# Integration with Rmarkdown This is an example of integrating a Tracktables report into a RMarkdown document. ```r library(tracktables) options(markdown.HTML.header = system.file("misc", "datatables.html", package = "knitr")) oldFileLocations <- system.file("extdata",package="tracktables") dir.create(file.path(getwd(),"IGVDirectory"), showWarnings = FALSE,recursive = TRUE) file.copy(oldFileLocations, file.path(getwd(),"IGVDirectory"), recursive = TRUE) ``` ``` ## [1] TRUE ``` ```r fileLocations <- file.path(getwd(),"IGVDirectory","extdata") ``` Next the samplesheet of metadata and filesheet of locations is created. ```r bigwigs <- dir(fileLocations,pattern="*.bw",full.names=TRUE) intervals <- dir(fileLocations,pattern="*.bed",full.names=TRUE) bigWigMat <- cbind(gsub("_Example.bw","",basename(bigwigs)), bigwigs) intervalsMat <- cbind(gsub("_Peaks.bed","",basename(intervals)), intervals) FileSheet <- merge(bigWigMat,intervalsMat,all=TRUE) FileSheet <- as.matrix(cbind(FileSheet,NA)) colnames(FileSheet) <- c("SampleName","bigwig","interval","bam") SampleSheet <- cbind(as.vector(FileSheet[,"SampleName"]), c("EBF","H3K4me3","H3K9ac","RNAPol2"), c("ProB","ProB","ProB","ProB")) colnames(SampleSheet) <- c("SampleName","Antibody","Species") ``` The tracktables report is created from a call to \texttt{maketracktable}. By default all paths are created relative the directory specified by \texttt{basedirectory}. ```r HTMLreport <- maketracktable(fileSheet=FileSheet, SampleSheet=SampleSheet, filename="IGVEx3.html", basedirectory=getwd(), genome="mm9") ``` ``` ## tracktables uses the Datatables javascript libraries. ## For information on Datatables see http://datatables.net/ ``` ```r cat(HTMLreport) ```