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Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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scanpy.api.tl.diffmap documentation #827

Closed veghp closed 3 years ago

veghp commented 4 years ago

Please consider mentioning explicitly in the documentation of scanpy.api.tl.diffmap that "the 0-th column is the steady-state solution, which is non-informative in diffusion maps", as mentioned here: https://github.com/theislab/single-cell-tutorial/blob/master/latest_notebook/Case-study_Mouse-intestinal-epithelium_1906.ipynb. Also that it's not plotted by default, cf. https://github.com/theislab/scanpy/issues/675.

It is very important for those who want to use these coordinates (adata.obsm["X_diffmap"]).

ivirshup commented 3 years ago

This issue has been mentioned on Scanpy. There might be relevant details there:

https://scanpy.discourse.group/t/how-are-the-diffusion-plots-generated/400/2