Plot query cells on top of reference cells in UMAP

Question

[saicchan]

Using MapQuery, I've successfully mapped the cells of my query dataset onto the UMAP coordinates of my reference dataset. However, I would like to visualize both the reference dataset cells (preferably in grey, in the background) and the query dataset cells (colored, in the foreground) in the same UMAP plot. Is this possible?

Thank you very much for any suggestions!

Answer 1

[Bastien Hervé]

In the metadata of your Seurat object you know which cell is coming from the query or the reference. If you set this information in a column named for example origin. You can plot a UMAP with DimPlot and set group.by="origin"