plotUncertainty {snpStats} | R Documentation

## Plot posterior probabilities of genotype assignment

### 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 dc208@cam.ac.uk

### Examples

    ## No example available yet

[Package snpStats version 1.44.0 Index]