t\ty += 30\n\t}\n\n\t//\n\tconst renderedsymbols = Object.keys(bysymbol)\n\tif (renderedsymbols.length) {\n\t\tleng\n\t\t\t.append('text')\n\t\t\t.text('Symbols')\n\t\t\t.attr('y', y)\n\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t.each(function () {\n\t\t\t\tx = this.getBBox().width\n\t\t\t})\n\n\t\tlet x1\n\t\tfor (const symbolname in bysymbol) {\n\t\t\tconst s = bysymbol[symbolname]\n\t\t\tconst g = leng.append('g').on('click', () => {\n\t\t\t\ts.hidden = !s.hidden\n\t\t\t\tsvg.selectAll('.twodmaf-' + symbolname).style('display', s.hidden ? 'none' : '')\n\t\t\t\tlabel.style('text-decoration', s.hidden ? 'line-through' : '')\n\t\t\t})\n\n\t\t\tx1 = x + 20\n\t\t\tg.append('path')\n\t\t\t\t.attr('transform', 'translate(' + x1 + ',' + y + ')')\n\t\t\t\t.attr('d', symbolgen.type(symbols[symbolname]).size(100)())\n\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t.attr('fill', 'none')\n\t\t\t\t.each(function () {\n\t\t\t\t\tx1 += this.getBBox().width\n\t\t\t\t})\n\n\t\t\t//x+=10\n\t\t\tconst label = g\n\t\t\t\t.append('text')\n\t\t\t\t.text(s.label ? s.label + ' (' + s.numlines + ')' : '')\n\t\t\t\t.attr('y', y + 2)\n\t\t\t\t.attr('x', x1)\n\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t.style('text-decoration', s.hidden ? 'line-through' : '')\n\t\t\ty += 30\n\t\t}\n\t\ty += 30\n\t}\n\n\t// gene table - sort genes\n\tconst g2m = {},\n\t\tg1 = {},\n\t\tg2 = {},\n\t\tgs = {}\n\tfor (const m of mlst) {\n\t\tif (!m.gene) continue\n\t\tif (!(m.gene in g2m)) {\n\t\t\tg2m[m.gene] = []\n\t\t}\n\t\tg2m[m.gene].push(m)\n\t\tif (m.set_1) {\n\t\t\tg1[m.gene] = 1\n\t\t} else if (m.set_2) {\n\t\t\tg2[m.gene] = 1\n\t\t} else if (m.set_share) {\n\t\t\tgs[m.gene] = 1\n\t\t}\n\t}\n\tconst genelst = []\n\tfor (const n in g1) {\n\t\tgenelst.push(n)\n\t}\n\tfor (const n in g2) {\n\t\tif (!(n in g1)) {\n\t\t\tgenelst.push(n)\n\t\t}\n\t}\n\tfor (const n in gs) {\n\t\tif (!(n in g1) && !(n in g2)) {\n\t\t\tgenelst.push(n)\n\t\t}\n\t}\n\tconst table = tdgenetable\n\t\t.append('div')\n\t\t.style('height', shareheight + sample1height + 'px')\n\t\t.style('margin', '10px')\n\t\t.style('padding', '10px')\n\t\t.style('border', 'solid 1px #ccc')\n\t\t.style('overflow-y', 'scroll')\n\t\t.style('resize', 'both')\n\t\t.append('table')\n\t{\n\t\tconst tr = table.append('tr')\n\t\ttr.append('td').text('Gene')\n\t\ttr.append('td').text(pdata.setname[1] + ' only')\n\t\ttr.append('td').text(pdata.setname[2] + ' only')\n\t\ttr.append('td').text('Shared')\n\t}\n\tlet bg = true\n\tfor (const name of genelst) {\n\t\tconst tr = table.append('tr')\n\t\tif (bg) {\n\t\t\ttr.style('background-color', '#f3f3f3')\n\t\t}\n\t\tbg = !bg\n\t\ttr.append('td').text(name)\n\t\tlet mlst = []\n\t\tif (name in g2m) {\n\t\t\tmlst = g2m[name]\n\t\t}\n\t\tconst s1 = [],\n\t\t\ts2 = [],\n\t\t\tss = []\n\t\tfor (const m of mlst) {\n\t\t\tif (m.set_share) ss.push(m)\n\t\t\telse if (m.set_1) s1.push(m)\n\t\t\telse if (m.set_2) s2.push(m)\n\t\t}\n\t\tlet td = tr.append('td')\n\t\tif (s1.length) {\n\t\t\tfor (const m of s1) {\n\t\t\t\tconst div = td\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.style('color', m.style.fillhl)\n\t\t\t\t\t.text(m.mname || '')\n\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\tclick(event.target, m, select_set1)\n\t\t\t\t\t})\n\n\t\t\t\tif (m.labelIsVisible) {\n\t\t\t\t\tclick(div.node(), m, select_set1)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\ttd = tr.append('td')\n\t\tif (s2.length) {\n\t\t\tfor (const m of s2) {\n\t\t\t\tconst div = td\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.style('color', m.style.fillhl)\n\t\t\t\t\t.text(m.mname || '')\n\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\tclick(event.target, m, select_set2)\n\t\t\t\t\t})\n\n\t\t\t\tif (m.labelIsVisible) {\n\t\t\t\t\tclick(div.node(), m, select_set1)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\ttd = tr.append('td')\n\t\tif (ss.length) {\n\t\t\tfor (const m of ss) {\n\t\t\t\tconst div = td\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t.style('color', m.style.fillhl)\n\t\t\t\t\t.text(m.mname || '')\n\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\tclick(event.target, m, select_share)\n\t\t\t\t\t})\n\n\t\t\t\tif (m.labelIsVisible) {\n\t\t\t\t\tclick(div.node(), m, select_set1)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tfunction click(butt, m, select) {\n\t\tif (m.selected) {\n\t\t\tbutt.style.border = ''\n\t\t\tm.selected = false\n\t\t} else {\n\t\t\tbutt.style.border = 'solid 1px black'\n\t\t\tm.selected = true\n\t\t}\n\t\tconst found = select.filter(d => {\n\t\t\treturn d.gene == m.gene && d.class == m.class && d.mname == m.mname\n\t\t})\n\t\tfound\n\t\t\t.selectAll('rect')\n\t\t\t.attr('fill-opacity', m.selected ? 0.5 : m.style.fillopacity)\n\t\t\t.attr('fill', m.selected ? m.style.fillhl : m.style.fill)\n\t\tfound\n\t\t\t.selectAll('circle,ellipse,line')\n\t\t\t.attr('stroke-opacity', m.selected ? 1 : m.style.strokeopacity)\n\t\t\t.attr('stroke', m.selected ? m.style.strokehl : m.style.stroke)\n\t\t\t.attr('stroke-width', m.selected ? 2 : 1)\n\t\tif (m.selected) {\n\t\t\t// add mobile label\n\t\t\tlet x = Math.max(20, m.radius),\n\t\t\t\ty = 0\n\t\t\tif ((m.set_1 || m.set_share) && m.maf1 >= 0.8) {\n\t\t\t\tx = -m.radius\n\t\t\t\ty = m.radius * 2\n\t\t\t}\n\t\t\tconst g = found\n\t\t\t\t.append('g')\n\t\t\t\t.attr('class', 'sja_2dmaf_mlabel')\n\t\t\t\t.attr('transform', 'translate(' + x + ',' + y + ')')\n\t\t\tlet w\n\t\t\tg.append('text')\n\t\t\t\t.text(m.labelAs ? m.labelAs : m.gene + ' ' + m.mname)\n\t\t\t\t.attr('fill', m.style.fillhl)\n\t\t\t\t.attr('dominant-baseline', 