plotMahal {CATALYST} | R Documentation

## Biaxial plot

### Description

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

### Usage

    plotMahal(x, ...)

    ## S4 method for signature 'dbFrame'
    plotMahal(x, which, cofactor = 50, out_path = NULL, name_ext = NULL)

### Arguments

`x` | a `dbFrame`.
`...` | optional arguments.
`which` | character string. Specifies which barcode to plot.
`cofactor` | numeric. Cofactor used for asinh transformation.
`out_path` | character string. If specified, outputs will be generated here.
`name_ext` | character string. If specified, will be appended to file name.

### Value

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

### Author(s)

Helena Lucia 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)
    re <- assignPrelim(x = sample_ff, y = sample_key)
    re <- estCutoffs(x = re)
    re <- applyCutoffs(x = re)
    plotMahal(x = re, which = "B3")

[Package CATALYST version 1.10.3 Index]