How to Visualization NMF coloc result?

[yifanfu01]

Problem

How to Visualization NMF coloc result?

I referred https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html this tutorial.
After cell 27, I got the similar dot plot for the celltype loadings.
But How could I visualize or plot spatial figure with this factors?
Such as I chose total_n_factors=9, I would like to plot the spots marked as fact_0, fact_1, ... Like your article figure 4e.

• [Yes ] I follow the instructions from the cell2location tutorial (using on scvi-tools).
• [Yes ] I have adjusted required hyperparameters to my dataset and tissue N_cells_per_location and detection_alpha.
• [N.A. ] I have provided 10X reaction/inlet as batch_key for reference NB regression.
• [Yes ] I have checked scverse Discourse and old Cell2location Community Forum, and did not find a solution.

Description of the data input and hyperparameters

I used Jupyter and Py3.9

I use a normal Visium spatial result.

Single cell reference data: number of cells, number of cell types, number of genes

I used the paired scRNA-seq data with full annotation.

Single cell reference data: technology type (e.g. mix of 10X 3' and 5')

Spatial data: about 2900 spots.