Hi, I am following this workflow. At step 6.1 second paragraph it says here we only visualize up-regulated pathways! I wonder how should I change the codes to visualize the down-regulated pathways? A beginner is writing this!
A second question I have is, in last paragraph of same part (6.1) it says we can use Pathview to visualize RNA-Seq data (exp.fc) on all interesting pathways! I wonder is it something else than what I got from the output of
> pv.out.lits <- sapply(path.ids2, function(pid) pathview(gene.data=exp.fc,
+ pathway.id=pid, species="spo", out.suffix=out.suffix, gene.idtype="KEGG"))