@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/mavb-5JAD6CPN.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../src/mavb.js"],
+  "sourcesContent": ["import { select as d3select } from 'd3-selection'\nimport * as client from './client'\nimport { renderSandboxFormDiv } from '../dom/sandbox.ts'\nimport { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport blocklazyload from './block.lazyload'\nimport { d3lasso } from '../common/lasso'\n\n/*\ndifferential gene expression viewer\n\nma: MA plot\nv: Volcano plot\nb: boxplot\n\n\n\n************ mavb object **********\n- hostURL\n- jwt\n- filename\n- genome {}\n- tracks []\n- holder\n- data []\n- ma_dotarea\n- vo_dotarea\n- hastvalue\n\tif false, tvalue is missing\n\totherwise, requires tvaluemin/max\n- tvaluemin\n- tvaluemax\n\n*/\n\nconst hlcolor = '#ffa200'\n\nconst tip = new client.Menu()\n\nexport function mavbparseinput(mavb, sayerror, holder, jwt) {\n\t/*\n\tcalled by embedding api\n\t*/\n\tif (!mavb.dataname) {\n\t\tmavb.dataname = 'Differential expression'\n\t}\n\tif (mavb.input) {\n\t\tconst textinput = mavb.input\n\t\tdelete mavb.input\n\t\tconst err = parseRaw(\n\t\t\t{\n\t\t\t\tgenome: mavb.genome,\n\t\t\t\tfilename: mavb.dataname,\n\t\t\t\tholder: holder,\n\t\t\t\ttracks: mavb.tracks,\n\t\t\t\thostURL: mavb.hostURL,\n\t\t\t\tjwt: jwt\n\t\t\t},\n\t\t\ttextinput.trim().split('\\n')\n\t\t)\n\t\tif (err) {\n\t\t\tsayerror('Error with diferential gene expressionn data: ' + err)\n\t\t}\n\t\treturn\n\t}\n\tlet request\n\tif (mavb.url) {\n\t\trequest = new Request(mavb.hostURL + '/urltextfile', {\n\t\t\tmethod: 'POST',\n\t\t\theaders: { 'content-type': 'application/json' },\n\t\t\tbody: JSON.stringify({ url: mavb.url, jwt: jwt })\n\t\t})\n\t\tdelete mavb.url\n\t} else if (mavb.file) {\n\t\trequest = new Request(mavb.hostURL + '/textfile', {\n\t\t\tmethod: 'POST',\n\t\t\theaders: { 'content-type': 'application/json' },\n\t\t\tbody: JSON.stringify({ file: mavb.file, jwt: jwt })\n\t\t})\n\t\tdelete mavb.file\n\t} else {\n\t\tsayerror('neither .input nor .url given for MA-Volcano plot')\n\t\treturn\n\t}\n\tconst wait = holder\n\t\t.append('div')\n\t\t.style('margin', '20px')\n\t\t.style('color', '#aaa')\n\t\t.style('font-size', '1.5em')\n\t\t.text('Loading differential gene expression data ...')\n\n\tfetch(request)\n\t\t.then(data => {\n\t\t\treturn data.json()\n\t\t})\n\t\t.then(data => {\n\t\t\tif (data.error) throw { message: data.error }\n\t\t\tif (!data.text) throw { message: 'no data loaded' }\n\n\t\t\tconst err = parseRaw(\n\t\t\t\t{\n\t\t\t\t\tgenome: mavb.genome,\n\t\t\t\t\tfilename: mavb.dataname,\n\t\t\t\t\tholder: holder,\n\t\t\t\t\ttracks: mavb.tracks,\n\t\t\t\t\thostURL: mavb.hostURL,\n\t\t\t\t\tjwt: jwt\n\t\t\t\t},\n\t\t\t\tdata.text.trim().split('\\n')\n\t\t\t)\n\t\t\tif (err) throw { message: 'Error with differential gene expression data: ' + err }\n\t\t})\n\t\t.catch(err => {\n\t\t\tsayerror(err.message)\n\t\t\tif (err.stack) console.log(err.stack)\n\t\t})\n\t\t.then(() => {\n\t\t\twait.remove()\n\t\t})\n}\n\nexport function mavbui(genomes, hostURL, jwt, holder, sandbox_header) {\n\t/*\n\tcreate GUI to collect user input\n\t*/\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('Differential gene expression viewer')\n\t\tpane.body.style('margin', '10px')\n\t}\n\tinputdiv.append('div').style('margin-top', '30px').style('color', '#858585').html(`\n\t\t<p>Interactive MA and Volcano plot for exploring differentially expressed genes.</p>\n\t\t<a href=https://docs.google.com/document/d/1gEhywyMzMQRM10NFvsObw1yDSWxVY7pxYjsQ2-nd6x4/edit?usp=sharing target=_blank>File format</a>\n\t\t`)\n\n\tfunction cmt(t, red) {\n\t\tsaydiv.style('color', red ? 'red' : 'black').text(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(\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tgenome: genomes[usegenome],\n\t\t\t\t\t\t\tfilename: file.name,\n\t\t\t\t\t\t\thostURL: hostURL,\n\t\t\t\t\t\t\tjwt: jwt,\n\t\t\t\t\t\t\tholder,\n\t\t\t\t\t\t\tsandbox_header\n\t\t\t\t\t\t},\n\t\t\t\t\t\tevent.target.result.trim().split('\\n')\n\t\t\t\t\t)\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\tif (pane) pane.pane.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\nfunction parseRaw(mavb, lines) {\n\t/*\n\tsee top for attributes\n\t*/\n\tif (mavb.tracks) {\n\t\tfor (const t of mavb.tracks) {\n\t\t\tt.iscustom = true\n\t\t}\n\t}\n\n\tconst [err, header] = parseHeader(lines[0].trim())\n\tif (err) {\n\t\treturn err\n\t}\n\tmavb.hastvalue = header.includes('tvalue')\n\n\tconst data = []\n\n\tlet errpvalue = 0\n\tlet errpvalueadj = 0\n\tlet errlogfc = 0\n\n\tfor (let i = 1; i < lines.length; i++) {\n\t\tconst line = lines[i]\n\t\tif (line == '') continue\n\t\tif (line[0] == '#') continue\n\t\tconst lst = line.trim().split('\\t')\n\t\tconst m = {}\n\t\tfor (let j = 0; j < header.length; j++) {\n\t\t\tm[header[j]] = lst[j]\n\t\t}\n\t\tif (!m.gene) {\n\t\t\treturn '(line ' + (i + 1) + ') missing gene'\n\t\t}\n\t\tm.gene = m.gene.replace(/\"/g, '')\n\n\t\tif (!m.logfoldchange) {\n\t\t\treturn '(line ' + (i + 1) + ') missing log fold change'\n\t\t}\n\t\t{\n\t\t\tconst v = Number.parseFloat(m.logfoldchange)\n\t\t\tif (Number.isNaN(v)) {\n\t\t\t\terrlogfc++\n\t\t\t\tcontinue\n\t\t\t\t//return '(line '+(i+1)+') invalid value for log fold change: '+m.logfoldchange\n\t\t\t}\n\t\t\tm.logfoldchange = v\n\t\t}\n\n\t\tif (!m.averagevalue) {\n\t\t\treturn '(line ' + (i + 1) + ') missing average value'\n\t\t}\n\t\t{\n\t\t\tconst v = Number.parseFloat(m.averagevalue)\n\t\t\tif (Number.isNaN(v)) {\n\t\t\t\treturn '(line ' + (i + 1) + ') invalid value for average value: ' + m.averagevalue\n\t\t\t}\n\t\t\tm.averagevalue = v\n\t\t}\n\n\t\tif (!m.pvalue) {\n\t\t\terrpvalue++\n\t\t\tcontinue\n\t\t} else {\n\t\t\tconst v = Number.parseFloat(m.pvalue)\n\t\t\tif (Number.isNaN(v)) {\n\t\t\t\t// ignore lines