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Here is my working R code for the task. It can be simplified as 3 lines.

# example of controling individual track

#theURL=”http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&wgRna=hide&cpgIslandExt=pack&ensGene=hide&mrna=hide&intronEst=hide&mgcGenes=hide&hgt.psOutput=on&cons44way=hide&snp130=hide&snpArray=hide&wgEncodeReg=hide&pix=1000&refGene=pack&knownGene=hide&rmsk=hide“

# example of controling via session

theURL=”http://genome-preview.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=sterding&hgS_otherUserSessionName=mm9_piRNA&hgt.psOutput=on&pix=1000“

# read regions

toPlot=read.table(“../data/piRNA.clusters.coordinates.cpg.bed”, header=T)

## paralle version

# library(multicore)

# mclapply(1:nrow(toPlot), function(i) screenshotUCSC(theURL, “”, as.character(toPlot$chr[i]), toPlot$start[i]-2000, toPlot$end[i]+1999, paste(“region_”, i, “_”, toPlot$name[i],”.pdf”, sep=””)), mc.cores=10)

# anti-robot version 

# UCSC Policy: Program-driven use of this software is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day.

for(i in 1:nrow(toPlot)){

    screenshotUCSC(theURL, “”, as.character(toPlot$chr[i]), toPlot$start[i]-2000, toPlot$end[i]+1999, paste(“region_”, i, “_”, toPlot$name[i],”.pdf”, sep=””))

    Sys.sleep(5) 

}

# merge script

mergePDF(“piRNAs_ucsc_screeshot.pdf”, list.files(pattern=”region_.*.pdf”))

try(system(“rm region_.*.pdf”))

####### lib ############

# Here is an R script wrote by Aaron Statham which saves UCSC to pdfs –

# you can choose which genome and tracks to display by altering the ‘url’ parameter. ‘trackfile’ is the url of a file describing the custom tracks (beds/bigwigs) to display

mergePDF <- function(output="merged.pdf", sourcefiles=c("source1.pdf","source2.pdf”,”source3.pdf”))

{

    # create the command string and call the command using system()

    # merging command from http://hints.macworld.com/article.php?story=2003083122212228

    command=paste(“gs -q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite”,paste(“-sOutputFile”,output, sep=”=”), paste(sourcefiles, collapse=” “),sep=” “)

    try(system(command))

}

#  Reference: http://www.biostars.org/post/show/6132/batch-viewing-of-ucsc-browser-graphic/

screenshotUCSC <- function(url, trackfile, chr, start, end, filename) {

        oldpen <- options("scipen")

        options(scipen=100)

        temp <- readLines(paste(url, "&hgt.customText=", trackfile, "&position=",chr,":",start,"-",end, sep=””))

        #cat(temp,”\n”)

        pdfurl <- paste("http://genome-preview.ucsc.edu/trash“,gsub(“.*trash”,””,gsub(“.pdf.*”,””,temp[grep(“.pdf”, temp, fixed=TRUE)][1])), “.pdf”, sep=””)

        cat(pdfurl,”\n”);

        options(scipen=oldpen)

        download.file(pdfurl, filename, mode=”wb”, quiet=TRUE)

}

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