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Question: Pathview: Exporting non native KEGG pathway ignoring same.layer argument
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gravatar for guillermo.marco
15 months ago by
Spain
guillermo.marco30 wrote:

When using pathview to save the following Sus scrofa KEGG pathway same.layer = TRUE argument seems to be ignored when also using kegg.native = FALSE. This is not happening with all the KEGG pathways, however I can't a find a repeat behavior.
Pathway PDF is generated in two sheets with legend on second page. You can check PDF result here: https://www.dropbox.com/s/4o97z1b8ji7diuh/ssc05166.pathview.pdf?dl=0

> genes

100158242 100152267    396960    397628 100738612 100127464    396875 100048932      <NA> 100520726 100624161    767625 100152590 100153002 100141423    397087 100521665 100523914
-3.253765 -3.253765 12.723644 -2.054660 -2.294707 -2.294707 -2.280152 -2.017907  7.720049 -4.358978 -2.883958 -5.870893  2.869302 -2.442875  3.030740 -3.383227  2.012139 -2.406322

pathview(gene.data = genes, pathway.id = "ssc05166", species = "ssc", kegg.native = FALSE, same.layer = TRUE, limit = list(10, cpd=1))
ADD COMMENTlink modified 15 months ago by Luo Weijun1.4k • written 15 months ago by guillermo.marco30
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gravatar for Luo Weijun
15 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
You are right same.layer = TRUE together with kegg.native = FALSE should produce a same page with both graph and legend. But in the R code you actually used above, same.layer = FALSE, i.e. pathview(gene.data = genes, pathway.id = "ssc05166", species = "ssc", kegg.native = FALSE, same.layer = FALSE, limit = list(10, cpd=1)) -------------------------------------------- On Wed, 8/24/16, guillermo.marco [bioc] <noreply@bioconductor.org> wrote: Subject: [bioc] Pathview: Exporting non native KEGG pathway ignoring same.layer argument To: luo_weijun@yahoo.com Date: Wednesday, August 24, 2016, 8:43 AM Activity on a post you are following on support.bioconductor.org User guillermo.marco wrote Question: Pathview: Exporting non native KEGG pathway ignoring same.layer argument: When using pathview to save the following Sus scrofa KEGG pathway same.layer = TRUE argument seems to be ignored when also using kegg.native = FALSE. So pathway is generated in two sheets with legend on second page. You can check PDF result here: https://www.dropbox.com/s/4o97z1b8ji7diuh/ssc05166.pathview.pdf?dl=0 > genes 100158242 100152267 396960 397628 100738612 100127464 396875 100048932 <na> 100520726 100624161 767625 100152590 100153002 100141423 397087 100521665 100523914 -3.253765 -3.253765 12.723644 -2.054660 -2.294707 -2.294707 -2.280152 -2.017907 7.720049 -4.358978 -2.883958 -5.870893 2.869302 -2.442875 3.030740 -3.383227 2.012139 -2.406322 pathview(gene.data = genes, pathway.id = "ssc05166", species = "ssc", kegg.native = FALSE, same.layer = FALSE, limit = list(10, cpd=1)) Post tags: Pathview, rgraphviz, graphviz, KEGG You may reply via email or visit Pathview: Exporting non native KEGG pathway ignoring same.layer argument
ADD COMMENTlink written 15 months ago by Luo Weijun1.4k

Did mistake when writing the original post, but edited later. Could you please the code (edited in question) and report if you're also getting two pages instead of one?

 

ADD REPLYlink written 15 months ago by guillermo.marco30
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