plotYields {CATALYST}R Documentation

Yield plot

Description

Distribution of barcode separations and yields as a function of separation cutoffs.

Usage

plotYields(x, ...)

## S4 method for signature 'dbFrame'
plotYields(x, which = 0, out_path = NULL,
  name_ext = NULL, plotly = TRUE)

Arguments

x

a dbFrame.

...

optional arguments.

which

0, numeric or character. Specifies which barcode(s) to plot. Valid values are IDs that occur as row names of bc_key(x); 0 (the default) will generate a summary plot with all barcodes.

out_path

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

name_ext

character string. If specified, will be appended to the plot's name.

plotly

logical. Should an interactive plot be rendered?

Details

The overall yield that will be achieved upon application of the specified set of separation cutoffs is indicated in the summary plot. Respective separation thresholds and their resulting yields are included in each barcode's plot. The separation cutoff value should be chosen such that it appropriately balances confidence in barcode assignment and cell yield.

Value

plots the distribution of barcode separations and yields upon debarcoding as a function of separation cutoffs. If available, currently used separation cutoffs as well as their resulting yields will be indicated in the plot's main title.

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)

# all barcodes summary plot
plotYields(x = re, which = 0)

# plot for specific sample
plotYields(x = re, which = "C1")


[Package CATALYST version 1.8.6 Index]