plotEvents {CATALYST} | R Documentation

## Event plot

### Description

Plots normalized barcode intensities for a given barcode.

### Usage

    plotEvents(x, ...)

    ## S4 method for signature 'dbFrame'
    plotEvents(x, which = "all", n_events = 100,
      out_path = NULL, name_ext = NULL)

### Arguments

`x` | a `dbFrame`.
`...` | optional arguments.
`which` | `"all"`, numeric or character. Specifies which barcode(s) to plot. Valid values are IDs that occur as row names in the `bc_key` of the supplied `dbFrame`, or 0 for unassigned events.
`n_events` | numeric. Specifies number of events to plot. Defaults to 100.
`out_path` | character string. If specified, outputs will be generated here.
`name_ext` | character string. If specified, will be appended to the file name.

### Value

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 recoomended to remove such populations or reconsider their separation cutoffs.

### 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)

    # view preliminary assignments
    re <- assignPrelim(x = sample_ff, y = sample_key)
    plotEvents(x = re, which = "D1", n_events = 1000)

    # apply deconvolution parameters
    re <- estCutoffs(re)
    re <- applyCutoffs(x = re)
    plotEvents(x = re, which = "D1", n_events = 500)

[Package CATALYST version 1.8.7 Index]