pathview produce 3 output files : what are they?

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4.5 years ago

okna0215 ▴ 10

Hello all.

Pathview produces 3 output files with the following command :

pathview(gene.data = foldchanges, pathway.id = '00040', speices = 'hsa', same.layer = F)

hsa00040.pathview.png (this plot have red or green colors (representing foldchanges))
hsa00040.png (some are colored in green)
hsa00040.xml (I have no idea)

Could you please tell me the difference between these files? What are green colors meaning in hsa00040.png?

pathview RNA-Seq • 2.3k views

ADD COMMENT • link 4.5 years ago by okna0215 ▴ 10

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Assuming you're using the Bioconductor package pathview, I suggest you read the doc and the vignette.

ADD REPLY • link 4.5 years ago by Jean-Karim Heriche 27k

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Yes it is bioconductor package. According to manual : 1. hsa00040.pathview.png : original KEGG pathway map 2. hsa00040.png (some are colored in green) : layered map with given values (foldchanges) 3. hsa00040.xml : data file

ADD REPLY • link 4.5 years ago by okna0215 ▴ 10

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