Can I get information of each sample in a project?

[sqs1020]

Hi,

Is there a way to see clusters of each sample/group from an ArchR project like "split.by" option in Seurat (see attached scrreenshot)?
PA.p3 <- DimPlot(PA.combined.sct, reduction = "umap", label = TRUE, repel = TRUE, split.by = "group")
Idents(PA.combined.sct) = "orig.ident"
PA.p4 <- DimPlot(PA.combined.sct, reduction = "umap", repel = TRUE, split.by = "group")

Thanks!

[rcorces]

perhaps you want the highlightCells argument?

highlightCells	A character vector of cellNames describing which cells to hightlight if using plotAs = "points" (default if discrete). The remainder of cells will be colored light gray.

https://www.archrproject.com/reference/plotEmbedding.html

[sqs1020]

Thank you for the infromation. I saw the highlightCells argument. The cells should in Embedding CellNames. Does that mean I could I only see 1 cell per time? How can I highlight a group of cells at one time? Thank you!

[rcorces]

The function documentation is very explicit. And you have not provided the highlightCells argument the correct input. It wants a character vector of cellNames.

highlightCells	A character vector of cellNames describing which cells to hightlight if using plotAs = "points" (default if discrete). The remainder of cells will be colored light gray.