Coloring a dimplot with my own color vector

[ghost]

Hello,

I would like to color all cells in a DimPlot with a precomputed color vector. Is there any easy way to do so? My problem is that the data has been clustered. Therefore, using cols=myVector will use the first entries of the vector as colors for the clusters.
Is there a way to tell DimPlot to ignore group.by?
Alternatively, how can we tell DimPlot to group.by cell name? (effectively creating as many classes as cells)

Thank you

[samuel-marsh]

Hi,

So if your intent is to color the cells individually then yes you can just create @meta.data column that contains the cell names and then use group.by on that column (Don't forget to add + NoLegend() too).

pbmc[["cell_names"]] <- colnames(pbmc)
DimPlot(pbmc, group.by = "cell_names") + NoLegend()

Best,
Sam

[ghost]

Sorry for the delay of reply. I think I was not clear in my enquiry. The group.by sent you off track.

I want to color the cells with precomputed values. For instance, the relative normalized expression of two genes (but that could be anything). For that, I can create my color vector as:

Creates a vector of relative counts between two genes

counts <- as.matrix(GetAssayData(object = obj, assay = "RNA", slot = "counts"))
MyGenes <- c("XXX","YYY")
maxGene1<-max(counts[MyGenes[1],])
maxGene2<-max(counts[MyGenes[2],])
relCounts<-counts[MyGenes[1],]/maxGene1-counts[MyGenes[2],]/maxGene2

Build a color vector based on relative counts

rbPal <- colorRampPalette(c('darkred',"yellow",'darkcyan'))
datcol <- rbPal(10)[as.numeric(cut(relCounts,breaks = 10))]

length(colnames(obj))
[1] 7707
length(datcol)
[1] 7707

Now, I want to use that color vector to color all cells according to their relative expression. Again, the later detail is just that. what matters is coloring a cell in the vector of cells with the corresponding color in the vector of colors. The following does not work:

DimPlot(obj,reduction="tsne", group.by = "cell_names") + NoLegend()+ scale_color_manual(values = datcol)

The plot should look like what we get with "features = MyGenes, blend=TRUE, combine = FALSE", but it does not.

[timoast]

If you want a continuous color scale, you should use FeaturePlot() rather than DimPlot(). FeaturePlot() can plot any continuous values stored in the object metadata, and then you can apply your own colorscale using standard ggplot2 functions