[BioC] pathview

Luo Weijun luo_weijun at yahoo.com
Wed Oct 2 18:46:51 CEST 2013

Hi Hilary,
It straightforward to include in pathview options to output the native kegg graphs in other format, like PDF or postscript. I originally had that in the early development phase of pathview. But I decided not to do that, because the file size of raster image format like PDF output from R is huge (> 10 times the size of PNG output), and without any gain of resolution. Note that pathview output resolution is limited by the source KEGG graphs (in PNG), which are usually not extremely high as they are raster image. Therefore it is better stick to PNG. I believe many journals are okay with PNG. You may always do the format conversion in adobe illustrator etc for pulication purpose.
You are right you need to use the latest/development version to use the Kegg gene IDs for many minor species like in your case. If you need to do pathway analysis on your species, the latest gage package also has a new function kegg.gsets, to compile pathway gene set any of the 2300 KEGG species and KEGG Orthology (with species="ko").

On Tue Oct 1 Hilary Smith wrote:

I just started using pathview (great program!) and was wondering if there is a way to make the images in eps format vs the .png files that are produced, so that I can use the images for publication in journals requiring eps. I don't think a standard postscript command like I normally use in R would work here, because the figure generation automatically occurs when I use the ">pathview" command. At present I am using the Development version of the package (see below) because I have a "non-model" organism (mosquito, Anopheles), and it seems I need to use the latest/development version to use the Kegg gene IDs for my organism (e.g., "AgaP_AGAP005583"). I can re-save and thus convert the PNG image as EPS in ADOBE, but I am not sure if that'll decrease resolution relative to making the format in EPS in R originally.

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