with invalid p value e.g. NA\n\t\t\t\terrpvalue++\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tm.pvalue = v\n\t\t}\n\n\t\tif (m.pvalueadj) {\n\t\t\tconst v = Number.parseFloat(m.pvalueadj)\n\t\t\tif (Number.isNaN(v)) {\n\t\t\t\terrpvalueadj++\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tm.pvalueadj = v\n\t\t}\n\n\t\tif (mavb.hastvalue) {\n\t\t\tif (!m.tvalue) {\n\t\t\t\treturn '(line ' + (i + 1) + ') missing T value'\n\t\t\t}\n\t\t\t{\n\t\t\t\tconst v = Number.parseFloat(m.tvalue)\n\t\t\t\tif (Number.isNaN(v)) {\n\t\t\t\t\treturn '(line ' + (i + 1) + ') invalid value for T value: ' + m.tvalue\n\t\t\t\t}\n\t\t\t\tm.tvalue = v\n\t\t\t}\n\t\t}\n\n\t\tdata.push(m)\n\t}\n\tif (data.length == 0) {\n\t\treturn 'No valid data'\n\t}\n\t// good data ready\n\tif (mavb.holder == undefined) {\n\t\tconst pane = client.newpane({ x: 100, y: 100 })\n\t\tpane.header.text(mavb.filename)\n\t\tmavb.holder = pane.body\n\t} else {\n\t\tmavb.holder.selectAll('*').remove()\n\t\t//Fix for rendering data correctly now that the mavb UI is in a div rather than consuming the entire sandbox and therefore not able to access the header\n\t\tif (mavb.sandbox_header !== undefined)\n\t\t\tmavb.holder.append('div').html('<span style=\"opacity:.5;font-size:.7em\">FILE: </span> ' + mavb.filename)\n\t}\n\tmavb.data = data\n\n\t// errors?\n\tif (errlogfc + errpvalue + errpvalueadj > 0) {\n\t\tconst div = mavb.holder.append('div').style('width', '800px')\n\t\tif (errlogfc) {\n\t\t\tclient.sayerror(div, errlogfc + ' lines dropped for invalid log fold change value')\n\t\t}\n\t\tif (errpvalue) {\n\t\t\tclient.sayerror(div, errpvalue + ' lines dropped for invalid P value')\n\t\t}\n\t\tif (errpvalueadj) {\n\t\t\tclient.sayerror(div, errpvalueadj + ' lines dropped for invalid adjusted P value')\n\t\t}\n\t}\n\n\trender(mavb)\n\n\treturn null\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\tlet i = htry('gene')\n\tif (i == -1) return ['gene missing from header']\n\theader[i] = 'gene'\n\ti = htry('logfc', 'log.foldchange')\n\tif (i == -1) return ['log.foldchange missing from header']\n\theader[i] = 'logfoldchange'\n\ti = htry('aveexpr', 'average.value')\n\tif (i == -1) return ['average.value missing from header']\n\theader[i] = 'averagevalue'\n\n\ti = htry('t', 't.value')\n\tif (i != -1) {\n\t\theader[i] = 'tvalue'\n\t}\n\n\ti = htry('p.value')\n\tif (i == -1) return ['p.value missing from header']\n\theader[i] = 'pvalue'\n\ti = htry('p.value.adjusted', 'adj.p.val', 'adjustedp-value(fdr)')\n\tif (i != -1) {\n\t\theader[i] = 'pvalueadj'\n\t}\n\treturn [null, header]\n}\n\nfunction render(mavb) {\n\t// range of absolute(t value) for setting dot radius\n\tif (mavb.hastvalue) {\n\t\tlet tmin = Math.abs(mavb.data[0].tvalue)\n\t\tlet tmax = 0\n\t\tfor (const d of mavb.data) {\n\t\t\tconst v = Math.abs(d.tvalue)\n\t\t\ttmin = Math.min(tmin, v)\n\t\t\ttmax = Math.max(tmax, v)\n\t\t}\n\t\tmavb.tvaluemin = tmin\n\t\tmavb.tvaluemax = tmax\n\t}\n\n\t// MA plot\n\n\tconst maplotdiv = mavb.holder\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.style('vertical-align', 'top')\n\t\t.style('margin', '20px')\n\n\tconst ma_svg = render_ma(maplotdiv, mavb)\n\n\t// volcano plot\n\n\tconst voplotdiv = mavb.holder\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.style('vertical-align', 'top')\n\t\t.style('margin', '20px')\n\n\tconst vo_svg = render_volcano(voplotdiv, mavb)\n\n\t// bottom row\n\n\tconst div3 = mavb.holder.append('div').style('margin', '20px')\n\n\t// row - 1\n\tconst textarea = div3\n\t\t.append('textarea')\n\t\t.style('display', 'inline-block')\n\t\t.attr('rows', 5)\n\t\t.attr('cols', 10)\n\t\t.style('resize', 'both')\n\t\t.attr('placeholder', 'Enter genes, separate by space or newline')\n\t// row - 2\n\tconst div31 = div3\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.style('margin-left', '10px')\n\t\t.style('vertical-align', 'top')\n\tdiv31\n\t\t.append('button')\n\t\t.style('display', 'block')\n\t\t.text('Show gene labels')\n\t\t.on('click', event => {\n\t\t\tconst str = textarea.property('value').trim()\n\t\t\tif (str == '') return\n\t\t\tconst genes = new Set()\n\t\t\tfor (const n of str.split(/[\\s\\n\\t]+/)) {\n\t\t\t\tgenes.add(n.toUpperCase())\n\t\t\t}\n\t\t\tif (genes.size == 0) return\n\t\t\tfor (const d of mavb.data) {\n\t\t\t\tif (!d.ma_label && genes.has(d.gene.toUpperCase())) {\n\t\t\t\t\thltoggle(d, mavb)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\tdiv31\n\t\t.append('button')\n\t\t.style('display', 'block')\n\t\t.text('Remove all labels')\n\t\t.on('click', event => {\n\t\t\tfor (const d of mavb.data) {\n\t\t\t\tif (d.ma_label) {\n\t\t\t\t\thltoggle(d, mavb)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\tdiv31\n\t\t.append('div')\n\t\t.style('margin-top', '10px')\n\t\t.style('color', '#858585')\n\t\t.style('font-size', '.8em')\n\t\t.html(\n\t\t\t'<span style=\"font-size:1.3em\">TIP:</span> click circles to toggle highlight on genes;<br>drag to move a gene label around.'