dotplot.genotypes: Show a visual representation of a slice of a genotype matrix

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

Description

Show a visual representation of a slice of a genotype matrix

Usage

## S3 method for class 'genotypes'
dotplot(gty, size = 2, meta = NULL, shape = c("point",
  "tile", "nothing"), color.by = NULL, force = FALSE, ...)

Arguments

gty	a genotypes object
size	numeric; size of points
meta	dataframe of additional sample metadata to be joined to the input before plotting
shape	if "point", each genotype call is represented by a circle; if "tile", the effect will be like a heatmap
color.by	column in meta to use for color-coding points; otherwise use genotype calls
force	logical; if TRUE, issues a stern warning before trying to make a huge plot which might hang the R session
...	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 hidden. Points are spaced evenly along the x-axis to facilitate visual inspection; marker spacing in genomic coordinates is indicated in a track along the bottom of the plot which connects each column to its relative genomic position. At present, the function will only do a single chromosome at a time.

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

Value

a grid of genotype calls, laid out horizontally in genomic coordinates

See Also

plot.clusters for intensity plots by marker

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