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MA / MD plot for differential binding results

Source: R/plot_md.R
plot_md.Rd

Plots log2 fold-change (y-axis) against average abundance/normalized binding counts (x-axis), with points coloured by significance status. Optionally labels a user-provided set of peaks with ggrepel::geom_label_repel().

Usage

plot_md(
  object,
  x_var = "Conc",
  y_var = "Fold",
  fdr_var = "FDR",
  cutoff_y = 1,
  cutoff_FDR = 0.05,
  y_max = 3,
  y_min = -3,
  label_var = NULL,
  peaks = NULL,
  title = "MD Plot",
  colors = c("red", "grey70", "blue")
)

Arguments

object

A data.frame or tibble — typically the output of DiffBind::dba.report() coerced to a data frame.

x_var

Character. Column with average abundance(normalized binding counts). Default "Conc".

y_var

Character. Column with log2 fold-change. Default "Fold".

fdr_var

Character. Column with FDR values. Default "FDR".

cutoff_y

Numeric. log2FC threshold for coloring. Default 1.

cutoff_FDR

Numeric. FDR threshold for coloring. Default 0.05.

y_max

Numeric. Upper y-axis limit. Default 3.

y_min

Numeric. Lower y-axis limit. Default -3.

label_var

Character. Column used for peak labels. Default NULL.

peaks

Character vector. Peak IDs to label. Default NULL.

title

Character. Plot title. Default "MD Plot".

colors

Character vector of length 3. Colors for up-regulated, no-change, and down-regulated points. Default c("red", "grey70", "blue").

Value

A ggplot2::ggplot object.

Examples

if (FALSE) { # \dontrun{
plot_md(
  object  = my_peaks,
  x_var   = "Conc",
  y_var   = "Fold",
  fdr_var = "FDR",
  title   = "MD plot — degron vs notag"
)
} # }