00 Date 20140922 Author Tom Carroll Sanjay Khadayate Anne Pajon Ziwei Liang Maintainer Tom Carroll Description Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages biocViews Sequencing ReportWriting VignetteBuil ID: 38556
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Package`tracktables'November13,2020TypePackageTitleBuildIGVtracksandHTMLreportsVersion1.24.0Date2014-09-22AuthorTomCarroll,SanjayKhadayate,AnnePajon,ZiweiLiangMaintainerTomCarroll&#xtc.i;&#xnfom; tic;&#xs@gm; il.;om0;DescriptionMethodstocreatecomplexIGVgenomebrowsersessionsanddynamicIGVreportsinHTMLpages.biocViewsSequencing,ReportWritingVignetteBuilderknitrLicenseGPL&#xtc.i;&#xnfom; tic;&#xs@gm; il.;om0;(=3)LazyLoadyesDependsR&#xtc.i;&#xnfom; tic;&#xs@gm; il.;om0;(=3.0.0)ImportsIRanges,GenomicRanges,XVector,Rsamtools,XML,tractor.base,stringr,RColorBrewer,methodsSuggestsknitr,BiocStyleCollate tracktablesFunctions.R git_urlhttps://git.bioconductor.org/packages/tracktablesgit_branchRELEASE_3_12git_last_commit26c4770git_last_commit_date2020-10-27Date/Publication2020-11-12Rtopicsdocumented:igvParam..........................................2Intervals...........................................6makebedtable........................................6MakeIGVSampleMetadata.................................7MakeIGVSession......................................8MakeIGVSessionXML...................................9maketracktable.......................................10Index131 2igvParam igvParamParametersfordisplayingbigwigs,bamsandintervalsinIGV DescriptionUseigvParam(object))tocreateaparameterobjecttocontrolIGVdisplayinvokedfrommake-tracktable()reportorfrommakeIGVSession()XMLles.Parametersforbigwig,bamandintervalslesmaybeprovided.SeeIGVmanualforafulldescriptionofoptions.UsageigvParam(bigwig.altColor="darkgrey",bigwig.color="darkgrey",bigwig.autoScale="true",bigwig.displayMode="COLLAPSED",bigwig.featureVisibilityWindow=-1,bigwig.fontSize=10,bigwig.normalize="false",bigwig.renderer="BAR_CHART",bigwig.sortable="true",bigwig.visible="true",bigwig.windowFunction="mean",bigwig.baseline=0,bigwig.drawBaseline="true",bigwig.flipAxis="false",bigwig.maximum=50,bigwig.minimum=0,bigwig.type="LINEAR",interval.altColor="darkgrey",interval.color="darkgrey",interval.autoScale="true",interval.displayMode="character",interval.featureVisibilityWindow=-1,interval.fontSize=10,interval.height=40,interval.normalize="false",interval.renderer="BASIC_FEATURE",interval.sortable="true",interval.visible="true",interval.windowFunction="count",bam.altColor="darkgrey",bam.color="darkgrey",bam.autoScale="true",bam.displayMode="EXPANDED",bam.featureVisibilityWindow=-1,bam.fontSize=10,bam.showSpliceJunctions="false",bam.colorByTag="",bam.colorOption="UNEXPECTED_PAIR",bam.flagUnmappedPairs="false",bam.groupByTag="",bam.maxInsertSize=1000,bam.minInsertSize=50,bam.shadeBasesOption="QUALITY",bam.shadeCenters="true",bam.showAllBases="false",bam.sortByTag="")igvParam(bigwig.altColor="darkgrey",bigwig.color="darkgrey",bigwig.autoScale="true",bigwig.displayMode="COLLAPSED",bigwig.featureVisibilityWindow=-1,bigwig.fontSize=10,bigwig.normalize="false",bigwig.renderer="BAR_CHART",bigwig.sortable="true",bigwig.visible="true",bigwig.windowFunction="mean",bigwig.baseline=0,bigwig.drawBaseline="true",bigwig.flipAxis="false",bigwig.maximum=50,bigwig.minimum=0,bigwig.type="LINEAR",interval.altColor="darkgrey",interval.color="darkgrey",interval.autoScale="true