plotEvents {CATALYST} | R Documentation

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

[Package CATALYST version 1.18.1 Index]