Getting percentages of contamination

[sameehan2301]

Hello,
Thank you for this nice tool. I was wondering how could I interpret the data? How do I demonstrate that one sample has more ambient RNA contamination as compared to the other? Is there some code that I am missing from the vignette?

I would like to demonstrate the percentage of contamination in sample A vs sample B.
Please let me know.
Thank you,
Regards,
Sam.

[joshua-d-campbell]

Hi @sameehan2301, thanks for using our tool! You can make a boxplot/violin plot to show the differences in contamination between two samples. There are several ways you can do this. For an example, I will import 2 PBMC datasets and run decontX using the singleCellTK package:

library(singleCellTK)
pbmc3k <- importExampleData("pbmc3k")
pbmc6k <- importExampleData("pbmc6k")
sce <- cbind(pbmc3k, pbmc6k)
sce <- decontX(sce, batch = sce$Sample)

If you ran decontX with the data in a SingleCellExperiment object, then you can use the plotSCEViolinColData function from the singleCellTK package:

library(singleCellTK)
plotSCEViolinColData(inSCE = sce, coldata = "decontX_contamination", groupBy = "sample", ylab = "Contamination", boxplot = FALSE)

Or you can extract the contamination vector and use whatever plotting tool you want:

contamination <- sce$decontX_contamination
sample <- sce$sample
boxplot(contamination ~ sample)

Hope that helps. I'm going to move this to a Discussion so others can see it as well.