\n\t\t)\n\t// row - 3\n\tconst div32 = div3\n\t\t.append('div')\n\t\t.style('display', 'inline-block')\n\t\t.style('margin-left', '30px')\n\t\t.style('vertical-align', 'top')\n\tdiv32\n\t\t.append('button')\n\t\t.text('Get MA plot')\n\t\t.style('display', 'block')\n\t\t.on('click', event => {\n\t\t\tclient.to_svg(ma_svg.node(), 'MAplot')\n\t\t})\n\tdiv32\n\t\t.append('button')\n\t\t.text('Get volcano plot')\n\t\t.style('display', 'block')\n\t\t.on('click', event => {\n\t\t\tclient.to_svg(vo_svg.node(), 'Volcano')\n\t\t})\n}\n\nfunction render_ma(holder, mavb) {\n\t/*\nm {}\n- gene\n- logfoldchange\n- averagevalue\n- pvalue\n\nadd:\n- ma_circle\n*/\n\tconst avlst = []\n\tlet minlogfc = 0,\n\t\tmaxlogfc = 0\n\tfor (const d of mavb.data) {\n\t\tminlogfc = Math.min(minlogfc, d.logfoldchange)\n\t\tmaxlogfc = Math.max(maxlogfc, d.logfoldchange)\n\t\tavlst.push(d.averagevalue)\n\t}\n\n\tavlst.sort((a, b) => a - b) // ascend\n\tconst minav = avlst[0]\n\tconst maxav = avlst[avlst.length - 1]\n\n\tlet yaxisw,\n\t\txaxish,\n\t\twidth,\n\t\theight,\n\t\txpad,\n\t\typad,\n\t\tboxh,\n\t\ttoppad = 50,\n\t\trightpad = 50,\n\t\tradius\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('Average expression value').attr('fill', 'black').attr('text-anchor', 'middle')\n\tconst ylab = svg.append('text').text('log2(fold change)').attr('fill', 'black').attr('text-anchor', 'middle')\n\tmavb.ma_dotarea = svg.append('g')\n\tconst box = mavb.ma_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\n\tconst xscale = scaleLinear().domain([minav, maxav])\n\tconst yscale = scaleLinear().domain([minlogfc, maxlogfc])\n\t// radius scale by range of abs(t-value)\n\tlet radiusscale\n\tif (mavb.hastvalue) {\n\t\tradiusscale = scaleLinear().domain([mavb.tvaluemin, mavb.tvaluemax])\n\t}\n\n\tconst dotg = mavb.ma_dotarea\n\t\t.selectAll()\n\t\t.data(mavb.data)\n\t\t.enter()\n\t\t.append('g')\n\t\t.each(function (d) {\n\t\t\td.ma_g = this\n\t\t})\n\tconst circle = dotg\n\t\t.append('circle')\n\t\t.attr('stroke', 'black')\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.ma_circle = this\n\t\t})\n\t\t.on('mouseover', circlemouseover)\n\t\t.on('mouseout', circlemouseout)\n\t\t.on('click', (event, d) => {\n\t\t\tcircleclick(d, mavb, event.clientX, event.clientY)\n\t\t})\n\n\tconst logfc0line = mavb.ma_dotarea.append('line').attr('stroke', '#ccc').attr('shape-rendering', 'crispEdges')\n\n\t// boxplot\n\tconst bpg = svg.append('g')\n\tconst bpthroughline = bpg.append('line').attr('stroke', hlcolor).attr('shape-rendering', 'crispEdges')\n\tconst percentile05line = bpg.append('line').attr('stroke', hlcolor).attr('shape-rendering', 'crispEdges')\n\tconst percentile95line = bpg.append('line').attr('stroke', hlcolor).attr('shape-rendering', 'crispEdges')\n\tconst bpbox = bpg.append('rect').attr('fill', 'white').attr('stroke', hlcolor).attr('shape-rendering', 'crispEdges')\n\tconst bpmedianline = bpg.append('line').attr('stroke', hlcolor).attr('shape-rendering', 'crispEdges')\n\tconst avpercentile05 = avlst[Math.ceil(avlst.length * 0.05)]\n\tconst avpercentile95 = avlst[Math.ceil(avlst.length * 0.95)]\n\tconst avpercentile25 = avlst[Math.ceil(avlst.length * 0.25)]\n\tconst avpercentile75 = avlst[Math.ceil(avlst.length * 0.75)]\n\tconst avmedian = avlst[Math.ceil(avlst.length / 2)]\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\t\tradius = Math.max(width, height) / 80 // minimum radius\n\t\tconst maxradius = radius * 3\n\n\t\txscale.range([0, width])\n\t\tyscale.range([height, 0])\n\t\tif (radiusscale) radiusscale.range([radius, maxradius])\n\n\t\tcircle.each(d => {\n\t\t\td.ma_radius = radiusscale ? radiusscale(Math.abs(d.tvalue)) : radius\n\t\t})\n\n\t\tboxh = radius * 3\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 + boxh + ypad) + ')')\n\t\txlab.attr('x', yaxisw + xpad + width / 2).attr('y', toppad + height + ypad + boxh + ypad + xaxish - 5)\n\t\tylab.attr('transform', 'translate(15,' + (toppad + height / 2) + ') rotate(-90)')\n\t\tmavb.ma_dotarea.attr('transform', 'translate(' + (yaxisw + xpad) + ',' + toppad + ')')\n\t\tbox.attr('width', width).attr('height', height)\n\t\tdotg.attr('transform', d => {\n\t\t\treturn 'translate(' + xscale(d.averagevalue) + ',' + yscale(d.logfoldchange) + ')'\n\t\t})\n\t\tcircle.attr('r', d => {\n\t\t\treturn d.ma_radius\n\t\t})\n\t\tlogfc0line.attr('x2', width).attr('y1', yscale(0)).attr('y2', yscale(0))\n\n\t\tbpg.attr('transform', 'translate(' + (yaxisw + xpad) + ',' + (toppad + height + ypad) + ')')\n\t\tconst p05 = xscale(avpercentile05),\n\t\t\tp25 = xscale(avpercentile25),\n\t\t\tp50 = xscale(avmedian),\n\t\t\tp75 = xscale(avpercentile75),\n\t\t\tp95 = xscale(avpercentile95)\n\t\tpercentile05line.attr('x1', p05).attr('x2', p05).attr('y2', boxh)\n\t\tpercentile95line.attr('x1', p95).attr('x2', p95).attr('y2', boxh)\n\t\tbpmedianline.attr('x1', p50).attr('x2', p50).attr('y2', boxh)\n\t\tbpbox\n\t\t\t.attr('x', p25)\n\t\t\t.attr('width', p75 - p25)\n\t\t\t.attr('height', boxh)\n\t\tbpthroughline\n\t\t\t.attr('x1', p05)\n\t\t\t.attr('x2', p95)\n\t\t\t.attr('y1', boxh / 2)\n\t\t\t.attr('y2', boxh / 2)\n\n\t\tsvg.attr('width', yaxisw + xpad + width + rightpad).attr('height', toppad + height + ypad + boxh + ypad + xaxish)\n\t\tclient.axisstyle({\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\tclient.axisstyle({\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\t// add lasso for ma plot\n\t// TODO: remove follow line after testing\n\tadd_lasso(dotg.selectAll('circle'), svg, 'vo_circle')\n\treturn svg\n}\n\nfunction render_volcano(holder, mavb) {\n\t/*\nm {}\n- gene\n- logfoldchange\n- averagevalue\n- pvalue\n\nadd:\n- vo_circle\n*/\n\tlet minlogfc = 0,\n\t\tmaxlogfc = 0,\n\t\tminlogpv = 0,\n\t\tmaxlogpv = 0\n\tfor (const d of mavb.data) {\n\t\tminlogfc = Math.min(minlogfc, d.logfoldchange)\n\t\tmaxlogfc = Math.max(maxlogfc, d.logfoldchange)\n\t\tif (d.pvalue == 0) {\n\t\t\tcontinue\n\t\t} else {\n\t\t\tconst v = -Math.log(d.pvalue, 10)\n\t\t\tminlogpv = Math.min(minlogpv, v)\n\t\t\tmaxlogpv = Math.max(maxlogpv, v)\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\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('-log(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\tif (mavb.hastvalue) radiusscale = scaleLinear().domain([mavb.tvaluemin, mavb.tvaluemax])\n\tconst dotg = mavb.vo_dotarea\n\t\t.selectAll()\n\t\t.data(mavb.data)\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 circle = dotg\n\t\t.append('circle')\n\t\t.attr('stroke', 'black')\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\t.on('click', (event, d) => {\n\t\t\tcircleclick(d, mavb, event.clientX, event.clientY)\n\t\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 (\n\t\t\t\t'translate(' + xscale(d.logfoldchange) + ',' + yscale(d.pvalue == 0 ? maxlogpv : -Math.log(d.pvalue, 10)) + ')'\n\t\t\t)\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\tclient.axisstyle({\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\tclient.axisstyle({\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.data[0].pvalueadj != undefined) {\n\t\t// enable pvalue switching between adjusted and unadjusted\n\t\tconst row = holder.append('div').style('margin', '20px')\n\t\trow.append('span').text('Select P value for Volcano plot:')\n\t\tconst select = row\n\t\t\t.append('select')\n\t\t\t.style('margin-left', '5px')\n\t\t\t.on('change', event => {\n\t\t\t\tminlogpv = 0\n\t\t\t\tmaxlogpv = 0\n\t\t\t\tconst useun = select.node().selectedIndex == 0\n\t\t\t\tfor (const d of mavb.data) {\n\t\t\t\t\tconst pv = useun ? d.pvalue : d.pvalueadj\n\t\t\t\t\tif (pv == 0) continue\n\t\t\t\t\tconst v = -Math.log(pv, 10)\n\t\t\t\t\tminlogpv = Math.min(minlogpv, v)\n\t\t\t\t\tmaxlogpv = Math.max(maxlogpv, v)\n\t\t\t\t}\n\t\t\t\tyscale.domain([minlogpv, maxlogpv])\n\t\t\t\tclient.axisstyle({\n\t\t\t\t\taxis: yaxisg.call(d3axis.axisLeft().scale(yscale)),\n\t\t\t\t\tcolor: 'black',\n\t\t\t\t\tshowline: true\n\t\t\t\t})\n\t\t\t\tdotg.attr('transform', d => {\n\t\t\t\t\tconst pv = useun ? d.pvalue : d.pvalueadj\n\t\t\t\t\treturn 'translate(' + xscale(d.logfoldchange) + ',' + yscale(pv == 0 ? maxlogpv : -Math.log(pv, 10)) + ')'\n\t\t\t\t})\n\t\t\t\tylab.text(useun ? '-log(P value)' : '-log(adjusted P value)')\n\t\t\t})\n\t\tselect.append('option').text('Unadjusted P value')\n\t\tselect.append('option').text('Adjusted P value')\n\t}\n\n\t// add lasso for volcano plot\n\t// TODO: remove follow line after testing\n\tadd_lasso(dotg.selectAll('circle'), svg, 'ma_circle')\n\treturn svg\n}\n\n// example of lasso function and usage\nfunction add_lasso(selectable_items, svg, other_svg_item_key) {\n\tconst lasso = d3lasso().items(selectable_items).targetArea(svg)\n\n\tfunction mavb_lasso_start() {\n\t\t// set all dots to initial state when lasso starts\n\t\tsvg\n\t\t\t.selectAll('.possible')\n\t\t\t.style('fill-opacity', 0)\n\t\t\t.classed('not_possible', true)\n\t\t\t.classed('selected', false)\n\t\t\t.each(d => {\n\t\t\t\td3select(d[other_svg_item_key]).attr('fill-opacity', 0)\n\t\t\t})\n\n\t\t// TODO: remove following commented code after review\n\t\t// here, there are many circles, so rather than applying style to add circles,\n\t\t// only previously selected circles are reverted back to normal\n\t\t// can use like following as well, for detail example see mds.scatterplot.js\n\t\t// lasso.items()\n\t\t// \t.style('fill-opacity', 0)\n\t\t// \t.classed('not_possible', true)\n\t\t// \t.classed('selected', false)\n\t\t// \t.each((d) =>{\n\t\t// \t\td3select(d[other_svg_item_key]).attr('fill-opacity', 0)\n\t\t// \t})\n\t}\n\n\tfunction mavb_lasso_draw() {\n\t\t// Style the possible dots, when selected using lasso\n\t\tlasso\n\t\t\t.possibleItems()\n\t\t\t.style('fill-opacity', 0.9)\n\t\t\t.classed('not_possible', false)\n\t\t\t.classed('possible', true)\n\t\t\t.each(d => {\n\t\t\t\td3select(d[other_svg_item_key]).attr('fill-opacity', 0.9)\n\t\t\t})\n\t}\n\n\tfunction mavb_lasso_end() {\n\t\t// do something, like show menu or open info panel for selected samples\n\t}\n\n\t// perform following custom drag events after original lasso drag events finish in lasso.js\n\tlasso.on('start', mavb_lasso_start).on('draw', mavb_lasso_draw).on('end', mavb_lasso_end)\n\n\tsvg.call(lasso)\n}\n\nfunction circlemouseover(event, d) {\n\ttip.clear().show(event.clientX, event.clientY)\n\tconst lst = [\n\t\t{ k: 'gene', v: d.gene },\n\t\t{ k: 'average value', v: d.averagevalue },\n\t\t{ k: 'log fold change', v: d.logfoldchange },\n\t\t{ k: 'P value', v: d.pvalue }\n\t]\n\tif (d.pvalueadj != undefined) {\n\t\tlst.push({ k: 'adjusted P value', v: d.pvalueadj })\n\t}\n\tif (d.tvalue != undefined) {\n\t\tlst.push({ k: 'T value', v: d.tvalue })\n\t}\n\t// rest of the attributes\n\tfor (const k in d) {\n\t\tif (\n\t\t\tk == 'gene' ||\n\t\t\tk == 'averagevalue' ||\n\t\t\tk == 'logfoldchange' ||\n\t\t\tk == 'pvalue' ||\n\t\t\tk == 'pvalueadj' ||\n\t\t\tk == 'tvalue'\n\t\t) {\n\t\t\tcontinue\n\t\t}\n\t\tconst v = d[k]\n\t\tif (typeof v != 'string') {\n\t\t\tcontinue\n\t\t}\n\t\tlst.push({ k: k, v: v })\n\t}\n\n\tclient.make_table_2col(tip.d, lst)\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\nfunction hltoggle(d, mavb) {\n\tif (d.ma_label) {\n\t\t// remove existing labels\n\t\td.ma_label.remove()\n\t\td.ma_labelbg.remove()\n\t\td.ma_label = null\n\t\td.vo_label.remove()\n\t\td.vo_labelbg.remove()\n\t\td.vo_label = null\n\t\td3select(d.ma_circle).attr('fill-opacity', 0)\n\t\td3select(d.vo_circle).attr('fill-opacity', 0)\n\t\treturn\n\t}\n\n\t// to highlight this gene\n\n\t// move this gene to the top of the stack so it won't be blocked\n\tmavb.ma_dotarea.node().appendChild(d.ma_g)\n\n\td.ma_labelbg = d3select(d.ma_g)\n\t\t.append('text')\n\t\t.text(d.gene)\n\t\t.attr('x', d.ma_radius + 5)\n\t\t.attr('y', 0)\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('font-size', 14)\n\t\t.attr('font-family', client.font)\n\t\t.attr('fill', 'none')\n\t\t.attr('stroke', 'white')\n\t\t.attr('stroke-width', 3)\n\td.ma_label = d3select(d.ma_g)\n\t\t.append('text')\n\t\t.text(d.gene)\n\t\t.attr('x', d.ma_radius + 5)\n\t\t.attr('y', 0)\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('font-size', 14)\n\t\t.attr('fill', 'black')\n\t\t.attr('font-family', client.font)\n\t\t.on('mousedown', (event, d) => {\n\t\t\tlabelmousedown(d.ma_label, d.ma_labelbg, event)\n\t\t})\n\n\tmavb.vo_dotarea.node().appendChild(d.vo_g)\n\td.vo_labelbg = d3select(d.vo_g)\n\t\t.append('text')\n\t\t.text(d.gene)\n\t\t.attr('x', d.vo_radius + 5)\n\t\t.attr('y', 0)\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('font-size', 