plotMahal {CATALYST} | R Documentation

## Biaxial plot

### Description

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

### Usage

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

### Arguments

`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.

### Value

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

### Author(s)

Helena L Crowell helena.crowell@uzh.ch

### References

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.

### Examples

    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")

[Package CATALYST version 1.18.1 Index]