Closed DaianeH closed 11 months 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,
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).
ktplots
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,