14)\n\t\t.attr('font-family', client.font)\n\t\t.attr('fill', 'none')\n\t\t.attr('stroke', 'white')\n\t\t.attr('stroke-width', 3)\n\td.vo_label = d3select(d.vo_g)\n\t\t.append('text')\n\t\t.text(d.gene)\n\t\t.attr('x', d.vo_radius + 5)\n\t\t.attr('y', 0)\n\t\t.attr('dominant-baseline', 'central')\n\t\t.attr('font-size', 14)\n\t\t.attr('fill', 'black')\n\t\t.attr('font-family', client.font)\n\t\t.on('mousedown', (event, d) => {\n\t\t\tlabelmousedown(d.vo_label, d.vo_labelbg, event)\n\t\t})\n\td3select(d.ma_circle).attr('fill-opacity', 0.8)\n\td3select(d.vo_circle).attr('fill-opacity', 0.8)\n}\n\nfunction labelmousedown(label, labelbg, evt) {\n\tevent.preventDefault()\n\tconst labx = Number.parseFloat(label.attr('x'))\n\tconst laby = Number.parseFloat(label.attr('y'))\n\tconst x0 = evt.clientX\n\tconst y0 = evt.clientY\n\tconst body = d3select(document.body)\n\tbody\n\t\t.on('mousemove', event => {\n\t\t\tlabel.attr('x', labx + event.clientX - x0).attr('y', laby + event.clientY - y0)\n\t\t\tlabelbg.attr('x', labx + event.clientX - x0).attr('y', laby + event.clientY - y0)\n\t\t})\n\t\t.on('mouseup', event => {\n\t\t\tbody.on('mousemove', null).on('mouseup', null)\n\t\t})\n}\n\nfunction circleclick(d, mavb, mousex, mousey) {\n\tif (mavb.tracks) {\n\t\t// have bigwig tracks\n\t\tif (!d.ma_label) {\n\t\t\t// this gene is not highlighted, will show the tracks\n\t\t\tconst pane = client.newpane({ x: mousex + 20, y: mousey - 50 })\n\t\t\tpane.header.text(d.gene)\n\t\t\tshowTracks(mavb, d.gene, pane.body)\n\t\t}\n\t}\n\thltoggle(d, mavb)\n}\n\nfunction showTracks(mavb, gene, holder) {\n\tfetch(\n\t\tnew Request(mavb.hostURL + '/genelookup', {\n\t\t\tmethod: 'POST',\n\t\t\theaders: { 'content-type': 'application/json' },\n\t\t\tbody: JSON.stringify({ deep: 1, input: gene, genome: mavb.genome.name, jwt: mavb.jwt })\n\t\t})\n\t)\n\t\t.then(data => {\n\t\t\treturn data.json()\n\t\t})\n\t\t.then(data => {\n\t\t\tif (data.error) throw { message: data.error }\n\t\t\tif (!data.gmlst || data.gmlst.length == 0) throw { message: 'No genes can be found for ' + gene }\n\n\t\t\tconst chr2pos = new Map()\n\t\t\tfor (const m of data.gmlst) {\n\t\t\t\tif (!chr2pos.has(m.chr)) {\n\t\t\t\t\tchr2pos.set(m.chr, { chr: m.chr, start: m.start, stop: m.stop })\n\t\t\t\t}\n\t\t\t\tchr2pos.get(m.chr).start = Math.min(m.start, chr2pos.get(m.chr).start)\n\t\t\t\tchr2pos.get(m.chr).stop = Math.max(m.stop, chr2pos.get(m.chr).stop)\n\t\t\t}\n\t\t\tconst coord = [...chr2pos][0][1]\n\n\t\t\t// create new tklst but don't push gene tracks in .tracks[]\n\t\t\tconst tklst = [...mavb.tracks]\n\t\t\tclient.first_genetrack_tolist(mavb.genome, tklst)\n\n\t\t\t// import block causes duplication\n\t\t\tblocklazyload({\n\t\t\t\tholder: holder,\n\t\t\t\thostURL: mavb.hostURL,\n\t\t\t\tjwt: mavb.jwt,\n\t\t\t\tgenome: mavb.genome,\n\t\t\t\tchr: coord.chr,\n\t\t\t\tstart: coord.start,\n\t\t\t\tstop: coord.stop,\n\t\t\t\ttklst: tklst,\n\t\t\t\tnobox: true\n\t\t\t})\n\t\t})\n\t\t.catch(err => {\n\t\t\tclient.sayerror(holder, err.message)\n\t\t\tif (err.stack) console.log(err.stack)\n\t\t})\n}\n"],
+  "mappings": 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+  "names": ["sayerror", "event", "i", "d"]
+}

package/dist/mds.fimo-CQFREH3A.js

@@ -0,0 +1,509 @@
+import {
+  appear2 as appear,
+  axisstyle,
+  font,
+  gmlst2loci,
+  keyupEnter,
+  make_table_2col
+} from "./chunk-YS7Y257H.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-PITPUAWX.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-K6CZAEBF.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import {
+  dofetch
+} from "./chunk-XJYVMXMZ.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-ZSNZPH6G.js";
+import "./chunk-ET2KFCXK.js";
+import {
+  axisTop
+} from "./chunk-LMG7Y5IN.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-6XKAOSQE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// src/mds.fimo.js
+var headerheight = 80;
+var headerunderpad = 5;
+async function init(obj) {
+  window.obj = obj;
+  obj.errdiv = obj.div.append("div");
+  try {
+    init_ui(obj);
+    await do_query(obj);
+  } catch (e) {
+    obj.errdiv.text(e.message || e);
+    if (e.stack) console.log(e.stack);
+  }
+}
+function init_ui(obj) {
+  obj.motifrowheight = 16;
+  obj.gaincolor = "red";
+  obj.losscolor = "blue";
+  obj.flankspan = 15;
+  if (!obj.fimo_thresh) obj.fimo_thresh = 1e-3;
+  if (!obj.minabslogp) obj.minabslogp = 1;
+  obj.tip = new Menu();
+  const table = obj.div.append("table").style("border-spacing", "3px").style("border-collapse", "separate").style("margin", "10px");
+  {
+    const tr = table.append("tr");
+    tr.append("td").text("Flanking sequence (#nt)");
+    const td = tr.append("td");
+    td.append("input").attr("type", "number").style("margin", "0px 10px").style("width", "100px").property("value", obj.flankspan).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      const v = Number.parseInt(event.target.value);
+      if (v < 10) {
+        window.alert("Enter integer above 10");
+        return;
+      }
+      if (v == obj.flankspan) return;
+      obj.flankspan = v;
+      do_query(obj);
+    });
+    td.append("span").style("font-size", "0.7em").style("opacity", 0.5).text("Press ENTER to update");
+  }
+  {
+    const tr = table.append("tr");
+    tr.append("td").text("P-value cutoff");
+    const td = tr.append("td");
+    td.append("input").attr("type", "number").style("margin", "0px 10px").style("width", "100px").property("value", obj.fimo_thresh).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      const v = Number.parseFloat(event.target.value);
+      if (v <= 0) {
+        window.alert("Enter a p value between 0 to 1");
+        return;
+      }
+      if (v == obj.fimo_thresh) return;
+      obj.fimo_thresh = v;
+      do_query(obj);
+    });