",interval.displayMode="character",interval.featureVisibilityWindow=-1,interval.fontSize=10,interval.height=40,interval.normalize="false",interval.renderer="BASIC_FEATURE",interval.sortable="true",interval.visible="true",interval.windowFunction="count",bam.altColor="darkgrey",bam.color="darkgrey",bam.autoScale="true",bam.displayMode="EXPANDED",bam.featureVisibilityWindow=-1,bam.fontSize=10, igvParam3bam.showSpliceJunctions="false",bam.colorByTag="",bam.colorOption="UNEXPECTED_PAIR",bam.flagUnmappedPairs="false",bam.groupByTag="",bam.maxInsertSize=1000,bam.minInsertSize=50,bam.shadeBasesOption="QUALITY",bam.shadeCenters="true",bam.showAllBases="false",bam.sortByTag="")Argumentsbigwig.altColorAcharactervectorofalternatecolourforbigwigsdisplayedinIGV.bigwig.colorAcharactervectorofmaincolourforbigwigsdisplayedinIGV.bigwig.displayModeAcharactervectorofdisplaymodeforbigwigsdisplayedinIGV.bigwig.featureVisibilityWindowAnumericvectoroffeaturevisibilitywindowforbigwigsdisplayedinIGV(Defaut-1).bigwig.fontSizeAnumericvectoroffontsizeforbigwigsdisplayedinIGV.bigwig.autoScaleAcharactervector("true"/"false")toindicatewhetherdataisautoscaledforbig-wigsdisplayedinIGV(Default"true").bigwig.normalizeAcharactervector("true"/"false")toindicatewhetherdataisnormalisedforbigwigsdisplayedinIGV(Default"false").bigwig.rendererAcharactervectorofrendererforbigwigsdisplayedinIGV(Default"BAR_CHART").bigwig.sortableAcharactervector("true"/"false")toindicatewhetherdataissortableforbig-wigsdisplayedinIGV(Default"true").bigwig.visibleAcharactervector("true"/"false")toindicatewhetherdataisvisibleforbigwigsdisplayedinIGV(Default"true").bigwig.windowFunctionAcharactervector("true"/"false")ofwindowfunctionforbigwigsdisplayedinIGV(Default"mean").bigwig.baselineAnumericvectorofbaselinebigwigsdisplayedinIGV.bigwig.drawBaselineAcharactervector("true"/"false")ofwhethertodrawbaselineforbigwigsdis-playedinIGV(Default"true").bigwig.flipAxisAcharactervector("true"/"false")toindicatewhethertoipaxisforbigwigsdisplayedinIGV(Default"false").bigwig.maximumAnumericvectorofmaximumvaluetodisplayforbigwigsdisplayedinIGV(Default50).bigwig.minimumAnumericvectorofminimumvaluetodisplayforbigwigsdisplayedinIGV(Default0).bigwig.typeAcharactervectorofdisplaytypeforbigwigsdisplayedinIGV(Default"LIN-EAR"). 4igvParaminterval.altColorAcharactervectorofalternatecolourforintervalsdisplayedinIGV.interval.colorAcharactervectorofmaincolourforintervalsdisplayedinIGV.interval.autoScaleAcharactervector("true"/"false")toindicatewhetherdataisautoscaledforin-tervalsdisplayedinIGV(Default"false").interval.displayModeAcharactervectorofdisplaymodeforintervalsdisplayedinIGV(Default"COLLAPSED").interval.featureVisibilityWindowAnumericvectoroffeaturevisibilitywindowforintervalsdisplayedinIGV(Defaut-1).interval.fontSizeAnumericvectoroffontsizeforintervalsdisplayedinIGV.interval.heightAnumericvectorofheightforintervalsdisplayedinIGV.interval.normalizeAcharactervector("true"/"false")toindicatewhetherdataisnormalisedforintervalsdisplayedinIGV(Default"false").interval.rendererAcharactervectorofrendererforintervalsdisplayedinIGV(Default"BA-SIC_FEATURE").interval.sortableAcharactervector("true"/"false")toindicatewhetherdataissortableforinter-valsdisplayedinIGV(Default"true").interval.visibleAcharactervector("true"/"false")toindicatewhetherdataisvisibleforintervalsdisplayedinIGV(Default"true").interval.windowFunctionAcharactervector("true"/"false")ofwindowfunctionforintervalsdisplayedinIGV(Default"count").bam.altColorAcharactervectorofalternatecolourforbamlesdisplayedinIGV.bam.colorAcharactervectorofmaincolourforbamlesdisplayedinIGV.bam.autoScaleAcharactervector("true"/"false")toindicatewhetherdataisautoscaledforbamlesdisplayedinIGV(Default"false").bam.displayModeAcharactervectorofdisplaymodeforbamlesdisplayedinIGV(Default"EXPANDED").bam.featureVisibilityWindowAnumericvectoroffeaturevisibilitywindowforbamlesdisplayedinIGV(Defaut-1).bam.fontSizeAnumericvectoroffontsizeforintervalsdisplayedinIGV.bam.showSpliceJunctionsAcharactervector("true"/"false")toindicatewhethertoshowsplicejuntionsforbamlesdisplayedinIGV(Default"false").bam.colorByTagAcharactervectortoindicatewhethertocolourreadsbyTagsforBamles(Defualt=""). igvParam5bam.colorOptionAcharactervectorofoptiontohighlightTagsforBamles(Defualt="UNEX-PECTED_PAIR").bam.flagUnmappedPairsAcharactervector("true"/"false")toindicatewhethertoafunmappedpairsforbamlesdisplayedinIGV(Default"false").bam.groupByTagAcharactervector("true"/"false")toindicatehowtogroupsreadsbyTagforbamlesdisplayedinIGV(Default"").bam.maxInsertSizeAnumericvectorofmaximuminsertsizetodisplayforBamles.bam.minInsertSizeAnumericvectorofminimuminsertsizetodisplayforBamles.bam.shadeBasesOptionAcharactervectorofoptiontoshadebasesforBamles(Default"QUALITY").bam.shadeCentersAcharactervector("true"/"false")toindicatewhethertoshadecentresforbamlesdisplayedinIGV(Default"false").bam.showAllBasesAcharactervector("true"/"false")toindicatetoshowallbasesforbamlesdisplayedinIGV(Default"false").bam.sortByTagAcharactervector("true"/"false")toindicatehowtosortreadsbyTagforbamlesdisplayedinIGV(Default"").ValueAnigvParamclassobjecttousewithmaketracktable,MakeIGVSessionandmakeIGVSessionMXLAuthor(s)ThomasCarrollExamples##SimpleinitialisationofanIGVParamobjectigvDisplayParamsigvParam()##MorecustominitialisationofanIGVParamobject.igvDisplayParamsigvParam(bigwig.color="red",bigwig.autoScale="false",bigwig.minimum=10,bigwig.maximum=100)#SeefullparametersandIGVonlinemanualformoredetailsoncustomistions##UseigvParamswithmaketracktablesfunctiontocustomisebigwigdisplaycolouranddatarange.fileLocationssystem.file("extdata",package="tracktables")bigwigsdir(fileLocations,pattern="*.bw",full.names=TRUE)intervalsdir(fileLocations,pattern="*.bed",full.names=TRUE)bigWigMatcbind(gsub("_Example.bw","",basename(bigwigs)), 6makebedtablebigwigs)intervalsMatcbind(gsub("_Peaks.bed","",basename(intervals)),intervals)fileSheetmerge(bigWigMat,intervalsMat,all=TRUE)fileSheetas.matrix(cbind(fileSheet,NA))colnames(fileSheet)c("SampleName","bigwig","interval","bam")SampleSheetcbind(as.vector(fileSheet[,"SampleName"]),c("EBF","H3K4me3","H3K9ac","RNAPol2"),c("ProB","ProB","ProB","ProB"))colnames(SampleSheet)c("SampleName","Antibody","Species")MakeIGVSession(SampleSheet,fileSheet,igvdirectory=getwd(),"Example","mm9",igvParams=igvDisplayParams) IntervalsExamplegenomicintervals DescriptionThisdatasetcontainspeaksfromanin-houseEBF1ChIP-seqUsagedata(Intervals)Details•IntervalsGRangesobjectcontainingEBF1peaksValueAGRangesobjectwithtworows