Alexey Sergushichev
Alexey Sergushichev
@mjsteinbaugh @llrs I was again thinking about this issue and still don't want to remove `theme_bw()` or something equivalent, as this is rather complex plot, and want for it to...
Actually, may be I don't need much from `theme_bw()`, just remove the background and change major grid lines, so I guess we do can remove the call: ``` with(pRaw, ggplot(data=curve)...
fixed by https://github.com/ctlab/fgsea/commit/7f9ac2844bb88762728a78534e195ebe26c73ecd
@ChristianRohde please check if the BiocParallel example above works for you or not.
@mvhunter1 Is it the problem of some particular dataset or it hangs on different inputs?
@mvhunter1 Does it fail for the example dataset? Does setting `nperm=1000` help? It looks like a different problem, not the one described in this issue, so please create another issue...
Reopening, as this question arises regularly
@Close-your-eyes I guess you can use that as well if it works for you. Although I would say that logFC can be estimated more directly by the differential expression method.
Hi, it's a good question. I wasn't able to quickly find an easy way to do this. You can try to modify the plot yourself, as plotEnrichment function returns ggplot...
Additionally, you can use fgsea::plotEnrichment function source code as a template, and make your own function.