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 1.8.5 Index]