show the mean of several genes in spatial scanpy figure

[sophieRAIBAUD]

... Hello

I would like to plot the "log1p_total_counts" of a visium transcriptomic dataset (AnnData object with n_obs × n_vars) using sc.pl.spatial

sc.pl.spatial(adatal, img_key="hires", color=["gene1", "gene2", "gene3"]) --> gives 3 images (the 3 genes are plotted stacked on 3 images)

But instead of I would like to plot the mean of the 3 genes on 1 image

is it possible ?? I hope the question is clear :) Manys thanks for your help Sophie

[MertDemirdizen]

I am looking for the same thing. Did you find a way to do that?

[sophieRAIBAUD]

unfortunatly not :(

[MertDemirdizen]

Check this out. It helped me a lot. https://github.com/Teichlab/limbcellatlas/issues/1#issuecomment-1146685471

[sophieRAIBAUD]

many thanks !!

[giovp]

hi @MertDemirdizen @sophieRAIBAUD sorry for late reply. This type of functionality is planned to be added to squidpy (there is an issue also there discussing the same). I'd close this here since the scanpy spatial plot will be deprecated, feel free to reopen/ping me in the squidpy repo directly

[sophieRAIBAUD]

OK thanks @giovp when do you plan to add this new fonctionnality ? @MertDemirdizen : I don't understand how to add the intensity according to the post (https://github.com/Teichlab/limbcellatlas/issues/1#issuecomment-1146685471) could you help me ? many thanks !