Single Cell Density Scatter Plot with Seruat

Question

[FreeTimeTravel]

I am currently working in a department which requested a figure just like the one seen in Fig 1C in this article. The FeatureScatter function does not appear to allow density functions nor does Nebulosa allow for scatter plots. Does anyone know how create this figure within Seurat?

Answer 1

[rpolicastro]

Extract the UMAP coordinates with the Embeddings function, and plot them using the geom_pointdensity geometry from ggpointdensity.

[FreeTimeTravel]

Thank you but the X and Y axis need to be expression of two different genes, not UMAP or other graph coordinates.

[rpolicastro]

The same advice applies, but instead of Embeddings use GetAssayData and subset the two genes.