plotYields {CATALYST} | R Documentation

## Yield plot

### Description

Distribution of barcode separations and yields as a function of separation cutoffs.

### Usage

    plotYields(x, ...)

    ## S4 method for signature 'dbFrame'
    plotYields(x, which = 0, out_path = NULL,
      name_ext = NULL, plotly = TRUE)

### Arguments

`x` | a `dbFrame`.
`...` | optional arguments.
`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, outputs will be generated here.
`name_ext` | character string. If specified, will be appended to the plot's name.
`plotly` | logical. Should an interactive plot be rendered?

### 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

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's main title.

### Author(s)

Helena Lucia Crowell crowellh@student.ethz.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)
    re <- assignPrelim(x = sample_ff, y = sample_key)
    re <- estCutoffs(x = re)

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

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

[Package CATALYST version 1.4.2 Index]