Pathview: Exporting non native KEGG pathway to PNG
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@guillermomarco-11336
Last seen 4.4 years ago
Spain

Hello,

I'm trying to export a KEGG using the Pathview package. I'm interested on KEGG non-native plot (kegg.native = F). It works like a charm however it only exports the plot to PDF format. Is there any workaround to generate the plot also in PNG format?

pathview(gene.data  = geneList,
                     pathway.id = "hsa04110",
                     species    = "hsa",
                     limit      = list(10, cpd=1),
                     kegg.native = F)

I've been trying with keggview.graph() but I got stuck.

Regards,
Guillermo.

pathview bioconductor graphics graphviz Pathview • 892 views
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 21 days ago
United States
Guillermo, Currently, Pathview only outputs graphviz view (non-native KEGG graphs) in pdf format. If you png file is desirable you may open that in Illustrator and save it in png or other formats. We will add the png format option if we see more need from the users. Weijun
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Thanks for the fast answer!

Regards,
Guillermo.

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dondelelcaro ▴ 10
@dondelelcaro-11528
Last seen 4.7 years ago
USA/Champaign/University of Illinois

If you use the patch that I just created (https://github.com/dondelelcaro/pathview) you can call png() before calling pathview(...,write.plot=FALSE) if that's helpful.

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