plotQTL: Create an object needed to create QTL plots.

In ellisztamas/arghqtl: Tools for plotting and downstream analysis of R/QTL objects in R

Description

Creates a list of information needed to plot QTL across a genome, for all or only a subset of chromsomes.

Usage

plotQTL(chr = 1:5, marker_locations, nlanes = 2, left_gap = 2, right_gap = 2)

Arguments

chr	a numeric vector listing which chromosomes are to be plotted.
marker_locations	A data.frame listing marker positions on each chromosome. Should include a column labelled 'Position' and another labelled 'Chromosome'.
nlanes	the number of lanes to plot for each chromosome.
left_gap, right_gap	Additional space on the left- and right-hand sides of each chromosome for additional labels.

Details

For each chromosome specified a 'track' is created, which is further divided into lanes for plotting QTL from different years or experiments. QTL positions and their confidence intervals are plotted to the centre of these lanes, and dividing lanes plotted between each lane. These lane centres and margin positions can be used to add extra information, such as lane labels above the chromosome.

The gap between chromosomes can be adjusted to include further embellishments, and the plot will rescale automatically.

Value

A list of two tables detailing:

1. Chromosomes to be plotted

2. Number of chromosome tracks to be included

3. Number of lanes on each track

4. Lists of marker positions for each track

5. Lengths of each track

6. Gap to the left of each track

7. Gap to the right of each track

8. Table of x-axis poisitions of the centres of each lane.

9. Table of x-axis poisitions of the margins of each lane.

10. Optional list of labels for each lane.

ellisztamas/arghqtl documentation built on March 18, 2021, 9:44 p.m.