REQUEST | doDimPlot | Plot NA values of grouping values in background about scpubr

[enblacar]

Hi @jaakoobb,

Thank you for using my package! There is no straight away parameter that handles this, as I do not generally expect NA in the metadata variables to plot, as they are also handled by na.value parameter in SCpubr::do_DimPlot().

However, I found a workaround for this. In short:

• You turn your metadata variable from a factor to a character (if it is a factor).
• Select all the NA values and turn them into a character value - i.e: "Remove".
• Set the metadata variable as the Idents of the Seurat object via the Seurat::Idents() function.
• Plot the DimPlot using the idents.keep parameter and providing all the values but the one you wish to bring to the back.

And that should do it. Here is a code example of it:

sample$seurat_clusters <- as.character(sample$seurat_clusters)
sample$seurat_clusters[is.na(sample$seurat_clusters)] <- "Remove"
sample$seurat_clusters <- as.factor(sample$seurat_clusters)
Seurat::Idents(sample)  <- sample$seurat_clusters

# Plot.
p <- SCpubr::do_DimPlot(sample, 
                        idents.keep = levels(sample)[levels(sample) != "Remove"])
p

This is how it looks with this hotfix:

I will consider coding a workaround for this behaviour for the next update. Hope this helps in the meantime!

Enrique