Lisa Sikkema

Hi! I have exactly the same problem, is anyone looking into this yet?

Hi Quentin, When you plot a categorical variable for the first time, scanpy stores the colors for each category in adata.uns, that's why it is modifying your adata. For continuous...

This is probably addressed in #2267

This happens after using anndata.concat if I remember correctly @Mari123i ? Then better to check out the [anndata GitHub](https://github.com/scverse/anndata/blob/dbe85e55012d5d5204ab34f6d885c8964d36414d/docs/index.rst) and submit your issue there

Interesting! Yes I think it would

Hi @UboCA, You can use the `row_palette` argument for this, as in this example: ```python import scanpy as sc adata = sc.datasets.pbmc3k_processed() sc.pl.stacked_violin( adata, var_names=["PTPRC", "RER1"], groupby="louvain", row_palette="tab10", # swap_axes=True,...

I have the same problem. Did anyone find a solution yet?

I think they just forgot to add one line (based on my understanding of the code and the MNN code in R). I created a fork with the corrected code,...

Thanks a lot for the quick response! I'm not sure if I understand though: I get that the model parameters for calculating the reference embedding aren't changed, but this should...

Okay interesting! It actually sounds like the current default defeats the purpose of scArches as a whole, with no batch correction being performed during the mapping (at least at the...