plot.clusters: Plot 2D hybridization intensities at a few markers

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Plot 2D hybridization intensities at a few markers

Usage

## S3 method for class 'clusters'
plot(x, markers = NULL, theme.fn = ggplot2::theme_bw,
  force = FALSE, hilite = NULL, ...)

Arguments

x	a genotypes object
markers	indexing vector for selecting markers from x
theme.fn	a function specifying formatting options for the resulting ggplot
force	logical; if TRUE, issues a stern warning before trying to make a huge plot which might hang the R session
hilite	name of one or more samples to highlight on the plot
...	ignored

Details

Each point represents a genotype call for a single sample. Points are coloured according to numeric genotype call (0/1/2/N), with missing (N) calls in grey. Samples for which the quality filter is set are shown as open circles.

Since the return value is a ggplot, the user can add modify it at will. To recover the underlying dataframe, use ...$data.

Value

2D intensity plots, one panel per marker (via ggplot)

See Also

dotplot.genotypes for compact plotting of genotype calls only

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.