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ebi-gene-expression-group / scanpy-scripts

Scripts for using scanpy
Apache License 2.0
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Make sure that paga without basis uses color if given #100

Closed pcm32 closed 3 years ago

pcm32 commented 3 years ago

Currently paga is missing the color attribute, which should explain why when it is given on Galaxy on plot trajectory it has no effect:

scanpy-cli plot paga --use-key 'paga' --layout fa --legend-loc 'right margin' \
    --threshold 0.01  --solid-edges connectivities \
    --color 'cell_type,ENSMUSG00000023274,ENSMUSG00000053977' \
    --node-size-scale 1.0 --edge-width-scale 1.0 --show-obj stdout \
    --output-format anndata --output-obj output.h5  --input-format 'anndata' input.h5   \
    --fig-size '4,4' --fig-dpi 80 --fig-fontsize 10 --frameoff ./output.png

image

After the required releases everywhere, this should fix https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/issues/232

pcm32 commented 3 years ago

After these changes on the conda env, in Galaxy I produced the desired plot (with the same job redone):

image

pcm32 commented 3 years ago

We might want to pin to Scanpy 1.7.2, recent Scanpy 1.8.0 is breaking a lot of tests I would suggest.

pcm32 commented 3 years ago

Thanks for review and fixes @pinin4fjords. I'll try to get in the other plotting fix one of these nights and then go for a release.