plotUncertainty: Plot posterior probabilities of genotype assignment

In NikNakk/snpStats: SnpMatrix and XSnpMatrix classes and methods

Description

The snpStats package allows for storage of uncertain genotype assignments in a one byte "raw" variable. The probabilities of assignment form a three-vector, subject to the linear constraint that they sum to 1.0; their possible values are grouped into 253 different classes. This function displays counts of these classes on a two-dimensional isometric plot.

Usage

plotUncertainty(snp, nlevels = 10, color.palette = heat.colors(nlevels))

Arguments

snp	One or more columns of a SnpMatrix object
nlevels	Probability cells are coloured according to frequency. This argument gives the number of colours that can be used
color.palette	The colour palette to be used

Details

The plot takes the form of an equilateral triangle in which each apex represents a certain assignment to one of the three genotypes. A point within the triangle represents, by the perpendicular distance from each side, the three probabilities. Each of the 253 probability classes is represented by a hexagonal cell, coloured according to its frequency in the data, which is also written within the cell

Author(s)

David Clayton [e-mail]

Examples

## No example available yet

NikNakk/snpStats documentation built on May 7, 2019, 6:18 p.m.