Question

Hightlight genes/metabolites in Pathview and ReactomePA

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emisecherre • 0

@emisecherre-23089

Last seen 4.3 years ago

Hello ! I would like to use Pathview and ReactomePA to visualize my pathways. I have a list of genes and metabolites of interest, and i would like to know how to highlight them (different color for exemple) in the pathway maps returned by these packages ? Thanks for your answer

pathview ReactomePA • 1.5k views

ADD COMMENT • link updated 4.4 years ago by James W. MacDonald 67k • written 4.4 years ago by emisecherre • 0

score 0 · Answer 1 · 2020-06-25

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 14 hours ago

United States

There are vignettes for pathview and ReactomePA that show how to do that. Is there something in particular that you don't understand?

ADD COMMENT • link 4.4 years ago James W. MacDonald 67k

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For ReactomePA, i don't get if theres an other way to color nodes than using p-values as i want to color genes and metabolites from my lists. And for pathview, i see its described on the section "8.1 Compound and gene data", but i really don't understand which parameters i have to change to color specific elements...

ADD REPLY • link 4.4 years ago emisecherre • 0