How can I colour UMAP by sample batches

Question

[cabioc]

Hi

I would like to label single cell RNAseq UMAP dots by sample batch Under Seurat.like this

The sample batchs showed on the colnames by their first 6 letters and digits (like AAA001xx, AAA002xx and BBB001xx) on the counts matrix (dta). So I firstly tried to split them using plates<-substr(colnames(dta), 0, 6), and then DimPlot(dta, reduction = "umap", group.by= plates, label=FALSE). It didn't work.

I think I completely went a wrong direction. Can someone help?

[swbarnes2]

Is this Seurat?

[cabioc]

0 just now cabioc • 0

Sorry, I forgot mention. It is Seurat.

[cabioc]

Sorry, I forgot mention. It is Seurat.

Answer 1

[fracarb8]

Seurat groups and splits based on the values in the metadata table ([e-mail]). If you want group.by= plates to work, you need to add the column plates to [e-mail].

[e-mail]$plates <- substr(rownames([e-mail]), 0, 6)

[cabioc]

Thank you! It works now

Answer 2

[Jautis]

I would use color, which will be added to a legend. Seurat DimPlot has a cols option which you would feed the vector of names by cell (this should be in your metadata for the cells). I don't think you need to split them first.