Scale in plot_genes_per_cell_type

[ChristinaSteyn]

Hi there,

Thank you for your assistance with Cell2location thus far! Could you please explain to me what the scale represents in the plots generated from the plot_genes_per_cell_type. I have run the scripts and gotten an output looking something like this:

I've now adjusted the scale to run from 0 to 1 but I was wondering what the values represent and why there are some negative values (are these scaled counts?).

Thank you in advance!

[vitkl]

These are standard scanpy spatial plots - not specific to the cell2location package. Please refer to their documentation.
Here vmax option is set to a high quantile of the count distribution. When you have too few counts you get the plots like you observe.