plotEvents {CATALYST}R Documentation

Event plot

Description

Plots normalized barcode intensities for a given barcode.

Usage

plotEvents(x, ...)

## S4 method for signature 'dbFrame'
plotEvents(x, which = "all", n_events = 100, out_path = NULL, name_ext = NULL)

Arguments

x

a dbFrame.

...

optional arguments.

which

"all", numeric or character. Specifies which barcode(s) to plot. Valid values are IDs that occur as row names in the bc_key of the supplied dbFrame, or 0 for unassigned events.

n_events

numeric. Specifies number of events to plot. Defaults to 100.

out_path

character string. If specified, outputs will be generated here.

name_ext

character string. If specified, will be appended to the file name.

Value

Plots intensities normalized by population for each barcode specified by which: Each event corresponds to the intensities plotted on a vertical line at a given point along the x-axis. Events are scaled to the 95% quantile of the population it has been assigned to. Barcodes with less than 50 event assignments will be skipped; it is strongly recoomended to remove such populations or reconsider their separation cutoffs.

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)

# view preliminary assignments
re <- assignPrelim(x = sample_ff, y = sample_key)
plotEvents(x = re, which = "D1", n_events = 1000)

# apply deconvolution parameters
re <- estCutoffs(re)
re <- applyCutoffs(x = re)
plotEvents(x = re, which = "D1", n_events = 500)


[Package CATALYST version 1.10.3 Index]