[BioC] info on pathview

[Luo Weijun]

Dear Mori,
Thank you for the
note and interest in Pathview.
For KEGG view, we
map the user data onto native KEGG graph. And the resolution is really bounded
by the original KEGG graph. The argument res in the keggview.native function is
there to help the development process and will be removed eventually. It has
little effect if you want to achieve higher resolution. As you note that it may
change Pathview stamp font size (and gene label sizes when same.layer=F).
I would recommend you
sticking to the default resolution setting, which has been optimized over the
development process. The graphs in the Pathview papers and tutorials were all
generated using the default resolution setting. We can’t really do anything to improve
the original KEGG graph. However, improper conversion of the PNG image into PDF
format (for instance, in some journal editing process) may lower the
resolution. HTH.
Weijun





________________________________
From: Mori Elisa <emori at sienabiotech.it>
To: "'luo_weijun at yahoo.com'" <luo_weijun at yahoo.com> 
Sent: Monday, July 1, 2013 5:16 AM
Subject: info on pathview



Dear Weijun,

I am using your R package Pathview to download Kegg pathway, mapping genes with my data.
I would like first of all, thank you for this useful and beautiful package!
But I am not able to change the resolution of the picture. I would like to include the picture in a publication and I need 1000 dpi resolution. I tried to change it but, using Kegg visualization (kegg.native = TRUE) and in the same layer (same.layer = TRUE), the resolution changes only the size of gene names and not the entire resolution. Is it possible to change it? And which is the resolution you used in your paper?

Thank you in advance,
Best regards,
Elisa

Elisa Mori, PhD
Data Analysis
Tel :(+39) 0577 381 462
emori at sienabiotech.it

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