makebedtableMakeHTMLpagesforintervallesorGRanges. DescriptionCreatesHTMLpagesforintervallesorGRanges(TracktablesIntervalReport).Usagemakebedtable(grangesObject,name,basedirectory) MakeIGVSampleMetadata7ArgumentsgrangesObjectAGRangesobject.nameCharacterofthenameforIntervalHTMLreport.basedirectoryCharacterofthedirectorytowhichHTMLreportiswriten.ValueAcharacteroflelocationfortheTracktablesHTMLReportAuthor(s)ThomasCarrollExamplesdata(Intervals)htmlpagemakebedtable(Intervals,"EBF_PeaksTable.html",getwd()) MakeIGVSampleMetadataMakesamplemetadataleforusewithIGV. DescriptionCreatessamplemetadataleforIGVfromaSamplesheetofmetadataandFileSheetofleloca-tions.UsageMakeIGVSampleMetadata(SampleSheet,fileSheet,igvdirectory)ArgumentsSampleSheetAdata.frameobjectwithmetadatainformationforsamples.Firstcolumnmustcontainuniquesampleids.fileSheetAdata.frameoflelocations.Firstcolumnmustcontaintheuniquesampleids.igvdirectoryAcharacterofthedirectorytowhichsamplemetadataleiswritten.ValueAcharacteroflelocationfortheIGVsampleinformationle.Author(s)ThomasCarroll 8MakeIGVSessionExamplesfileLocationssystem.file("extdata",package="tracktables")bigwigsdir(fileLocations,pattern="*.bw",full.names=TRUE)intervalsdir(fileLocations,pattern="*.bed",full.names=TRUE)bigWigMatcbind(gsub("_Example.bw","",basename(bigwigs)),bigwigs)intervalsMatcbind(gsub("_Peaks.bed","",basename(intervals)),intervals)fileSheetmerge(bigWigMat,intervalsMat,all=TRUE)fileSheetas.matrix(cbind(fileSheet,NA))colnames(fileSheet)c("SampleName","bigwig","interval","bam")SampleSheetcbind(as.vector(fileSheet[,"SampleName"]),c("EBF","H3K4me3","H3K9ac","RNAPol2"),c("ProB","ProB","ProB","ProB"))colnames(SampleSheet)c("SampleName","Antibody","Species")MakeIGVSampleMetadata(SampleSheet,fileSheet,igvdirectory=getwd()) MakeIGVSessionMakeIGVsessionXMLandsampleinformationle Description#'CreatesIGVsessionXMLandsampleinformationlefromaSamplesheetofmetadataandFileSheetoflelocations.UsageMakeIGVSession(SampleSheet,fileSheet,igvdirectory,XMLname,genomeName,locusName="All",colourBy=NULL,igvParams=igvParam())ArgumentsSampleSheetAdata.frameobjectwithmetadatainformationforsamples.Firstcolumnmustcontainuniquesampleids.fileSheetAdata.frameoflelocations.Firstcolumnmustcontaintheuniquesampleids.igvdirectoryAcharacterofthedirectorytowhichsamplemetadataleiswritten.XMLnameAcharacterofthenameforIGVsessionxmlgenomeNameAcharacterofgenomeforIGV(SeeIGVuserguidefordetails)locusNameAcharacteroflocustodisplayinigvonloading(SeeIGVuserguidefordetails)colourByCharacterdeningwhichsamplemetadatatobeusedforcolouringbigwigles MakeIGVSessionXML9igvParamsAnobjectofclassigvParamcontainingdisplayparametersforIGV.Whenpro-vidingalist,thislistmustbesamelengthasnumberofsamplesandeachele-menthavetwonumericvaluescorrespondingtominimumandmaximumvaluetobeusedinsettingdatarange.Currentlyonly"autoscale"oralistofminimumandmaximumvaluesareaccepted.ValueAcharacteroflelocationfortheIGVsessionXMLAuthor(s)ThomasCarrollExamplesfileLocationssystem.file("extdata",package="tracktables")bigwigsdir(fileLocations,pattern="*.bw",full.names=TRUE)intervalsdir(fileLocations,pattern="*.bed",full.names=TRUE)bigWigMatcbind(gsub("_Example.bw","",basename(bigwigs)),bigwigs)intervalsMatcbind(gsub("_Peaks.bed","",basename(intervals)),intervals)fileSheetmerge(bigWigMat,intervalsMat,all=TRUE)fileSheetas.matrix(cbind(fileSheet,NA))colnames(fileSheet)c("SampleName","bigwig","interval","bam")SampleSheetcbind(as.vector(fileSheet[,"SampleName"]),c("EBF","H3K4me3","H3K9ac","RNAPol2"),c("ProB","ProB","ProB","ProB"))colnames(SampleSheet)c("SampleName","Antibody","Species")MakeIGVSession(SampleSheet,fileSheet,igvdirectory=getwd(),"Example","mm9") MakeIGVSessionXMLMakeIGVsessionXML