mash_plot_pairwise_sharing: Create a ggplot of pairwise sharing of mash effects

In Alice-MacQueen/snpdiver: Explore SNP Effects on Multiple Phenotypes in Diversity Panels

Description

Given a correlation matrix, an RDS with a correlation matrix, or a mash object, create a ggplot of pairwise sharing of mash effects using get_pairwise_sharing and ggcorr.

Usage

mash_plot_pairwise_sharing(
  m = NULL,
  effectRDS = NULL,
  corrmatrix = NULL,
  reorder = TRUE,
  thr.r2 = NA,
  saveoutput = FALSE,
  filename = NA,
  suffix = "",
  ...
)

Arguments

m	An object of type mash
effectRDS	An RDS containing a correlation matrix.
corrmatrix	A correlation matrix
reorder	Logical. Should the columns be reordered by similarity?
thr.r2	Numeric. Value between 0 and 1. The r^2 value above which effects are considered to be linked; in this case, only the SNP with the more significant log10Bayes Factor value in mash is kept.
saveoutput	Logical. Should the output be saved to the path?
filename	Character string with an output filename. Optional.
suffix	Character. Optional. A unique suffix used to save the files, instead of the current date & time.
...	Other arguments to get_pairwise_sharing or ggcorr.

Value

A list containing a dataframe containing the correlations and a ggplot2 object containing the correlation plot.

Alice-MacQueen/snpdiver documentation built on Dec. 17, 2021, 8:41 a.m.