This relies on the data output that is being produced from RSeQC and ends up in one folder. All variables that this document is dependent on can be changed either in the header of by calling the document including parameters.
```r
RfunctionsDirectory = params$RfunctionsDirectory RseqFunctionsFile = paste(RfunctionsDirectory,"RSeQCfunctions.R", sep="/") source(RseqFunctionsFile) workingDirectory = params$workingDirectory resultsDir = params$resultsDir metaDataTableFile = params$metaDataTableTxt metaData = read.table(paste(workingDirectory,metaDataTableFile,sep= "/"), sep = "\t", header = TRUE,comment.char=""); plot = getTPKMPlots(resultsDir,metaData) plot
RfunctionsDirectory = params$RfunctionsDirectory RseqFunctionsFile = paste(RfunctionsDirectory,"RSeQCfunctions.R", sep="/") source(RseqFunctionsFile) workingDirectory = params$workingDirectory resultsDir = params$resultsDir metaDataTableFile = params$metaDataTableTxt metaData = read.table(paste(workingDirectory,metaDataTableFile,sep= "/"), sep = "\t", header = TRUE,comment.char=""); plot =getTINPlots(resultsDir,metaData) plot print ("")
RfunctionsDirectory = params$RfunctionsDirectory RseqFunctionsFile = paste(RfunctionsDirectory,"RSeQCfunctions.R", sep="/") source(RseqFunctionsFile) workingDirectory = params$workingDirectory resultsDir = params$resultsDir metaDataTableFile = params$metaDataTableTxt metaData = read.table(paste(workingDirectory,metaDataTableFile,sep= "/"), sep = "\t", header = TRUE,comment.char=""); plot =getGeneBodyCoveragePlots(resultsDir,metaData) plot[[1]] plot[[2]]
RfunctionsDirectory = params$RfunctionsDirectory RseqFunctionsFile = paste(RfunctionsDirectory,"RSeQCfunctions.R", sep="/") source(RseqFunctionsFile) workingDirectory = params$workingDirectory resultsDir = params$resultsDir metaDataTableFile = params$metaDataTableTxt metaData = read.table(paste(workingDirectory,metaDataTableFile,sep= "/"), sep = "\t", header = TRUE,comment.char=""); plot =getJunctionSaturationPlots(resultsDir,metaData) plot[[1]] plot[[2]]
RfunctionsDirectory = params$RfunctionsDirectory RseqFunctionsFile = paste(RfunctionsDirectory,"RSeQCfunctions.R", sep="/") source(RseqFunctionsFile) workingDirectory = params$workingDirectory resultsDir = params$resultsDir metaDataTableFile = params$metaDataTableTxt metaData = read.table(paste(workingDirectory,metaDataTableFile,sep= "/"), sep = "\t", header = TRUE,comment.char=""); plot =getClippingProfilePlots(resultsDir,metaData) plot[[1]] plot[[2]]
RfunctionsDirectory = params$RfunctionsDirectory RseqFunctionsFile = paste(RfunctionsDirectory,"RSeQCfunctions.R", sep="/") source(RseqFunctionsFile) workingDirectory = params$workingDirectory resultsDir = params$resultsDir metaDataTableFile = params$metaDataTableTxt metaData = read.table(paste(workingDirectory,metaDataTableFile,sep= "/"), sep = "\t", header = TRUE,comment.char=""); if(any(colnames(metaData) == "Type")){ if(any(metaData$Type=="PE")){ plot =getClippingProfilePlots(resultsDir,metaData) plot[[1]] plot[[2]] } }else{ print("No info about paired end reads") }
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