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Question: info on pathview
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gravatar for Luo Weijun
5.1 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
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@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 Please??consider the environment before printing ________________________________ La Siena Biotech S.p.A., nella qualit? di titolare, tratta i Suoi dati??esclusivamente per le finalit? amministrative e contabili della propria??attivit?, anche in occasione della loro comunicazione a terzi.??L?informativa estesa ivi comprensiva del diritti ex art. 7 ? visionabile??su www.sienabiotech.com? . The Company, Siena Biotech SpA, as data??controller, deals with your personal data only for administrative and??accounting purposes of its activities, even in case of the communication??to third parties. The information which includes the rights of section 7??is available on: www.sienabiotech.com? ???
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