plot.haplinStrat: Plotter function for haplinStrat results.

Description

This will automatically plot all haplinStrat results on one figure.

Usage

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

Value

ggplot object.

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

This function uses the same style as plot.haplinSlide and plots all of the haplinStrat results on one figure, for easy comparison. NB: those estimates that have infinite confidence interval will not be plotted.