clustering using leiden algorithm

Hello I'm trying to perform clustering on my data using scanpy.

I used this tutorial: https://github.com/mousepixels/sanbomics_scripts/blob/main/single_cell_analysis_complete_class.ipynb

My question is how I can store the plot generated using this command line in a file (png format for example):

sc.pl.umap(adata, color = ['leiden', 'Sample'], frameon = False)

Thank you

leiden scanpy scrna-seq

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written 3.1 years ago by dalibenam64 •

Easiest way is the save argument: sc.pl.umap(adata, color=['leiden', 'Sample'], frameon=False, save='myplot.png')

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written 3.1 years ago by LChart

thank you very much

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written 3.1 years ago by dalibenam64 •

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