DescriptionCreatessessionXMLforIGVfromaFileSheetoflelocations.UsageMakeIGVSessionXML(fileSheet,igvdirectory,XMLname,genomeName,locusName="All",colourBy=NULL,igvParams=igvParam()) 10maketracktableArgumentsfileSheetAdata.frameoflelocations.Firstcolumnmustcontaintheuniquesampleids.igvdirectoryAcharacterofthedirectorytowhichIGVXMLsessioniswritten.XMLnameAcharacterofthenameforIGVsessionxmlgenomeNameAcharacterofgenomeforIGV(SeeIGVuserguidefordetails)locusNameAcharacteroflocustodisplayinigvonloading(SeeIGVuserguidefordetails)colourByCharactervectorofRGBcolourstouseforcolouringdisplayedBigWigsigvParamsAnobjectofclassigvParamcontainingdisplayparametersforIGV.Whenpro-vidingalist,thislistmustbesamelengthasnumberofsamplesandeachele-menthavetwonumericvaluescorrespondingtominimumandmaximumvaluetobeusedinsettingdatarange.Currentlyonly"autoscale"oralistofminimumandmaximumvaluesareaccepted.ValueAcharacteroflelocationfortheIGVsessionXMLAuthor(s)ThomasCarrollExamplesfileLocationssystem.file("extdata",package="tracktables")bigwigsdir(fileLocations,pattern="*.bw",full.names=TRUE)intervalsdir(fileLocations,pattern="*.bed",full.names=TRUE)bigWigMatcbind(gsub("_Example.bw","",basename(bigwigs)),bigwigs)intervalsMatcbind(gsub("_Peaks.bed","",basename(intervals)),intervals)fileSheetmerge(bigWigMat,intervalsMat,all=TRUE)fileSheetas.matrix(cbind(fileSheet,NA))colnames(fileSheet)c("SampleName","bigwig","interval","bam")MakeIGVSessionXML(fileSheet,igvdirectory=getwd(),"Example","mm9") maketracktableMakeHTMLpagesforIGVsessions(TracktablesExperimentReport) DescriptionCreatesHTMLtableofsamplemetadataandallrequiredlesforinteractingwithIGV. maketracktable11Usagemaketracktable(fileSheet,SampleSheet,filename,basedirectory,genome,colourBy=NULL,igvParams=igvParam())ArgumentsfileSheetAdataframecontainingsamplelelocations(e.g.BigWiglocations).SampleSheetAdataframecontainingsamplemetadatafilenameCharacterofnamefortracktablesHTMLreport.(.htmlprexisaddedautomat-ically)basedirectoryCharacterofdirectoryfortracktablesHTMLreport,IGVsessionsandanyin-tervallesgenomeCharacterofgenomeforIGV(SeeIGVuserguidefordetails)colourByCharacterdeningwhichsamplemetadatatobeusedforcolouringbigwiglesigvParamsAnobjectofclassigvParamcontainingdisplayparametersforIGV.Whenpro-vidingalist,thislistmustbesamelengthasnumberofsamplesandeachele-menthavetwonumericvaluescorrespondingtominimumandmaximumvaluetobeusedinsettingdatarange.Currentlyonly"autoscale"oralistofminimumandmaximumvaluesareaccepted.ValueAnobjectcontainingXMLdocument(HTMLInternalDocument,XMLInternalDocument,XMLAbstractDocument)Author(s)ThomasCarrollExamplesfileLocationssystem.file("extdata",package="tracktables")bigwigsdir(fileLocations,pattern="*.bw",full.names=TRUE)intervalsdir(fileLocations,pattern="*.bed",full.names=TRUE)bigWigMatcbind(gsub("_Example.bw","",basename(bigwigs)),bigwigs)intervalsMatcbind(gsub("_Peaks.bed","",basename(intervals)),intervals)fileSheetmerge(bigWigMat,intervalsMat,all=TRUE)fileSheetas.matrix(cbind(fileSheet,NA))colnames(fileSheet)c("SampleName","bigwig","interval","bam")SampleSheetcbind(as.vector(fileSheet[,"SampleName"]),c("EBF","H3K4me3","H3K9ac","RNAPol2"),c("ProB","ProB","ProB","ProB"))colnames(SampleSheet)c("SampleName","Antibody","Species") 12maketracktableHTMLreportmaketracktable(fileSheet,SampleSheet,"IGV_Example.html",basedirectory=getwd(),"mm9") IndexdatasetsIntervals,6igvParam,2igvParam-class(igvParam),2Intervals,6makebedtable,6MakeIGVSampleMetadata,7MakeIGVSession,8MakeIGVSessionXML,9maketracktable,1013