+    td.append("span").style("font-size", "0.7em").style("opacity", 0.5).text("Press ENTER to update");
+  }
+  {
+    const tr = table.append("tr");
+    tr.append("td").text("Minimum log10 p-value difference");
+    const td = tr.append("td");
+    td.append("input").attr("type", "number").style("margin", "0px 10px").style("width", "100px").property("value", obj.minabslogp).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      const v = Number.parseFloat(event.target.value);
+      if (v <= 0) {
+        window.alert("Enter a number above 0");
+        return;
+      }
+      if (v == obj.minabslogp) return;
+      obj.minabslogp = v;
+      do_query(obj);
+    });
+    td.append("span").style("font-size", "0.7em").style("opacity", 0.5).text("Press ENTER to update");
+  }
+  obj.wait = obj.div.append("div");
+  obj.svg = obj.div.append("svg");
+  obj.dynamic_g = obj.svg.append("g");
+  obj.legend = {};
+  obj.legend.logpvaluediv = obj.div.append("div");
+  may_init_factorprofiles(obj);
+}
+function may_init_factorprofiles(obj) {
+  if (!obj.factor_profiles) return;
+  if (!Array.isArray(obj.factor_profiles)) throw "factor_profiles is not array";
+  for (const profile of obj.factor_profiles) {
+    if (!profile.name) throw "name missing for a profile";
+    if (!profile.leftpad) profile.leftpad = 20;
+    if (!profile.width) profile.width = 300;
+    profile.headerg = obj.svg.append("g");
+    profile.textlabel = profile.headerg.append("text").text(profile.name).attr("x", profile.width / 2).attr("text-anchor", "middle").attr("y", -30);
+    if (profile.isgenevalue) {
+      profile.color = "green";
+      profile.axisg = profile.headerg.append("g");
+      continue;
+    }
+    if (profile.isgenevalueonesample) {
+      if (!profile.samplename) throw "samplename missing for isgenevalueonesample";
+      profile.barcolor = "#62945B";
+      profile.axisg = profile.headerg.append("g");
+      continue;
+    }
+    throw "unknown profile type";
+  }
+}
+function do_query(obj) {
+  appear(obj.wait.text("Loading..."));
+  obj.dynamic_g.selectAll("*").remove();
+  const arg = {
+    genome: obj.genome.name,
+    m: obj.m,
+    fimo_thresh: obj.fimo_thresh,
+    flankspan: obj.flankspan,
+    minabslogp: obj.minabslogp
+  };
+  return dofetch("fimo", arg).then((data) => {
+    if (data.error) throw "Error: cannot do motif finding: " + data.error;
+    if (obj.callback_once) {
+      obj.callback_once();
+      delete obj.callback_once;
+    }
+    if (!data.items || data.items.length == 0) throw "Found no motif change due to this mutation";
+    obj.wait.style("display", "none");
+    for (const m of data.items) {
+      if (m.attr) {
+        m.gene = m.attr["Transcription factor"];
+      } else {
+        m.gene = m.name;
+      }
+    }
+    return show_result(data, obj);
+  }).catch((e) => {
+    obj.wait.style("display", "block").text(e.message || e);
+    if (e.stack) console.log(e.stack);
+  });
+}
+async function show_result(data, obj) {
+  draw_motif_simplified(data, obj);
+  if (obj.factor_profiles) {
+    await get_gene_position(data, obj);
+    let width = Number.parseInt(obj.svg.attr("width"));
+    for (const profile of obj.factor_profiles) {
+      profile.headerg.attr("transform", "translate(" + (width + profile.leftpad) + "," + headerheight + ")");
+      profile.motifs = [];
+      for (const motif of data.items) {
+        const pg = motif.layer1_g.append("g").attr("transform", "translate(" + (width + profile.leftpad) + ",0)");
+        profile.motifs.push({
+          motif,
+          g: pg,
+          message: pg.append("text").text("Loading...").attr("dominant-baseline", "central").attr("fill", "#ccc")
+        });
+      }
+      width += profile.leftpad + profile.width;
+      obj.svg.attr("width", width + 5);
+      await load_factorprofile(obj, profile);
+      for (const m of data.items) {
+        m.bgbox.attr("width", width);
+        m.coverbox.attr("width", width);
+      }
+    }
+  }
+}
+function draw_motif_simplified(data, obj) {
+  const ntwidth = 14;
+  const motifgraphwidth = ntwidth * data.refseq.length;
+  const ntfontsize = 16;
+  const rulerheight = 30;
+  {
+    const x = (obj.m.pos - data.refstart + 0.5) * ntwidth;
+    const g2 = obj.dynamic_g.append("g").attr("transform", "translate(" + x + "," + headerheight + ")");
+    g2.append("rect").attr("x", -ntwidth / 2).attr("y", -10).attr("width", ntwidth).attr("height", 10).attr("fill", "#666");
+    g2.append("text").attr("y", -15).attr("text-anchor", "middle").text(obj.m.chr + ":" + obj.m.pos + " " + obj.m.ref + ">" + obj.m.alt);
+  }
+  let svgheight = headerheight + headerunderpad;
+  const rowspace = 1;
+  const g = obj.dynamic_g.append("g").attr("transform", "translate(0," + svgheight + ")");
+  for (const [i, motif] of data.items.entries()) {
+    motif.g = g.append("g").attr("transform", "translate(0," + (obj.motifrowheight * (i + 0.5) + rowspace * i) + ")");
+    motif.layer1_g = motif.g.append("g");
+    motif.layer2_g = motif.g.append("g");
+    motif.bgbox = motif.layer1_g.append("rect").attr("y", -obj.motifrowheight / 2).attr("width", motifgraphwidth).attr("height", obj.motifrowheight).attr("fill", "white");
+    const x = (motif.start - data.refstart) * ntwidth;
+    const w = (Math.min(motif.stop, data.refstop) - motif.start) * ntwidth;
+    motif.layer1_g.append("rect").attr("x", x).attr("y", -obj.motifrowheight / 2).attr("width", w).attr("height", obj.motifrowheight).attr("fill", motif.gain ? obj.gaincolor : obj.losscolor).attr("fill-opacity", motif.logpvaluediff / (motif.gain ? data.valuemax : data.valuemin));
+    let str;
+    if (motif.strand == "+") {
+      str = ">  " + motif.name + "  >";
+    } else {
+      str = "<  " + motif.name + "  <";
+    }
