Generate GVCF plots — plotGvcf • rPHG2

Generates general GVCF metrics plots for genome-wide GVCF statistics

Usage

plotGvcf(object, ...)

# S4 method for class 'PHGMetrics'
plotGvcf(
  object,
  metricId = NULL,
  f = NULL,
  nRow = NULL,
  nCol = NULL,
  tag = "A",
  mData = NULL,
  mVar = NULL,
  colorOverride = NULL,
  sampleOrder = NULL
)

Arguments

object: A PHGMetrics object containing the gVCF data.
...: Additional arguments, for use in specific methods
metricId: A character vector specifying the ID of the metric to be plotted. Only a single ID is supported.
f: A formula object defining the plot.
nRow: An integer specifying the number of rows in the plot layout.
nCol: An integer specifying the number of columns in the plot layout.
tag: What tag type do you want passed to final plot?
mData: Add optional metadata data.frame object for categorical plotting. This object must contain a singular column named sample, taxa, or line along with one or more columns containing categorical data for plotting.
mVar: If mData is specified, what categorical column do you want plotted? If NULL, the first non-sample/taxa/line column will be selected.
colorOverride: If colorOverride is specified, all default colors will be overridden with specified classic color or hex-based RGB value (e.g., #000FFF).
sampleOrder: A character vector of sample IDs for manual order override. If sampleOrder is specified, bars will be ordered based on order in vector object. Additionally, this can be used as a method to subset the base set for a given number of selected samples.

Value

A plot object generated from the specified gVCF data and layout.