'middle')\n\t\t\t\t.attr('text-anchor', 'start')\n\t\t\t\t.attr('font-size', m.radius)\n\t\t\t\t.each(function () {\n\t\t\t\t\tw = this.getBBox().width\n\t\t\t\t})\n\t\t\tg.append('rect')\n\t\t\t\t.attr('y', -m.radius / 2)\n\t\t\t\t.attr('width', w)\n\t\t\t\t.attr('height', m.radius)\n\t\t\t\t.attr('fill', 'black')\n\t\t\t\t.attr('fill-opacity', 0)\n\t\t\t\t.on('mouseover', event => d3select(event.target).attr('fill-opacity', 0.2))\n\t\t\t\t.on('mouseout', event => d3select(event.target).attr('fill-opacity', 0))\n\t\t\t\t.on('mousedown', event => {\n\t\t\t\t\tconst x0 = x,\n\t\t\t\t\t\ty0 = y,\n\t\t\t\t\t\tmx = event.clientX,\n\t\t\t\t\t\tmy = event.clientY,\n\t\t\t\t\t\tbody = d3select(document.body)\n\t\t\t\t\tbody.on('mousemove', event => {\n\t\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\t\tx = x0 + event.clientX - mx\n\t\t\t\t\t\ty = y0 + event.clientY - my\n\t\t\t\t\t\tg.attr('transform', 'translate(' + x + ',' + y + ')')\n\t\t\t\t\t})\n\t\t\t\t\tbody.on('mouseup', () => {\n\t\t\t\t\t\tbody.on('mousemove', null).on('mouseup', null)\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t} else {\n\t\t\tfound.select('.sja_2dmaf_mlabel').remove()\n\t\t}\n\t}\n\treturn outtable\n}\n\nfunction d2maf_dotmover(event, m, tooltip) {\n\tif (!m.selected) {\n\t\td3select(event.target).attr('fill', m.style.fillhl).attr('fill-opacity', 0.2)\n\t}\n\ttooltip.clear()\n\ttooltip.show(event.clientX, event.clientY)\n\ttooltip.d\n\t\t.append('div')\n\t\t.html(\n\t\t\t(m.gene || 'no gene') +\n\t\t\t\t' <span style=\"color:' +\n\t\t\t\tm.style.fillhl +\n\t\t\t\t'\">' +\n\t\t\t\t(m.mname || '') +\n\t\t\t\t'</span>' +\n\t\t\t\t(m.class ? ' <span style=\"font-size:70%\">' + common.mclass[m.class].label + '</span>' : '')\n\t\t)\n}\n\nfunction d2maf_dotmout(event, m, tooltip) {\n\tif (!m.selected) {\n\t\td3select(event.ele)\n\t\t\t.attr('fill', m.style.fill)\n\t\t\t.attr('fill-opacity', m.style.fillopacity)\n\t\t\t.attr('stroke', m.style.stroke)\n\t}\n\ttooltip.hide()\n}\n\nfunction d2maf_minfo(event, header, m) {\n\tconst pane = client.newpane({ x: event.clientX + 30, y: event.clientY - 30 })\n\tpane.header.text((m.gene ? m.gene : 'No gene') + ' ' + (m.mname ? m.mname : ''))\n\tvar data = []\n\tfor (let i = 0; i < header.length; i++) {\n\t\tdata.push({ k: header[i], v: m[header[i]] })\n\t}\n\tclient.make_table_2col(pane.body, data)\n}\n\nfunction d2maf_click(data, person) {\n\tconst v = data.pairs[person]\n\tif (v.shown) {\n\t\tv.shown = false\n\t\tv.holder.remove()\n\t\tif (v.handle) {\n\t\t\tv.handle.attr('font-weight', 'normal')\n\t\t}\n\t} else {\n\t\tv.shown = true\n\t\tif (v.holder) {\n\t\t\tdata.showholder.node().appendChild(v.holder.node())\n\t\t} else {\n\t\t\tv.holder = d2maf_render(data.showholder, v)\n\t\t}\n\t\tif (v.handle) {\n\t\t\tv.handle.attr('font-weight', 'bold')\n\t\t}\n\t}\n}\n\nfunction d2maf_peopletable(data, holder) {\n\tconst plst = []\n\tfor (const n in data.pairs) {\n\t\tplst.push([n, data.pairs[n].mlst.length])\n\t}\n\n\tholder.selectAll('*').remove()\n\tconst searchrow = holder.append('div').style('margin-bottom', '5px')\n\n\tsearchrow.append('span').text(plst.length + ' individual' + (plst.length > 1 ? 