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dpeerlab / SEACells

SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
GNU General Public License v2.0
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cell-cell affinity matrix #49

Open ytliu01 opened 1 year ago

ytliu01 commented 1 year ago

Hi,

Thanks for this fantastic tool! I read the paper introducing SEACell and felt like the cell-cell affinity matrix ordered by meta cells is a useful visualization (Fig1,h in the paper). I'm wondering if the package has a plotting function to make such a visualization.

Thanks!

ManuSetty commented 1 year ago

We unfortunately do not have the functionality but it should be relatively straightforward to make this plot. The kernel matrix is stored in model.K and the order of cells is same as that of the input. You can then use the kernel in model.K as input to seaborn heatmap or clustermap to generate the visualization.