[BioC] Visualise KEGG pathway and highlight genes

Paolo Sonego paolo.sonego at gmail.com
Fri Apr 17 12:29:20 CEST 2009

Hi Daniel,
If you wish to convert the gif generated at the specific url (taking 
advantage of the KEGGSOAP package) to a PDF then you can use  the 
awesome EBImage package (which relies on the ImageMagick suit) in this way:

## Using the example from the KEGGSOAP manual

url <- color.pathway.by.objects("path:eco00260",
                c("eco:b0002", "eco:c00263"),
                c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))

filename="KEGGMAP.pdf" # the extension is mandatory 
im.gif <- readImage(url, TrueColor)
writeImage(im.gif, filename)


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