Scaling Gene Set Heatmap

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1

Hello,

I am currently trying to plot a selection of gene sets on a heat map via the following overall workflow:

1)DEG analysis
2)GSEA on DEG
3)sc.tl.score_genes() on ~20 relevant gene sets
4)using sc.pl.heatmap() to plot the gene sets

I set the standard_scale parameter to “vars” in order to scale all the gene set values to between 0 and 1, and it looks quite good. Is there a way to scale the gene set values so they instead fall between -1 and 1?

Thanks for all the great work and any help you can provide!

2

Hello,

I’m entirely sure about this but you may try vcenter, vmax, vmin. Let me know if it works!

Shahroze

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3

I ended up using the following solution that GitHub copilot generated for me, and it seems to work quite well. I basically use the sklearn MinMaxScaler to scale the column of the obs dataframe containing the score_gene() output for each gene set. Do you think this is appropriate in this context?

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4

I’m not sure to be honest, but it’s worth a shot to try. The parameters I suggested earlier are directly part of the heatmap function so may be easier to implement. Whatever gets you the result you’re looking for :slight_smile: