Question

Hightlight genes/metabolites in Pathview and ReactomePA

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emisecherre • 0

@emisecherre-23089

Last seen 4.4 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 4.5 years ago by James W. MacDonald 67k • written 4.5 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 1 day 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 4.5 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 4.5 years ago emisecherre • 0