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| <html> | |
| <head> | |
| <title>JBrowse feature rendering outside of browser</title> | |
| <link rel="stylesheet" type="text/css" href="css/genome.css"> | |
| <script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: './src'"></script> | |
| <script type="text/javascript" src="src/JBrowse/init.js"></script> | |
| <script> | |
| require([ | |
| 'dojo/cookie', | |
| 'dojo/_base/window', | |
| 'dojo/_base/array', | |
| 'dojo/dom', | |
| 'dojo/dom-construct', | |
| 'JBrowse/Browser', | |
| 'JBrowse/View/Track/Wiggle/XYPlot', | |
| 'JBrowse/Store/SeqFeature/BigWig', | |
| 'JBrowse/View/GranularRectLayout', | |
| 'JBrowse/Store/Sequence/StaticChunked' | |
| ], | |
| function ( | |
| cookie, | |
| win, | |
| array, | |
| dom, | |
| domConstruct, | |
| Browser, | |
| BigWigTrack, | |
| BigWigStore, | |
| Layout, | |
| StaticChunkedSequence | |
| ) { | |
| var trackConfig = { | |
| "urlTemplate" : "http://genomes.missouri.edu/bam/BoneDensityLumbarSpine.bfs.hg38-lifted.bed.bw", | |
| "type" : "JBrowse/View/Track/Wiggle/XYPlot", | |
| "label" : "BoneDensityGWAS", | |
| "scoreType" : "maxScore" | |
| }; | |
| var browser=new Browser({unitTestMode: true}); | |
| var mmin=0; | |
| var mmax=100000000; | |
| browser.view = { | |
| minVisible: function() { return mmin; }, | |
| maxVisible: function() { return mmax; } | |
| }; | |
| var store = new BigWigStore({ browser: browser, urlTemplate: trackConfig.urlTemplate }); | |
| var renderBlock=function(name,id,store,i,length) { | |
| domConstruct.create('div', { | |
| id: id, | |
| style: { | |
| position: "absolute", | |
| width: "3%", | |
| left: i*3.1+"%", | |
| border: "1px solid black" | |
| } | |
| }, win.body()); | |
| domConstruct.create('div', { | |
| id: id+'label', | |
| style: { | |
| position: "absolute", | |
| width: "3%", | |
| left: i*3.1+"%" | |
| }, | |
| innerHTML: name | |
| }, win.body()); | |
| var block={}; | |
| block.featureLayout = new Layout(0, length); | |
| block.featureNodes = new Array(); | |
| block.startBase = mmin; | |
| block.scale = 50/length; | |
| block.endBase = length; | |
| block.domNode=dom.byId(id); | |
| trackConfig.style={'pos_color':'hsl('+i*20+',50%,50%)'}; | |
| var track = new BigWigTrack({ | |
| config: trackConfig, | |
| browser: browser, | |
| store: store | |
| }); | |
| track.blocks=[block]; | |
| track.refSeq={"name":name}; | |
| track.label=dom.byId("label"); | |
| track.heightUpdateCallback = (function() { "update height" }); | |
| track.blockHeights=[100]; | |
| track.filterFeature=(function() { return true; }); | |
| track.fillBlock({ | |
| blockIndex: 0, | |
| block: block, | |
| scale: block.scale, | |
| leftBase: 0, | |
| rightBase: length | |
| }); | |
| } | |
| var chroms=[{"length":248956422,"name":"chr1","seqChunkSize":20000,"end":248956422,"start":0},{"length":242193529,"name":"chr2","start":0,"end":242193529,"seqChunkSize":20000},{"length":198295559,"name":"chr3","seqChunkSize":20000,"end":198295559,"start":0},{"length":190214555,"name":"chr4","start":0,"end":190214555,"seqChunkSize":20000},{"length":181538259,"name":"chr5","seqChunkSize":20000,"end":181538259,"start":0},{"length":170805979,"name":"chr6","start":0,"end":170805979,"seqChunkSize":20000},{"length":159345973,"name":"chr7","seqChunkSize":20000,"end":159345973,"start":0},{"length":145138636,"name":"chr8","start":0,"end":145138636,"seqChunkSize":20000},{"length":138394717,"name":"chr9","seqChunkSize":20000,"end":138394717,"start":0},{"length":133797422,"name":"chr10","start":0,"end":133797422,"seqChunkSize":20000},{"length":135086622,"name":"chr11","seqChunkSize":20000,"end":135086622,"start":0},{"length":133275309,"name":"chr12","start":0,"end":133275309,"seqChunkSize":20000},{"length":114364328,"name":"chr13","seqChunkSize":20000,"end":114364328,"start":0},{"length":107043718,"name":"chr14","start":0,"end":107043718,"seqChunkSize":20000},{"length":101991189,"name":"chr15","seqChunkSize":20000,"end":101991189,"start":0},{"length":90338345,"name":"chr16","start":0,"end":90338345,"seqChunkSize":20000},{"length":83257441,"name":"chr17","seqChunkSize":20000,"end":83257441,"start":0},{"length":80373285,"name":"chr18","start":0,"end":80373285,"seqChunkSize":20000},{"length":58617616,"name":"chr19","seqChunkSize":20000,"end":58617616,"start":0},{"length":64444167,"name":"chr20","start":0,"end":64444167,"seqChunkSize":20000},{"length":46709983,"name":"chr21","seqChunkSize":20000,"end":46709983,"start":0},{"length":50818468,"name":"chr22","start":0,"end":50818468,"seqChunkSize":20000},{"length":156040895,"name":"chrX","seqChunkSize":20000,"end":156040895,"start":0},{"length":57227415,"name":"chrY","start":0,"end":57227415,"seqChunkSize":20000},{"length":16569,"name":"chrM","seqChunkSize":20000,"end":16569,"start":0}]; | |
| array.forEach(chroms, function(chrom, i) { | |
| renderBlock(chrom.name,"display"+i,store,i,chrom.length); | |
| }); | |
| }); | |
| </script> | |
| </head> | |
| <body style="margin: 30px"> | |
| <div style="margin: 30px"> | |
| <h1>BigWig</h1> | |
| </div> | |
| </body> | |
| </html> |
Author
cmdcolin
commented
Dec 17, 2015
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