's' : ''))\n\n\t/*\nno buttons\n\n\t.append($('<div>')\n\t\t.append('<span>Patients, top '+data.peoplelimit+' of '+plst.length+'&nbsp;</span>')\n\t\t.append($('<input>').attr({type:'text',size:10,placeholder:'search'}).on('keyup',function(e){\n\t\t\tvar v=e.target.value\n\t\t\tif(v.length<2) {\n\t\t\t\tsja.d.menu.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tv=v.toLowerCase()\n\t\t\tvar hit=[]\n\t\t\tplst.forEach(function(p){\n\t\t\t\tif(p[0].toLowerCase().indexOf(v)!=-1) {\n\t\t\t\t\thit.push(p[0])\n\t\t\t\t}\n\t\t\t})\n\t\t\tif(hit.length==0) {\n\t\t\t\tsja.d.menu.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tsja.d.menu.showunder(e.target)\n\t\t\tfor(var i=0; i<Math.min(20,hit.length); i++) {\n\t\t\t\tsja.d.menu.append($('<div>').addClass('sja_menuoption').text(hit[i]).click((function(n){return function(){\n\t\t\t\t\tsja.f.d2maf_click(data,n)\n\t\t\t\t\tsja.d.menu.fadeOut()\n\t\t\t\t\te.target.value=''\n\t\t\t\t}})(hit[i])))\n\t\t\t}\n\t\t}))\n\t)\n\t.append($('<div>').css('margin-top','5px')\n\t\t.append($('<button>').text('more').click(function(){\n\t\t\tdata.peoplelimit=Math.min(plst.length,data.peoplelimit+10)\n\t\t\tsja.f.d2maf_peopletable(data)\n\t\t}))\n\t\t.append($('<button>').text('less').click(function(){\n\t\t\tdata.peoplelimit=Math.max(Math.min(5,parseInt(plst.length/3)),data.peoplelimit-10)\n\t\t\tsja.f.d2maf_peopletable(data)\n\t\t}))\n\t\t.append($('<button>').text('wider').click(function(){\n\t\t\tdata.peoplewidth+=100\n\t\t\tsja.f.d2maf_peopletable(data)\n\t\t}))\n\t\t.append($('<button>').text('narrower').click(function(){\n\t\t\tdata.peoplewidth=Math.max(150,data.peoplewidth-100)\n\t\t\tsja.f.d2maf_peopletable(data)\n\t\t}))\n\t\t.append($('<button>').text('screenshot').click(function(){\n\t\t\tvar a=document.createElement('a')\n\t\t\tdocument.body.appendChild(a)\n\t\t\t$(a).click(function(){\n\t\t\t\ta.download='2dmaf.patients.bar.svg'\n\t\t\t\ta.href=sja.f.to_svg(svg[0][0])\n\t\t\t\tdocument.body.removeChild(a)\n\t\t\t})\n\t\t\ta.click()\n\t\t}))\n\t)\n\t*/\n\n\tconst svg = holder.append('svg')\n\n\tconst space = 5,\n\t\taxish = 20,\n\t\trowh = data.rowh\n\tlet maxlabelw = 0\n\n\tfor (const s of plst) {\n\t\tsvg\n\t\t\t.append('text')\n\t\t\t.text(s[0])\n\t\t\t.attr('font-size', rowh)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.each(function () {\n\t\t\t\tmaxlabelw = Math.max(maxlabelw, this.getBBox().width)\n\t\t\t})\n\t\t\t.remove()\n\t}\n\n\tsvg.attr('width', maxlabelw + space + data.peoplewidth + 30).attr('height', axish + space + rowh * plst.length)\n\n\tplst.sort((a, b) => b[1] - a[1])\n\n\tlet maxmcount = 0\n\tfor (const k in data.pairs) {\n\t\tmaxmcount = Math.max(maxmcount, data.pairs[k].mlst.length)\n\t}\n\n\tconst ag = svg\n\t\t.append('g')\n\t\t.attr('transform', 'translate(' + (maxlabelw + space) + ',' + axish + ')')\n\t\t.call(\n\t\t\taxisTop()\n\t\t\t\t.scale(scaleLinear().domain([0, maxmcount]).range([0, data.peoplewidth]))\n\t\t\t\t.tickFormat(d3format('d'))\n\t\t\t\t.ticks(3)\n\t\t)\n\tclient.axisstyle({\n\t\taxis: ag,\n\t\tshowline: true,\n\t\tcolor: 'black'\n\t})\n\n\tconst wsf = data.peoplewidth / maxmcount\n\tlet y = axish + space\n\n\tfor (const s of plst) {\n\t\tconst person = s[0]\n\t\tdata.pairs[person].handle = svg\n\t\t\t.append('text')\n\t\t\t.text(person)\n\t\t\t.attr('class', 'sja_svgtext2')\n\t\t\t.attr('font-size', rowh - 2)\n\t\t\t.attr('font-family', client.font)\n\t\t\t.attr('x', maxlabelw)\n\t\t\t.attr('y', y + space + rowh / 2)\n\t\t\t.attr('text-anchor', 'end')\n\t\t\t.on('click', () => {\n\t\t\t\td2maf_click(data, person)\n\t\t\t})\n\t\tlet m1 = 0,\n\t\t\tm2 = 0,\n\t\t\tms = 0\n\t\tfor (const m of data.pairs[person].mlst) {\n\t\t\tif (m.set_1) m1++\n\t\t\telse if (m.set_2) m2++\n\t\t\telse if (m.set_share) ms++\n\t\t}\n\t\tconst g = svg.append('g').attr('transform', 'translate(' + (maxlabelw + space) + ',' + y + ')')\n\t\tif (m1 > 0) {\n\t\t\tg.append('rect')\n\t\t\t\t.attr('width', wsf * m1)\n\t\t\t\t.attr('height', rowh - 1)\n\t\t\t\t.attr('fill', data.color1)\n\t\t}\n\t\tif (ms > 0) {\n\t\t\tg.append('rect')\n\t\t\t\t.attr('x', wsf * m1)\n\t\t\t\t.attr('width', wsf * ms)\n\t\t\t\t.attr('height', rowh - 1)\n\t\t\t\t.attr('fill', data.colorshare)\n\t\t}\n\t\tif (m2 > 0) {\n\t\t\tg.append('rect')\n\t\t\t\t.attr('x', wsf * (m1 + ms))\n\t\t\t\t.attr('width', wsf * m2)\n\t\t\t\t.attr('height', rowh - 1)\n\t\t\t\t.attr('fill', data.color2)\n\t\t}\n\t\ty += rowh\n\t}\n}\n\n/*\nd2maf_genetable=function(data)\n{\nvar dsc=sja.datasets[data.dsname]\nvar hash={}\nfor(var n in data.pairs) {\n\tdata.pairs[n].mlst.forEach(function(m){\n\t\tif(!(m.gene in hash)) {\n\t\t\thash[m.gene]={\n\t\t\t\ts1:{},\n\t\t\t\ts2:{},\n\t\t\t\tshare:{},\n\t\t\t\ttotal:0\n\t\t\t}\n\t\t}\n\t\tif(m.set_1) {\n\t\t\tif(!(m.sample in hash[m.gene].s1)) {\n\t\t\t\thash[m.gene].s1[m.sample]=[]\n\t\t\t\thash[m.gene].total++\n\t\t\t}\n\t\t\thash[m.gene].s1[m.sample].push(m)\n\t\t} else if(m.set_2) {\n\t\t\tif(!(m.sample in hash[m.gene].s2)) {\n\t\t\t\thash[m.gene].s2[m.sample]=[]\n\t\t\t\thash[m.gene].total++\n\t\t\t}\n\t\t\thash[m.gene].s2[m.sample].push(m)\n\t\t} else {\n\t\t\tif(!