plotUncertainty:
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.
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