Question: Is there a way to visualize log fold changes for Reactome pathways in R?
gravatar for Gabriel
15 months ago by
Gabriel60 wrote:

With KEGG, we can use the tool Bioconductor to plot our pathways with the logfold changes for our datasets, using R. Like this:

Pathview visualization of fold changes This can also be done with WikiPathways and Cytoscape, by downloading the images and uploading the fold changes into cytoscape via R tools such as RCy3.

Can the same be done with Reactome? I preferrably want the pathways in the original representation as shown on the svg file on the reactome website. Like this: reactome svg patway image But with log fold changes. There is a way to do this in ReactomePA, but it shows the result in a dissociated network diagram that is hard to make sense out of.

ADD COMMENTlink written 15 months ago by Gabriel60
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