Zero value with scvi normalisation

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1

Hello,

I did a normalisation with scvi-tools. Now I want to use the dotplot function of scanpy.
Unfortunatly, the normalisation seems to have modified all the zero value to non zero. Thus when using the dotplot function I do not have anymore information about the % of cells expressing the genes. There si no more zero value so 100% of cells express each genes.

How would you deal with that ?

2

Hi, you can use the expression_cutoff argument in scanpy.pl.dotplot and adjust it or you can use the posterior_predictive_sample function to actually generate count data. However, this function does not support projecting to batches.