Spatially resolved heatmaps

[MertDemirdizen]

Hi,
Congrats on the great work.
Sorry for using your respiratory for an unrelated thing but I wondered how you plot two genes on the same spatial map as in Figure 5. If you can show me, I would appreciate it. Thank you very much in advance.

[brianpenghe]

Dear Mert,

You can plot that by hijacking cell2location's function to plot two cell abundances

If you want to plot two genes, you can save the gene values to the .obs of the adata object pretending that they are cell abundance scores; and then plot those "scores".

Hope that makes sense?

[MertDemirdizen]

Thank you very much,
It helped me a lot!

[brianpenghe]

Hello @MertDemirdizen , good news: we've now got a tool to do this. Please check this out: https://github.com/JPatrickPett/pseudo_rnascope.git