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zktuong / dandelion

dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
https://sc-dandelion.readthedocs.io/
GNU Affero General Public License v3.0
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TypeError: clone_overlap() got an unexpected keyword argument 'colorby' #392

Open NicolaasVanRenne opened 3 months ago

NicolaasVanRenne commented 3 months ago

Description of the bug

I am running the tutorial V(D)J analysis. When I run ddl.tl.clone_overlap(adata, groupby="leiden", colorby="leiden", weighted_overlap=True) I get this error: Traceback (most recent call last): File "", line 1, in TypeError: clone_overlap() got an unexpected keyword argument 'colorby'

No idea why it does not work.

I can remove the colorby by running ddl.tl.clone_overlap(adata, groupby="leiden", weighted_overlap=True)

But when I plot it, I get this lousy image:

shared_clonotype

I have no idea why this goes wrong....

Minimal reproducible example

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The error message produced by the code above

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OS information

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Version information

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Additional context

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zktuong commented 3 months ago

hi @NicolaasVanRenne ,

the function you called is ddl.tl.clone_overlap, which doesn't have the colorby option, hence that error message. https://sc-dandelion.readthedocs.io/en/latest/modules/dandelion.tools.clone_overlap.html

The reason why the lines are very thick is because you have specified: weighted_overlap=True - the thickness scales to the number of cells. if False, then it will just be a thin line like in the tutorial.