plot.atlasqtl: Plot function for S3 class "atlasqtl"

In hruffieux/atlasqtl: Flexible sparse regression for hierarchically-related responses using annealed variational inference

Plot function for S3 class "atlasqtl"

Description

This function provides functionality for plotting a so-called Manhattan plot with the positions and sizes of "hotspot" predictors (i.e., predictors associated with multiple responses).

Usage

## S3 method for class 'atlasqtl'
plot(
  x,
  thres = 0.5,
  fdr_adjust = FALSE,
  pch = 20,
  ylim_max = NULL,
  main = "Hotspot Manhattan plot",
  xlab = "Predictors",
  ylab = "Nb of associated responses",
  add = FALSE,
  ...
)

Arguments

x	an object with S3 class "atlasqtl".
thres	threshold to be applied on the posterior probabilities of association to define hotspots (default is 0.5, for the Median Probability Model).
fdr_adjust	if TRUE the threshold is applied on FDR estimates computed from the "atlasqtl" posterior probabilities of association, otherwise it is directly applied on the posterior probabilities of association (default is FALSE).
pch	type of points.
ylim_max	upper limit for y-axis (ignored if add is TRUE).
main	plot title (ignored if add is TRUE).
xlab	x-axis title (ignored if add is TRUE).
ylab	y-axis title (ignored if add is TRUE).
add	whether the plot should be overlaid on an existing plot.
...	additional arguments.

See Also

atlasqtl, print.atlasqtl, summary.atlasqtl, assign_bFDR

hruffieux/atlasqtl documentation built on April 12, 2025, 12:54 p.m.