plotMahal: Biaxial plot
In CATALYST: Cytometry dATa anALYSis Tools

Description Usage Arguments Value Author(s) References Examples

Histogram of counts and plot of yields as a function of separation cutoffs.

1	plotMahal(x, which, assay = "exprs", n = 1000)

`x`	a `SingleCellExperiment`.
`which`	character string. Specifies which barcode to plot.
`assay`	character string specifying which assay to use.
`n`	numeric. Number of cells to subsample; use NULL to include all.

Plots all inter-barcode interactions for the population specified by argument which. Events are colored by their Mahalanobis distance.

Helena L Crowell helena.crowell@uzh.ch

Zunder, E.R. et al. (2015). Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nature Protocols 10, 316-333.

data(sample_ff, sample_key)
sce <- prepData(sample_ff, by_time = FALSE)
sce <- assignPrelim(sce, sample_key)
sce <- estCutoffs(sce)
sce <- applyCutoffs(sce)
plotMahal(sce, which = "B3")