Question

Pathview: Exporting non native KEGG pathway ignoring same.layer argument

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guillermo.marco ▴ 30

@guillermomarco-11336

Last seen 7.8 years ago

Spain

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))

Pathview rgraphviz graphviz KEGG • 1.6k views

ADD COMMENT • link updated 8.3 years ago by Luo Weijun ★ 1.6k • written 8.3 years ago by guillermo.marco ▴ 30

score 0 · Answer 1 · 2016-08-25

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