Question

Pathview: Exporting non native KEGG pathway to PNG

2

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guillermo.marco ▴ 30

@guillermomarco-11336

Last seen 7.7 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 • 2.4k views

ADD COMMENT • link updated 8.2 years ago by dondelelcaro ▴ 10 • written 8.3 years ago by guillermo.marco ▴ 30

0

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dondelelcaro ▴ 10

@dondelelcaro-11528

Last seen 8.1 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.

ADD COMMENT • link 8.2 years ago dondelelcaro ▴ 10

score 2 · Accepted Answer · 2016-08-23

2

Entering edit mode

Luo Weijun ★ 1.6k

@luo-weijun-1783

Last seen 17 months 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