plotEvents: Event plot

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Event plot

Description

Plots normalized barcode intensities for a given barcode.

Usage

plotEvents(
  x,
  which = "all",
  assay = "scaled",
  n = 1000,
  out_path = NULL,
  out_name = "event_plot"
)

Arguments

x	a SingleCellExperiment.
which	"all", numeric or character specifying which barcode(s) to plot. Valid values are IDs that occur as rownames in the bc_key slot of the input SCE's metadata, or 0 for unassigned events.
assay	character string specifying which assay data slot to use. One of assayNames(x).
n	single numeric specifying the number of events to plot.
out_path	character string. If specified, events 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

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 recommended to remove such populations or reconsider their separation cutoffs.

Value

a list of ggplot objects.

Author(s)

Helena L Crowell [e-mail]

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)
sce <- prepData(sample_ff, by_time = FALSE)
sce <- assignPrelim(sce, sample_key)
plotEvents(sce, which = "D1")

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