[BioC] Retrieving KEGG pathway diagrams via KEGGSOAP

Paolo Sonego paolo.sonego at gmail.com
Fri Apr 17 16:52:20 CEST 2009

Dear Daren,

If you are in a Unix environment (Linux/Mac OS X), below there is a 
trivial example taking advantage of EBImage package and ImageMagick 
toolkit (sorry I can figure out how to use EBImage to combine the 
different images in a single pdf).

url <- mark.pathway.by.objects("path:hsa03050", c("hsa:5709", "hsa:10197"))
urls <- c(url, url, url) ## set different urls here
im.gif <- NULL
for (i in 1:length(urls)){
    im.gif <- readImage(urls[i], TrueColor)
    writeImage(im.gif, paste("pathway_", i, ".pdf", sep=""))

to combine the files in a single pdf:
system("convert pathway_* pathways.pdf")



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