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