Seurat: FeatureScatte split by orig.ident

[francescarivello]

I am using Seurat to analyze my inDrop experiments over different stimulation times. I stored the stimulation times in the meta.data of the Seurat object under orig.ident
I would like to plot using FeatureScatter the correlations between two genes which I do giving the following command:
FeatureScatter(combined_Seu_6clusters, feature1 = "VEGFA", feature2 = "EGR1", group.by = "orig.ident", pt.size = 2)

However this leads to one plot with all the stimulation times overlapping. I would like to see one plot per each stimulation time. In FeatureScatter I cannot add split.by = "orig.ident"

How to do otherwise?

[timoast]

Hi, we don't support this right now but could think about adding it in the future. In the meantime you could either subset the data and create different plots for different subsets, or extract the data using GetAssayData and create the plots using ggplot2.

[francescarivello]

Thank you Tim for the quick reply. I was also having some trouble on su setting a Seurat object based on orig.identity = 3h for example. Which kind of command should I give?

[timoast]

You can subset to keep idents == "3h" like so:

sub.obj <- subset(object, idents = "3h")

[satijalab]

I'll just add that I agree this would be a very useful enhancement