Plot MA using expression/readcount-based fold changes

Wrapper around `plot_ma(..., type = "expression")` that accepts a `SummarizedExperiment` or precomputed fold-change `data.frame`.

Usage

plot_ma_expression(
  x,
  se,
  samples = NULL,
  control = NULL,
  fc_method = "median",
  pseudocount = 0,
  sig_alpha = 0.05,
  x_label = NULL,
  y_label = NULL,
  title = NULL,
  ...
)

Arguments

x: Data.frame from `calculate_difference()`.
se: A `SummarizedExperiment` or data.frame supplying readcounts or precomputed fold changes.
samples: Optional sample grouping vector (passed to `plot_ma`).
control: Control level name (passed to `plot_ma`).
fc_method: Aggregation method for fold-change calculation (passed to `plot_ma`).
pseudocount: Pseudocount added when computing log ratios (passed to `plot_ma`).
sig_alpha: Numeric significance threshold for adjusted p-values (default: 0.05).
x_label: Optional x-axis label passed to `plot_ma`.
y_label: Optional y-axis label passed to `plot_ma`.
title: Optional plot title passed to `plot_ma`.
...: Additional arguments passed to `plot_ma()`.

Value

A `ggplot2` object representing the MA plot.

Examples

x <- data.frame(genes = paste0("g", seq_len(5)), mean = runif(5))
fc <- data.frame(genes = paste0("g", seq_len(5)), log2_fold_change = rnorm(5))
plot_ma_expression(x, se = fc)