Vladimir Shitov

Hi! `RecursionError` means that some recursive function exceeded the recursion limit. You can check, how big this limit is by running: ```python import sys print(sys.getrecursionlimit()) ``` You may increase it...

Faced exactly the same problem with file "GSE185477_GSM3178784_C41_SC_raw_counts.zip" from [GSE185477](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185477) The advice from @hurleyLi helped, thanks a lot! But the error is quite confusing. It would be great to read...

Hi! This is answered here: https://github.com/scverse/scanpy/issues/2669 TLDR: set a higher `span`, when calculating HVGs. 0.5 worked for me. For example, ```python sc.pp.highly_variable_genes(x, flavor='seurat_v3', n_top_genes=50, batch_key='sampleid', subset=True, span=0.5) ```

@ivirshup , this issue can be closed both as solved and as a duplicate. Also, please check my comment in https://github.com/scverse/scanpy/issues/2669

Maybe this library would help? https://github.com/TutteInstitute/datamapplot It is pretty new, but looks promising and is maintained by @lmcinnes, the author of UMAP

I also modified the code of @ivirshup a bit to colorize labels by their color on the scanpy plots: ```python from adjustText import adjust_text def gen_mpl_labels( adata, groupby, exclude=(), ax=None,...

@GirayEryilmaz , sure! Here's how I used it: ```python with plt.rc_context({"figure.figsize": (8, 8), "figure.dpi": 150, "figure.frameon": False}): ax = sc.pl.umap(adata, color=cell_type_key, show=False, legend_loc=None, frameon=False) gen_mpl_labels( adata, cell_type_key, exclude=("None",), # This...

> > @VladimirShitov can you give an example of how you use the gen_mpl_labels function? I tried it and got somewhat different results. For example it lacked the lines pointing...

Great tutorial, thank you, Karin! Maybe it makes sense to set the background for figures to white at the beginning of the notebook. Currently it is transparent, which looks weird...

Hi, @flying-sheep . As a workaround, you can create an additional column in `.obs`, which would be a concatenated cell type + condition. E.g. "Tcell_healthy", "Tcell_disease". Then just build a...