I am performing pathway analysis using the ReactomePA package and the clusterProfiler package. I did the pathway analysis and got 2 objects, one by using the enrichPathway() function from ReactomePA and one by using the enrichKEGG() function from clusterProfiler.
Both objects have the same class: enrichResult.
Now my question: I am able to do plots which each object itself, but can I also make a plot that shows the pathways of both objects? Or is there another way I can achieve this?
Thanks a lot for your help, I really like both packages!
Thanks, but the link gives me the 404 Error message.
how should i use the merge_result function? I read the clusterProfiler reference manual
simply putting in the list of enrichResults i want to merge doesn't work unfortunately....
Somehow the underscore in the URL malformatted it... the link above should be:
merge_results
expects multiple lists!The code below works (inspired by your use case):
It worked, but i got only 17 merged results and 16 plots even though i expected 39. The console put out the following:
Thanks for your help!
Please post your full code, ideally fully reproducible (thus using the included data set).... Your output as such is not very informative....
Alright, that's my code
I haven't fully checked your code, but based on the output you showed earlier: could it be that some of your input vectors consist of entrez ids that are not HUMAN entrez ids, or only of ids that are not (yet) annotated to a Reactome or KEGG pathway? That would explain that 'no gene cane be mapped'....
They're all human genes... when i did the enrichment analysis without merging both results it worked, so maybe the Error Message is related to the merge_result function...