Package 'gassocplot'

Title: Regional association plots
Description: This package is used plot regional association plots.
Authors: James Staley [aut, cre] (ORCID: <https://orcid.org/0009-0001-9520-5011>)
Maintainer: James Staley <[email protected]>
License: GPL-3
Version: 0.0.2
Built: 2026-06-02 07:45:46 UTC
Source: https://github.com/remlapmot/gassocplot

Help Index

assoc_plot

Description

assoc_plot plots a scatter graph of associations (e.g. log10 p-values)

Usage

assoc_plot(
  data,
  corr = NULL,
  corr.top = NULL,
  ylab = NULL,
  title = NULL,
  subtitle = NULL,
  type = "log10p",
  x.min = NULL,
  x.max = NULL,
  top.marker = NULL,
  legend = TRUE
)

Arguments

data

data.frame with markername (marker), chromosome (chr), position (pos) and either z-statistics (z) or probabilities (prob) columns
corr

correlation matrix between markers
corr.top

correlation statistics between the top marker and the rest of the markers
ylab

the y-axis label
title

title of the plot
subtitle

subtitle of the plot
type

the type of the plot either log10p or probabilities
x.min

start of region
x.max

end of region
top.marker

the top associated marker, i.e. the marker with the largest -log10p or probability
legend

add r2 legend

Author(s)

James R Staley <[email protected]>

assoc_plot_save

Description

assoc_plot_save saves a png of the assoc_plot with the correct dimensions

Usage

assoc_plot_save(x, file, width = 9, height = 7, dpi = 500)

Arguments

x

the plot
file

the filepath
width

the width of the plot
height

the height of the plot
dpi

the resolution of the plot

Author(s)

James R Staley <[email protected]>

stack_assoc_plot

Description

stack_assoc_plot plots stacked regional association plots

Usage

stack_assoc_plot(
  markers,
  z,
  corr = NULL,
  corr.top = NULL,
  traits,
  ylab = NULL,
  type = "log10p",
  x.min = NULL,
  x.max = NULL,
  top.marker = NULL,
  legend = TRUE
)

Arguments

markers

data.frame of markers with markername (marker), chromosome (chr) and position (pos)
z

matrix of Z-scores or probabilities with one column for each trait
corr

matrix of correlation statistics between markers
corr.top

correlation statistics between the top marker and the rest of the markers
traits

trait names
ylab

the y-axis label
type

the type of the plot either log10p or probabilities
x.min

start of region
x.max

end of region
top.marker

the top associated marker, i.e. the marker with the largest -log10p or probability
legend

add r2 legend

Author(s)

James R Staley <[email protected]>

stack_assoc_plot_save

Description

stack_assoc_plot_save saves a png of the assoc_plot with the correct dimensions

Usage

stack_assoc_plot_save(
  x,
  file,
  n_traits,
  width = NULL,
  height = NULL,
  dpi = 500
)

Arguments

x

the plot
file

the filepath
n_traits

the filepath
width

the width of the plot
height

the height of the plot
dpi

the resolution of the plot

Author(s)

James R Staley <[email protected]>