Question: pathview produce 3 output files : what are they?
0
gravatar for okna0215
6 weeks ago by
okna02150
okna02150 wrote:

Hello all.

Pathview produces 3 output files with the following command :

pathview(gene.data = foldchanges, pathway.id = '00040', speices = 'hsa', same.layer = F)
  1. hsa00040.pathview.png (this plot have red or green colors (representing foldchanges))

  2. hsa00040.png (some are colored in green)

  3. hsa00040.xml (I have no idea)

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

rna-seq pathview • 79 views
ADD COMMENTlink written 6 weeks ago by okna02150

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

ADD REPLYlink written 6 weeks ago by Jean-Karim Heriche23k

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 REPLYlink written 27 days ago by okna02150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1051 users visited in the last hour