[BioC] Visualise KEGG pathway and highlight genes

[Daren Tan]

This solution is exactly what I am looking for in my previous post.
How to improve the resolution ?

On Fri, Apr 17, 2009 at 6:29 PM, Paolo Sonego <paolo.sonego at gmail.com> wrote:
> 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
>
> library(KEGGSOAP)
> url <- color.pathway.by.objects("path:eco00260",
>               c("eco:b0002", "eco:c00263"),
>               c("#ff0000", "#00ff00"), c("#ffff00", "yellow"))
>
>
> library(EBImage)
> filename="KEGGMAP.pdf" # the extension is mandatory im.gif <- readImage(url,
> TrueColor)
> writeImage(im.gif, filename)
>
>
>
> Regards,
> Paolo
>
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