Daniel Dimitrov

Hmm, this seems like an OmniPathR issue @deeenes :pray:

Hi @RMOsborn012, Most of liana's plots return ggplot/patchwork objects and these can be modified to other colours. Also, for ComplexHeatmap I allow kwargs to be passed so one can adjust...

Hi @RMOsborn012, Yeah, I assume patchwork is making it too complicated. I will try to think how to enable palettes to be passed to the more complicated plots. Thanks for...

Hi @jjacob12, Sorry it took me a while to come back to you. Using your subset data, even with 1000 permutations it worked on my laptop. Also, there is nothing...

Hi @jjacob12, I believe the easiest way is to use [zellkonverter](https://www.bioconductor.org/packages/release/bioc/html/zellkonverter.html). `BiocManager::install("zellkonverter")` ``` sce

Tested your converted AnnData object in Python: ``` import scanpy as sc import liana as li adata = sc.read_h5ad("adata.h5ad") li.mt.rank_aggregate(adata, groupby='celltype', layer='logcounts', use_raw=False, verbose=True) adata.uns['liana_res'].head() ``` runs in ~ 30...

Hi @jjacob12 great :smiley:

Hi @reneemoerkens, Regarding the frequency heatmap, perhaps if the columns with cell types are categorical then the categories order would be kept - I haven't tried it, but might be...

Hi @hemadelon, I traced the interaction and it's original source is Cellinker: http://www.rna-society.org/cellinker/mysql_php/more.php?id=LR00955&species=Homo%20sapiens If you think that it's erroneous, I'm planning to update the PK of liana soon, and I...

Hi @reneemoerkens, If you could copy your code for the latter comment, I could see what you meant and try to implement it in a subsequent version. :) Glad to...