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Question: Pathview: Exporting non native KEGG pathway to PNG
2
gravatar for guillermo.marco
15 months ago by
Spain
guillermo.marco30 wrote:

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.

ADD COMMENTlink modified 14 months ago by dondelelcaro10 • written 15 months ago by guillermo.marco30
2
gravatar for Luo Weijun
15 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
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
ADD COMMENTlink written 15 months ago by Luo Weijun1.4k

Thanks for the fast answer!

Regards,
Guillermo.

ADD REPLYlink written 15 months ago by guillermo.marco30
0
gravatar for dondelelcaro
14 months ago by
dondelelcaro10
USA/Champaign/University of Illinois
dondelelcaro10 wrote:

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 COMMENTlink written 14 months ago by dondelelcaro10
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