plotEvents: Event plot

Description Usage Arguments Details Value Author(s) References Examples

View source: R/plotEvents.R

Description

Plots normalized barcode intensities for a given barcode.

Usage

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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 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

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

CATALYST documentation built on Nov. 8, 2020, 6:53 p.m.