+    motif.layer1_g.append("text").text(str).attr("x", x + w / 2).attr("dominant-baseline", "central").attr("text-anchor", "middle").attr("stroke", "white").attr("stroke-width", 3).attr("font-size", obj.motifrowheight - 3).attr("font-family", font).style("white-space", "pre");
+    motif.layer1_g.append("text").text(str).attr("x", x + w / 2).attr("dominant-baseline", "central").attr("text-anchor", "middle").attr("font-size", obj.motifrowheight - 3).attr("font-family", font).style("white-space", "pre");
+    motif.coverbox = motif.layer2_g.append("rect").attr("y", -obj.motifrowheight / 2).attr("width", motifgraphwidth).attr("height", obj.motifrowheight).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event) => {
+      motif.bgbox.attr("fill", "#f9fabd");
+      motif_tooltip(motif, obj, event);
+    }).on("mouseout", () => {
+      motif.bgbox.attr("fill", "white");
+      obj.tip.hide();
+    });
+  }
+  svgheight += (rowspace + obj.motifrowheight) * data.items.length + 20;
+  make_legend(data, obj);
+  obj.svg.attr("width", motifgraphwidth).attr("height", svgheight);
+}
+function motif_tooltip(motif, obj, event) {
+  obj.tip.clear();
+  if (motif.attr) {
+    obj.tip.d.append("div").text("MOTIF").style("font-weight", "bold");
+    const lst1 = [
+      { k: "P-values", v: htmlpvalue(motif, obj) },
+      { k: "Strand", v: motif.strand }
+    ];
+    make_table_2col(obj.tip.d, lst1);
+    obj.tip.d.append("div").text("FACTOR").style("font-weight", "bold");
+    const lst2 = [];
+    for (const k in motif.attr) {
+      lst2.push({ k, v: motif.attr[k] });
+    }
+    make_table_2col(obj.tip.d, lst2);
+  } else {
+    const lst = [
+      { k: "TF", v: motif.name },
+      { k: "P-values", v: htmlpvalue(motif, obj) },
+      { k: "Strand", v: motif.strand }
+    ];
+    make_table_2col(obj.tip.d, lst);
+  }
+  obj.tip.show(event.clientX, event.clientY);
+}
+function htmlpvalue(m, obj) {
+  return (m.pvalue_ref == void 0 ? '<span style="opacity:.5;padding:2px"><span style="font-size:.7em">REF</span> not found</span>' : '<span style="background-color:' + obj.losscolor + ';padding:2px;color:white;"><span style="font-size:.7em">REF</span> ' + m.pvalue_ref + "</span>") + "<br>" + (m.pvalue_alt == void 0 ? '<span style="opacity:.5;padding:2px"><span style="font-size:.7em">ALT</span> not found</span>' : '<span style="background-color:' + obj.gaincolor + ';padding:2px;color:white;"><span style="font-size:.7em">ALT</span> ' + m.pvalue_alt + "</span>");
+}
+function make_legend(data, obj) {
+  obj.legend.logpvaluediv.selectAll("*").remove();
+  const leftpad = 50, axistickh = 4, fontsize = 12, barw = 55, barh = 20;
+  obj.legend.logpvaluediv.append("span").text("Log10 p-value difference");
+  const svg = obj.legend.logpvaluediv.append("svg").attr("width", (leftpad + barw) * 2).attr("height", fontsize + axistickh + barh);
+  const axisg = svg.append("g").attr("transform", "translate(" + leftpad + "," + (fontsize + axistickh) + ")");
+  axisstyle({
+    axis: axisg.call(
+      axisTop().scale(
+        linear().domain([data.valuemin, 0, data.valuemax]).range([0, barw, barw * 2])
+      ).tickValues([data.valuemin, 0, data.valuemax]).tickSize(axistickh)
+    )
+  });
+  const gain_id = Math.random().toString();
+  const loss_id = Math.random().toString();
+  const defs = svg.append("defs");
+  {
+    const grad = defs.append("linearGradient").attr("id", loss_id);
+    grad.append("stop").attr("offset", "0%").attr("stop-color", obj.losscolor);
+    grad.append("stop").attr("offset", "100%").attr("stop-color", "white");
+  }
+  {
+    const grad = defs.append("linearGradient").attr("id", gain_id);
+    grad.append("stop").attr("offset", "0%").attr("stop-color", "white");
+    grad.append("stop").attr("offset", "100%").attr("stop-color", obj.gaincolor);
+  }
+  svg.append("rect").attr("x", leftpad).attr("y", fontsize + axistickh).attr("width", barw).attr("height", barh).attr("fill", "url(#" + loss_id + ")");
+  svg.append("rect").attr("x", leftpad + barw).attr("y", fontsize + axistickh).attr("width", barw).attr("height", barh).attr("fill", "url(#" + gain_id + ")");
+  svg.append("text").attr("x", leftpad - 5).attr("y", fontsize + axistickh + barh / 2).attr("font-family", font).attr("font-size", fontsize).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("fill", "black").text("Loss");
+  svg.append("text").attr("x", leftpad + barw * 2 + 5).attr("y", fontsize + axistickh + barh / 2).attr("font-family", font).attr("font-size", fontsize).attr("dominant-baseline", "central").attr("fill", "black").text("Gain");
+}
+async function get_gene_position(data, obj) {
+  obj.gene2position = {};
+  const factornames = /* @__PURE__ */ new Set();
+  for (const m of data.items) {
+    factornames.add(m.gene);
+  }
+  for (const genename of factornames) {
+    const pos = await get_one_gene_position(genename, obj);
+    if (pos) {
+      obj.gene2position[genename] = pos;
+    }
+  }
+}
+function get_one_gene_position(genename, obj) {
+  return dofetch("genelookup", { genome: obj.genome.name, input: genename, deep: 1 }).then((data) => {
+    if (!data.gmlst) return null;
+    const loci = gmlst2loci(data.gmlst);
+    return loci[0];
+  });
+}
+function load_factorprofile(obj, profile) {
+  if (profile.isgenevalue) {
+    return load_factorprofile_genevalue(obj, profile);
+  }
+  if (profile.isgenevalueonesample) {
+    return load_factorprofile_genevalueonesample(obj, profile);
+  }
+  throw "unknown profile type";
+}
+async function load_factorprofile_genevalueonesample(obj, profile) {
+  const arg = {
+    genome: obj.genome.name,
+    genes: [],
+    sample: profile.samplename
+  };
+  if (profile.mdslabel) {
+    arg.dslabel = profile.mdslabel;
+    arg.querykey = profile.querykey;
+    if (profile.samplegroup_attrlst) {
+      arg.getgroup = profile.samplegroup_attrlst;
+    }
+  } else {
+    arg.iscustom = 1;
+    arg.file = profile.file;
+    arg.url = profile.url;
