plotQTL_qtl: Plot QTL positions.

In ellisztamas/qtltools: Tools for plotting QTL

Description

Plot QTL positions and confidence intervals from an r/qtl object onto a plotQTL plot. 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, model_fit, lane, fill_cutoff = 0, col = 1,
  ...)

Arguments

plotQTL	A plotQTL object from plotQTL().
model_fit	A fitQTL object from r/qtl.
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.
...	Additional plotting commands.
qtlobject	A QTL object from r/qtl.

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