plotYields: Yield plot
In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

plotYields

R Documentation

Yield plot

Description

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.

Usage

plotYields(x, which = 0, out_path = NULL, out_name = "yield_plot")

Arguments

`x`	a `SingleCellExperiment`.
`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, yields plots for all barcodes specified via `which` will be written to a single PDF file in this location.
`out_name`	character strings specifying the output's file name when `!is.null(out_path)`; should be provided without(!) file type extension.

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

a list of ggplot objects.

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

# construct SCE & apply arcsinh-transformation
data(sample_ff, sample_key)
sce <- prepData(sample_ff)

# deconvolute samples & estimate separation cutoffs
sce <- assignPrelim(sce, sample_key)
sce <- estCutoffs(sce)

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

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

HelenaLC/CATALYST documentation built on Nov. 30, 2024, 4:04 a.m.