Further improvements for the advanced visualisation tutorial

scverse / scanpy-tutorials

Scanpy Tutorials.

https://scanpy-tutorials.readthedocs.io/

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Further improvements for the advanced visualisation tutorial #62

Open Hrovatin opened 1 year ago

Hrovatin commented 1 year ago

[ ] More notes on how to deal with more complex plots, e.g. DotPlot
[ ] Split up dotplot https://github.com/scverse/scanpy/issues/1956
[ ] Legend hierarchy https://github.com/scverse/scanpy/issues/2024
[ ] Access color palettes and make palettes taht were not yet added https://github.com/scverse/scanpy/issues/1881
[ ] Improve explanation of palettes (uns colors as list correspond to categories, how to generate palette for categorical with scanpy function).

VladimirShitov commented 1 year ago

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 when using Github's dark theme:

Also, I would suggest some standardization regarding how to call variables with Axes. In some places, they are called axes, and in some axs. I believe, axes is a more common approach.

And I believe, it is good to stick to PEP8 style in the code to teach the users good ;)

spatts14 commented 2 weeks ago

Hi I was wondering if it is possible to split the dotplot bases on condition? i.e you have cell type on x axis, gene on y axis, but have 2 dots per pairing (one for each condition)? I couldn't find documentation on how to do it, although seems like its mentioned here?

VladimirShitov commented 2 weeks ago

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 dotplot normally with this column