scanpy
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Single-cell analysis in Python. Scales to >1M cells.
Is it possible to have one figure pf spatial gene expression stack over (superimpose) another? The following function will give me two subplots instead of an integrated one `sc.pl.spatial(ada, img_key="hires",...
Hey, we moved from conda-forge to Bioconda -> https://github.com/scverse/scanpy/issues/1169 Unfortunately, this comes at a cost which is highly relevant for pipeline building. nf-core wants to add support for scverse data...
- [x] Other? Quick documentation fix, under sc.tl.louvain: https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.louvain.html The return info only includes `adata.obs['louvain']` and doesn't include `adata.uns['louvain']['params']`
- [ ] Additional function parameters / changed functionality / changed defaults? Hi there, it would be great to have the counts layer being added automatically to the anndata object...
Alternative to #2255 Fixes #2254, #2227 Puts all the diffmap specific logic inside the diffmap plotting function. ## TODO - [ ] consider the components argument - [ ] tests...
Fixes #2267 ## TODO - [ ] Tests - [ ] Changelog
Fixes https://github.com/scverse/scanpy/issues/2254 https://github.com/scverse/scanpy/issues/2227 Before there was a hard coded offset for the diffmap basis (https://github.com/scverse/scanpy/blob/8736fc3b02a6af3b7214481c2cf78a3f8f5e06bd/scanpy/plotting/_tools/scatterplots.py#L1077) and later it disappeared. This restores the offset for diffmap, and also provides an option...
**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing how to provide the necessary information for us to reproduce your bug. ### Minimal code sample (that we can copy&paste without having any data)...
- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [ ]...
Wish to add pyliger into sc.external. Here is the link: https://github.com/welch-lab/pyliger Thanks!
