Hi,

Identity is the identity of the cells in scRNA-seq data. It's not directly related with this plot, but with scRNA-seq data in general. So, the identity is any factor/categorical variable that describes each cell. The identity of the cells can be the sample, replicate, condition, cell cluster to which they belong to.

In your case it seems to be condition or sample. But you can set the identity to cell clusters/populations/types any variable that annotates each cell to a factor/categorical variable.

You can see the identity of your cells by typing:

Idents(pbmc) # assuming that pbmc is your seurat object

You can set the identity of your cells to another variable in your seurat object by doing:

Idents(pbmc) <- "replicate"

Where replicate is a variable in your seurat object - "pbmc" - annotating each cell as rep1 or rep2 (see the example here: https://satijalab.org/seurat/v3.0/interaction_vignette.html ).

I hope this answers your question,

António