plotscatter.HS: Haplotype and QTL Allele Scatter Plots

In geo047/HapSampler: QTL-marker haplotype builder

Description

Various scatter plots involving the sampled haplotypes and sampled QTL alleles.

Usage

## S3 method for class 'HS'
plotscatter(x, nbins = 10)

Arguments

x	a HS object, obtained from running hapsampler.
nbins	the number of bins for dividing the sampled haplotype frequency.

Details

A single graphic window is open, containing three plots.

The top left plot is of the sampled haplotypes within a chain verse the probability of that haplotype carrying QTL allele Q. The sammpled haplotypes are ordered based on their average allele Q probability (Prob(Q)). The results from each chain are coloured differently. This plot is useful for identifying those haplotypes that have been sampled differently across the parallel chains (i.e. we don't want points a long way away from the red fitted line).

The top right plot is of the sampled haplotypes across chains verse the probability of that haplotype carrying QTL allele Q. The sampled haplotypes are colour coded, depending upon frequency of being sampled across all n chains. The frequency ranges associated with the colours are given in the legend.

The bottom left plot is a scatter plot of the sampled QTL allele Q verse its probability.

Value

a plotting window is opened.

See Also

plotLike

geo047/HapSampler documentation built on May 17, 2019, 1:11 a.m.