plotQTL: Creates an object needed to create QTL plots.

In ellisztamas/qtltools: Tools for plotting QTL

Description

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

Usage

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

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. Defaults to two for Sweden vs. Italy. left_gap, right_gap left- and right-hand margin around each chromosome.

Details

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/qtltools documentation built on May 3, 2019, 10:42 p.m.