plotQTL_qtl: Plot QTL positions.

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

Description

Plot QTL positions and confidence intervals from onto a plotQTL plot. This can be done with a qtl object with a fitqtl object, or else with a cluster_qtl object. In the former case, maximum-likelihood positions are labelled with an upward arrow if the reference allele increases the phenotype, and vice versa.

Usage

plotQTL_qtl(
  plotQTL,
  qtl_object = NULL,
  model_fit = NULL,
  cluster_qtl = NULL,
  lane,
  fill_cutoff = NULL,
  col = 1,
  bg = col,
  ...
)

Arguments

plotQTL	A plotQTL object from plotQTL().
qtl_object	A QTL object from r/qtl. If this is specifed, model_fit should be as well, but cluster_qtl should not.
model_fit	A fitQTL object from r/qtl. If this is specifed, qtl_object should be as well, but cluster_qtl should not.
cluster_qtl	A cluster_qtl object listing information on QTL grouped into clusters. Usually the output of cluster_qtl(). If this is specified, qtl_object and model_fit should not be.
lane	Integer indicating which lane to plot to.
fill_cutoff	Threshold length of a confidence interval on QTL positions, above which points will be empty, and below which points will be filled.
col	Plotting colour for point estimates and credible intervals. Defaults to black.
bg	Plotting colour for the background of point estimates. This can be a single entry or a vector with an entry for each QTL to be plotted. Defaults to 'col'. If 'fill_cutoff' is also given, this overrides 'bg'.
...	Additional plotting commands passed to points() and segments().

Details

QTL with narrow confidence intervals are plotted with filled arrows. If confidence intervals are greater than a threshold number of centimorgans, arrows are plotted empty. This can be disabled by setting fill_cutoff to a larger number than the longest interval.

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