plot_man: Plot mediation exposure, mediator, and outcome per mediator

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

Plot mediation exposure, mediator, and outcome per mediator

Description

Plot mediation exposure, mediator, and outcome per mediator in M, as used in lotman & hitman, using ggplot2.

Usage

plot_man(
  E,
  M,
  Y,
  name = "top_mediators",
  main.v = "",
  xlab = "Log2 abundance",
  ylab = "Outcome",
  check.names = TRUE,
  manual.color = NULL
)

Arguments

E	A numeric vector of exposures.
M	A numeric matrix-like data object with one row per feature and one column per sample of mediators.
Y	A numeric vector of length(E) of outcomes. Only continuous, normally distributed outcomes currently supported.
name	Name of file to create. Set to NA to plot to screen instead of to file.
main.v	Character vector of main titles for plot.
xlab	Label for x-axis.
ylab	Label for y-axis.
check.names	Logical; should names(E)==colnames(M) & colnames(M)==names(Y) be checked?
manual.color	Vector passed to both scale_fill_manual and scale_color_manual.

Details

If manual.color is given, its length should be length(unique(E)).

Value

Invisibly, a ggplot2 object from the last row of M that was plotted.

jdreyf/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.