plot.haplinSlide: Plotter function for haplinSlide.

In Haplin: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes

Plotter function for haplinSlide.

Description

This will plot any haplinSlide object in one figure.

Usage

## S3 method for class 'haplinSlide'
plot(
  x,
  filename,
  title,
  windows,
  plot.signif.only = FALSE,
  signif.thresh = 0.05,
  y.lim,
  x.title,
  y.title,
  file.width,
  file.height,
  ...
)

Arguments

x	The haplinSlide object (NB: only the output produced by running haplinSlide with the table.output argument set to TRUE!)
filename	If the plot should be saved to the disk, give the name of the output file including the file extension.
title	If the user wishes to override the default title of the plot, give it here.
windows	Numerical vector. If given, this will only plot the chosen windows.
plot.signif.only	Logical: whether to filter out the "non-significant" markers from the plot. Default: FALSE, i.e., plot everything.
signif.thresh	The threshold defining the significant p-values: if plot.signif.only == TRUE, then only the markers with relative risk p-values lower than the threshold will be kept for plotting. Default: 0.05.
y.lim	Vector with two numbers setting the Y limits of the plotted graph.
x.title	Title for the X axis (default: "marker").
y.title	Title for the Y axis (default: "RR (log scale)").
file.width	Width (in inches) for the output plot, if a filename was given.
file.height	Height (in inches) for the output plot, if a filename was given.
...	other arguments (ignored).

Details

The haplinSlide object is a list of haplin results - by default in haptable form. This is used to plot the relative risk estimates for all the markers in one plot, to enable easy comparison. NB: those estimates that have infinite confidence interval will not be plotted.

Value

ggplot object.

Haplin documentation built on Sept. 11, 2024, 7:13 p.m.