(m.sample in hash[m.gene].share)) {\n\t\t\t\thash[m.gene].share[m.sample]=[]\n\t\t\t\thash[m.gene].total++\n\t\t\t}\n\t\t\thash[m.gene].share[m.sample].push(m)\n\t\t}\n\t})\n}\nvar genelst=[]\nfor(var n in hash) {\n\tgenelst.push([n,hash[n]])\n}\ngenelst.sort(function(a,b){\n\treturn b[1].total-a[1].total\n})\ndata.geneholder.empty()\ndata.geneholder.append($('<div>').css('margin-bottom','5px')\n\t.append($('<div>')\n\t\t.append('<span>Genes, top '+data.genelimit+' of '+genelst.length+'&nbsp;</span>')\n\t\t.append($('<input>').attr({type:'text',size:10,placeholder:'search'}).on('keyup',function(e){\n\t\t\tvar v=e.target.value\n\t\t\tif(v=='') {\n\t\t\t\tsja.d.menu.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tv=v.toLowerCase()\n\t\t\tvar hit=[]\n\t\t\tgenelst.forEach(function(i){\n\t\t\t\tif(i[0].toLowerCase().indexOf(v)==0) {\n\t\t\t\t\thit.push(i[0])\n\t\t\t\t}\n\t\t\t})\n\t\t\tif(hit.length==0) {\n\t\t\t\tsja.d.menu.hide()\n\t\t\t\treturn\n\t\t\t}\n\t\t\tsja.d.menu.showunder(e.target)\n\t\t\tvar d=$('<div>').css('width',300)\n\t\t\tsja.d.menu.append(d)\n\t\t\tfor(var i=0; i<Math.min(30,hit.length); i++) {\n\t\t\t\td.append($('<div>').addClass('sja_menuoption_y').text(hit[i]).click((function(gene){return 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   "names": ["event", "input", "event", "s", "i", "c", "a", "g", "tr", "mlst", "x", "y"]
 }

package/dist/{AppHeader-F4ZILRPL.js → AppHeader-C75X2TDR.js}

@@ -1,38 +1,37 @@
 import {
   makeButton,
   openSandbox
-} from "./chunk-FIY7FBE5.js";
+} from "./chunk-GNXCCFIB.js";
 import {
   InputSearch
-} from "./chunk-7VI6GDYZ.js";
+} from "./chunk-7HS6FJS2.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
-import "./chunk-WX2C2ZIZ.js";
-import "./chunk-CVWXP35F.js";
-import "./chunk-VYBTGBX5.js";
+import "./chunk-NHVAIOR2.js";
+import "./chunk-3J5ZD37S.js";
+import "./chunk-3HFUJA7U.js";
 import "./chunk-GEFYMVQM.js";
 import "./chunk-EG3MKQQH.js";
 import "./chunk-LGC254YE.js";
 import {
   get_tklst
-} from "./chunk-QB466XDY.js";
-import "./chunk-Q73DQFXR.js";
-import "./chunk-JOCEI72L.js";
+} from "./chunk-JLYMN7FE.js";
+import "./chunk-7BYHJTXX.js";
+import "./chunk-TQBLB23W.js";
 import "./chunk-6MSAGRRE.js";
 import "./chunk-MKAF2BHB.js";
 import {
   urlmap_default
-} from "./chunk-6RCKRFP3.js";
-import "./chunk-IPNHDLML.js";
+} from "./chunk-2CJ2LLB5.js";
+import "./chunk-CNRN4HZF.js";
 import {
   newSandboxDiv
 } from "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
-import "./chunk-3OM5JJ5X.js";
 import {
   block_init_default
-} from "./chunk-WMTED2QI.js";
+} from "./chunk-LUBGU7JN.js";
 import {
   throwMsgWithFilePathAndFnName
 } from "./chunk-RKJGIOIF.js";
@@ -44,15 +43,16 @@ import "./chunk-IQIXGTQV.js";
 import {
   first_genetrack_tolist,
   sayerror
-} from "./chunk-WTVD5AS2.js";
+} from "./chunk-QQESBFZD.js";
