polyqtlR (version 0.1.1)

plotRecLS: Plot the recombination landscape across the genome

Description

Function which visualises the recombination landscape in two ways: per linkage group, and per individual. For the first analysis, a rudimentary spline is also fitted to estimate the recombination rate along a grid of positions defined by gap, which is also returned by the function.

Usage

plotRecLS(
  recombination_data,
  plot_per_LG = TRUE,
  plot_per_ind = TRUE,
  gap = 1,
  ...
)

Value

A list with two elements, per_LG and per_individual. The first of these is itself a list with the same length as recombination_data, giving the estimated recombination rates along the linkage group. This rate is simply estimated as the (weighted) count of recombination breakpoints divided by the population size.

Arguments

recombination_data

Data on predicted recombination events, as returned by the function count_recombinations

plot_per_LG

Logical argument, plot recombination events per linkage group? By default TRUE.

plot_per_ind

Logical argument, plot recombination events per individual? By default TRUE.

gap

The size (in cM) of the gap used to define the grid of positions to define the window in which to estimate recombination rate. By default 1 cM. Interpolated positions are taken to be the centre of an interval, so a 1 cM gap would result in predictions for positions 0.5 cM, 1.5 cM etc.

...

Option to pass extra arguments to the plot function for the per_LG plots. This may lead to conflicts with arguments already declared internally (such as main for example).

Examples

data("Rec_Data_4x")
plotRecLS(Rec_Data_4x)