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zktuong / ktplotspy

Python library for plotting Cellphonedb results. Ported from ktplots R package.
https://ktplotspy.readthedocs.io/
MIT License
46 stars 12 forks source link

Plot using mtx format (not .h5ad) #29

Closed DaianeH closed 11 months ago

DaianeH commented 1 year ago

Hi,

I'm new to cellphonedb and just run it on a Seurat object in mtx format (as described here): https://github.com/ventolab/CellphoneDB/blob/master/notebooks/DEGs_calculation/0_prepare_your_data_from_Seurat.ipynb not in a .h5ad format. If I don't have a .h5ad, how can I define the adata parameter to plot using ktplotspy?

Thank you in advance,

zktuong commented 1 year ago

hi @DaianeH,

actually there's is an R-package for ktplots https://github.com/zktuong/ktplots. You can feed your Seurat object to it (but generally works better as SingleCellExperiment).