How to row normalize a matrixplot?
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3 months ago
bioinfo ▴ 150

Hello,

I made a heatmap with the command shown below. I was told that some of the genes are more lowly expressed that other so it s hard to see them on the same scale and was asked to row normalize the heatmap. How can I do that? For the heatmap I have already produced I used the normalized and logarithmized data.

sc.pl.matrixplot(adata, markers, groupby='leiden_0.4', cmap="Oranges", use_raw=True, swap_axes = True)

Thank you

scRNA-seq RNA-seq single-cell scanpy • 415 views
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You can give a try with the standard_scale argument. From the documentation:

standard_scale : Optional[Literal['var', 'group']] (default: None)

Whether or not to standardize the given dimension between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum.

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Thank you. That is what I ended up doing.

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