## ----knitr, echo=FALSE, results="hide"----------------------------------- library("knitr") opts_chunk$set(tidy=FALSE,dev="png",fig.show="hide", fig.width=4,fig.height=4.5, message=FALSE) ## ----style, eval=TRUE, echo=FALSE, results="asis"------------------------ BiocStyle::latex() ## ----include=FALSE------------------------------------------------------- library(knitr) opts_chunk$set( concordance=TRUE ) ## ----options, results="hide", echo=FALSE--------------------------------- options(digits=3, width=80, prompt=" ", continue=" ") ## ----inputdata, eval=TRUE------------------------------------------------ library(tracktables) fileLocations <- system.file("extdata",package="tracktables") 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") ## ----head_samplesheet, eval=TRUE----------------------------------------- head(SampleSheet) ## ----head_filesheet, eval=FALSE------------------------------------------ ## head(FileSheet) ## ----Filesheet, eval=TRUE,echo=FALSE------------------------------------- FileSheetEdited <- FileSheet FileSheetEdited[,2] <- file.path("pathTo",basename(FileSheetEdited[,2])) FileSheetEdited[1,3] <- file.path("pathTo",basename(FileSheetEdited[1,3])) head(FileSheetEdited) ## ----IGVsessionAndSample, eval=FALSE------------------------------------- ## ## MakeIGVSession(SampleSheet,FileSheet,igvdirectory=getwd(),"Example","mm9") ## ----maketracktable, eval=FALSE------------------------------------------ ## HTMLreport <- maketracktable(fileSheet=FileSheet, ## SampleSheet=SampleSheet, ## filename="IGVExample.html", ## basedirectory=getwd(), ## genome="mm9") ## ----maketracktable_WithColoursAndScales, eval=FALSE--------------------- ## ## igvDisplayParams <- igvParam(bigwig.autoScale = "false", ## bigwig.minimum = 1, ## bigwig.maximum = 5) ## ## ## HTMLreport <- maketracktable(FileSheet,SampleSheet,"IGVex2.html",getwd(),"mm9", ## colourBy="Antibody", ## igvParam=igvDisplayParams) ## ----maketracktable_relativePaths part1, eval=FALSE---------------------- ## ## library(tracktables) ## ## 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) ## fileLocations <- file.path(getwd(),"IGVDirectory","extdata") ## ----maketracktable_relativePaths part2, eval=FALSE---------------------- ## ## 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") ## ----maketracktable_relativePaths part3, eval=FALSE---------------------- ## ## HTMLreport <- maketracktable(fileSheet=FileSheet, ## SampleSheet=SampleSheet, ## filename="IGVEx3.html", ## basedirectory=file.path(getwd(),"IGVDirectory"), ## genome="mm9") ## ----maketracktable_absolutePaths, eval=FALSE---------------------------- ## ## urlForFiles <- "https://github.com/ThomasCarroll/tracktables-Data/raw/master/" ## ## # This will link to data and XMLs placed in github earlier. ## # In practice a dedicated FTP would be required for larger files. ## HTMLreport <- maketracktable(fileSheet=FileSheet,SampleSheet=SampleSheet, ## filename="IGVEx4.html",genome="mm9", ## basedirectory=urlForFiles, ## full.xml.paths=T, ## full.file.paths=T, ## writedirectory=file.path(getwd(),"IGVDirectory") ## ) ## ----maketracktable_hybridPaths, eval=FALSE------------------------------ ## ## # Example URL ## urlForFiles <- "https://github.com/ThomasCarroll/tracktables-Data/raw/master/" ## ## HTMLreport <- maketracktable(fileSheet=FileSheet,SampleSheet=SampleSheet, ## filename="IGVEx5.html",genome="mm9", ## basedirectory=urlForFiles, ## full.xml.paths=F, ## full.file.paths=T, ## writedirectory=file.path(getwd(),"IGVDirectory") ## ) ## ----maketracktable_asisPaths, eval=FALSE-------------------------------- ## urlForFiles <- "https://github.com/ThomasCarroll/tracktables-Data/raw/master/" ## ## HTMLreport <- maketracktable(fileSheet=FileSheet,SampleSheet=SampleSheet, ## filename="IGVEx6.html",genome="mm9", ## basedirectory=urlForFiles, ## full.xml.paths=F, ## full.file.paths=T, ## writedirectory=file.path(getwd(),"IGVDirectory"), ## use.path.asis=T ## ) ## ## ----sessionInfo, results='asis', eval=TRUE------------------------------ toLatex(sessionInfo())