+    arg.indexURL = profile.indexURL;
+  }
+  for (const g in obj.gene2position) {
+    const r = obj.gene2position[g];
+    arg.genes.push({
+      gene: g,
+      chr: r.chr,
+      start: r.start,
+      stop: r.stop
+    });
+  }
+  return dofetch("mdsgenevalueonesample", arg).then((data) => {
+    if (data.error) throw data.error;
+    for (const m of profile.motifs) {
+      m.message.text("No data");
+    }
+    if (data.nodata) return;
+    if (!data.result) throw "error";
+    let min = 0, max = 0;
+    for (const g in data.result) {
+      min = Math.min(min, data.result[g]);
+      max = Math.max(max, data.result[g]);
+    }
+    const scale = linear().domain([min, max]).range([0, profile.width]);
+    axisstyle({
+      axis: profile.axisg.call(axisTop().scale(scale).ticks(4)),
+      showline: 1
+    });
+    for (const m of profile.motifs) {
+      const v = data.result[m.motif.gene];
+      if (Number.isFinite(v)) {
+        m.message.text("");
+        m.g.append("rect").attr("y", -obj.motifrowheight / 2).attr("width", Math.max(1, scale(v))).attr("height", obj.motifrowheight).attr("shape-rendering", "crispEdges").attr("fill", profile.barcolor);
+      }
+    }
+    profile.textlabel.attr("x", profile.width / 2).attr("text-anchor", "middle").attr("y", -30);
+  }).catch((e) => {
+    if (e.stack) console.log(e.stack);
+    appear(obj.wait.text(e.message || e));
+  });
+}
+async function load_factorprofile_genevalue(obj, profile) {
+  profile.gene2result = /* @__PURE__ */ new Map();
+  for (const gene in obj.gene2position) {
+    const data = await factorprofile_genevalue_onegene_loadboxplot(obj, profile, gene);
+    if (data) {
+      factorprofile_genevalue_onegene_makeboxplot(obj, profile, gene, data);
+      profile.gene2result.set(gene, data);
+      factorprofile_genevalue_updatescale(obj, profile);
+    }
+  }
+  factorprofile_genevalue_finish(obj, profile);
+}
+function factorprofile_genevalue_onegene_makeboxplot(obj, profile, gene, data) {
+  if (data.nodata) return;
+  for (const m of profile.motifs) {
+    if (m.motif.gene != gene) continue;
+    m.boxplot = {
+      out: []
+    };
+    if (data.w1 != void 0) {
+      m.boxplot.hline = m.g.append("line").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
+      m.boxplot.linew1 = m.g.append("line").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
+      m.boxplot.linew2 = m.g.append("line").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
+      m.boxplot.box = m.g.append("rect").attr("fill", "white").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
+      m.boxplot.linep50 = m.g.append("line").attr("stroke", profile.color).attr("shape-rendering", "crispEdges");
+    }
+    if (data.out) {
+      for (const d of data.out) {
+        const circle = m.g.append("circle").attr("stroke", profile.color).attr("fill", "white").attr("fill-opacity", 0);
+        m.boxplot.out.push({
+          value: d.value,
+          circle
+        });
+      }
+    }
+  }
+}
+function factorprofile_genevalue_updatescale(obj, profile) {
+  let min = 0, max = 0;
+  for (const g of profile.gene2result.values()) {
+    min = Math.min(min, g.min);
+    max = Math.max(max, g.max);
+  }
+  const scale = linear().domain([min, max]).range([0, profile.width]);
+  const h = obj.motifrowheight - 2;
+  for (const [g, r] of profile.gene2result) {
+    for (const m of profile.motifs) {
+      if (m.motif.gene != g) continue;
+      const bp = m.boxplot;
+      if (!bp) continue;
+      if (bp.hline) {
+        const w1 = scale(r.w1);
+        const w2 = scale(r.w2);
+        const p25 = scale(r.p25);
+        const p50 = scale(r.p50);
+        const p75 = scale(r.p75);
+        bp.hline.transition().attr("x1", w1).attr("x2", w2);
+        bp.linew1.transition().attr("x1", w1).attr("x2", w1).attr("y1", -h / 2).attr("y2", h / 2);
+        bp.linew2.transition().attr("x1", w2).attr("x2", w2).attr("y1", -h / 2).attr("y2", h / 2);
+        bp.box.transition().attr("x", p25).attr("y", -h / 2).attr("width", p75 - p25).attr("height", h);
+        bp.linep50.transition().attr("x1", p50).attr("x2", p50).attr("y1", -h / 2).attr("y2", h / 2);
+      }
+      for (const d of bp.out) {
+        d.circle.transition().attr("cx", scale(d.value)).attr("r", h / 3);
+      }
+    }
+  }
+  axisstyle({
+    axis: profile.axisg.transition().call(axisTop().scale(scale).ticks(4)),
+    showline: 1
+  });
+}
+function factorprofile_genevalue_onegene_loadboxplot(obj, profile, gene) {
+  const r = obj.gene2position[gene];
+  const arg = {
+    genome: obj.genome.name,
+    gene,
+    chr: r.chr,
+    start: r.start,
+    stop: r.stop,
+    getgroup2boxplot: 1
+  };
+  if (profile.mdslabel) {
+    arg.dslabel = profile.mdslabel;
+    arg.querykey = profile.querykey;
+    if (profile.samplegroup_attrlst) {
+      arg.getgroup = profile.samplegroup_attrlst;
+    }
+  } else {
+    arg.iscustom = 1;
+    arg.file = profile.file;
+    arg.url = profile.url;
+    arg.indexURL = profile.indexURL;
+  }
+  return dofetch("mdsgeneboxplot", arg).then((data) => {
+    if (data.error) throw "Error: " + data.error;
+    if (data.nodata) throw "No data";
+    for (const m of profile.motifs) {
+      if (m.motif.gene == gene) {
+        m.message.text("");
+      }
+    }
+    return data;
+  }).catch((e) => {
+    if (e.stack) console.log(e.stack);
+    for (const m of profile.motifs) {
+      if (m.motif.gene == gene) {
+        m.message.text(e.message || e);
+      }
+    }
+  });
+}
+function factorprofile_genevalue_finish(obj, profile) {
+  let n = 0;
+  for (const g of profile.gene2result.values()) {
+    n = Math.max(n, g.n);
+  }
+  profile.textlabel.text(profile.name + " (n=" + n + ")").attr("x", profile.width / 2).attr("text-anchor", "middle").attr("y", -30);
+}
+export {
+  init
+};
+//# sourceMappingURL=mds.fimo-CQFREH3A.js.map