aldex.plot: Plot Method for ALDEx3 objects with pairwise comparisons

In ALDEx3: Linear Models for Sequence Count Data

Plot Method for ALDEx3 objects with pairwise comparisons

Description

Simple plots for an ALDEx3 object

Usage

aldex.plot(
  object,
  plot = c("volcano", "effect", "MA", "water"),
  contrast = NULL,
  threshold = 0.05,
  min.diff = 0.5,
  cohen = 0.5,
  sig.col = rgb(1, 0, 0, 0.5),
  water.show = 5,
  water.col = c("red", "blue"),
  water.names = TRUE,
  ...
)

Arguments

object	An object of class aldex
plot	type of plot (default='volcano')
contrast	the name of the comparison to plot, must be provided
threshold	FDR significance threshold (default=0.05)
min.diff	(default=0.5) used for MA (display), and waterfall (cutoff) plots
cohen	Cohen's d threshold for effect plot (slope)
sig.col	color for significant features
water.show	number features to show in waterfall plot
water.col	vector of colors for waterfall plot
water.names	logical, show names of features for waterfall plot
...	additional plot parameters (cex)

Details

Provides volcano, effect, MA and waterfall plots from an ALDEx3 object.

This method plots combinations of adjusted p-values from object$p.val.adj, posterior estimates, standard errors and log abundance values averaged across Monte Carlo samples. The result is returned as a single plot of the desired type. Effect plots use the ALDEx2-inspired diagnostics returned by aldex.effect. The contrast must identify exactly one binary model coefficient. Effect diagnostics and MA plots require logComp and logScale, which are not returned when aldex streams large jobs.

Value

the desired plot

Author(s)

Greg Gloor

ALDEx3 documentation built on Oct. 20, 2026, 1:07 a.m.