 import "./chunk-7YY2KB6H.js";
 import "./chunk-2BM5YZ6X.js";
 import {
   dofetch3
-} from "./chunk-5TRXIQ5D.js";
+} from "./chunk-VX3F7KVD.js";
 import {
   defaultcolor
-} from "./chunk-EHM2BRQX.js";
+} from "./chunk-HWETBYER.js";
+import "./chunk-BU73IBJJ.js";
 import "./chunk-L3BEUWSG.js";
 import "./chunk-JASS6SUY.js";
 import {
@@ -228,7 +228,7 @@ async function findgene2paint(str, app, genomename, jwt) {
       debugmode: app.debugmode
     };
     first_genetrack_tolist(g, par2.tklst);
-    import("./block-2GBSMOQ3.js").then((b) => new b.Block(par2)).catch((err) => {
+    import("./block-62RUXZ4B.js").then((b) => new b.Block(par2)).catch((err) => {
       app.error0(err);
     });
     return;
@@ -834,7 +834,7 @@ var AppHeader = class _AppHeader {
         debugmode: app.debugmode
       };
       first_genetrack_tolist(g, par.tklst);
-      import("./block-2GBSMOQ3.js").then((b) => new b.Block(par));
+      import("./block-62RUXZ4B.js").then((b) => new b.Block(par));
       app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
     });
     return g_browser_btn;
@@ -847,4 +847,4 @@ var AppHeader = class _AppHeader {
 export {
   AppHeader
 };
-//# sourceMappingURL=AppHeader-F4ZILRPL.js.map
+//# sourceMappingURL=AppHeader-C75X2TDR.js.map

package/dist/{DEanalysis-4WCLA5TG.js → DEanalysis-LU5YV4FN.js}

@@ -1,19 +1,19 @@
 import "./chunk-Q7EFDAC2.js";
 import {
   controlsInit
-} from "./chunk-4X2HPTBV.js";
-import "./chunk-3USEV6ZO.js";
+} from "./chunk-ZDEFIDSW.js";
+import "./chunk-H7ZEOS42.js";
 import "./chunk-LSSLEAD5.js";
-import "./chunk-5P67OVKQ.js";
+import "./chunk-V64JKUJY.js";
 import "./chunk-CLHA5AEH.js";
 import {
   axisstyle
-} from "./chunk-7VI6GDYZ.js";
+} from "./chunk-7HS6FJS2.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
-import "./chunk-WX2C2ZIZ.js";
-import "./chunk-CVWXP35F.js";
-import "./chunk-VYBTGBX5.js";
+import "./chunk-NHVAIOR2.js";
+import "./chunk-3J5ZD37S.js";
+import "./chunk-3HFUJA7U.js";
 import "./chunk-GEFYMVQM.js";
 import {
   roundValueAuto
@@ -25,11 +25,10 @@ import {
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
-import "./chunk-3OM5JJ5X.js";
 import "./chunk-RKJGIOIF.js";
 import "./chunk-P64DWRTC.js";
 import "./chunk-ROQ5WSLC.js";
-import "./chunk-WTVD5AS2.js";
+import "./chunk-QQESBFZD.js";
 import {
   Menu
 } from "./chunk-7YY2KB6H.js";
@@ -38,8 +37,9 @@ import {
 } from "./chunk-2BM5YZ6X.js";
 import {
   dofetch3
-} from "./chunk-5TRXIQ5D.js";
-import "./chunk-EHM2BRQX.js";
+} from "./chunk-VX3F7KVD.js";
+import "./chunk-HWETBYER.js";
+import "./chunk-BU73IBJJ.js";
 import {
   axisBottom,
   axisLeft
@@ -607,4 +607,4 @@ export {
   makeChartBtnMenu,
   openHiercluster
 };
-//# sourceMappingURL=DEanalysis-4WCLA5TG.js.map
+//# sourceMappingURL=DEanalysis-LU5YV4FN.js.map