search

zcang / COMMOT

MIT License
89 stars 13 forks source link

tradeseq is not working #16

Open bernard2012 opened 1 year ago

bernard2012 commented 1 year ago

Can you release a version without dependency on rpy2? It seems rpy2 relies on a very specific combination of Python and R. I have R 3.6 + Python 3.6, and R 4 + Python 3.10. But I do not have the Python 3.7 + R 3.6 combination that is required of using tradeseq. I tried using conda, but ended up with a mess, because apparently pip tries to install the most up to date version of pre-requisite packages that either do not compile or are not supported in older Python 3.7. All of these seem to be related to rpy2.

Can you put up a conda environment? Or release without rpy2?

ccruizm commented 1 year ago

Hello @bernard2012, could you figure this out? Also trying to implement commot+tradeseq but have faced the same problems 😕

biopzhang commented 1 year ago

I had similar problem here.

My set up is: MacOS Ventura Python==3.9.16, rpy2==3.5.11, anndata2ri==1.2 tradeSeq 1.10.0, R version 4.2.2

I made a couple of changes in the tools/_downstream_analysis.py and it worked. Feel free to access my modified one (https://github.com/biopzhang/COMMOT/blob/main/commot/tools/_downstream_analysis.py). If @zcang is interested, please investigate and consider to incorporate it to the repo. Nonetheless, I'm not a huge fan of rpy2, I would rather consider to directly run the R code in R environment and read the outputs from python (which is also painful) ...