plot_coverage: Peptide coverage

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Peptide coverage

Description

Plot the peptide coverage of the protein sequence

Usage

plot_coverage(
  dat,
  protein = dat[["Protein"]][1],
  states = NULL,
  show_blanks = TRUE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

dat	data imported by the read_hdx function
protein	selected protein
states	selected biological states for given protein
show_blanks	logical, indicator if the non-covered regions of the sequence are indicated in red
interactive	logical, whether plot should have an interactive layer created with with ggiraph, which would add tooltips to the plot in an interactive display (HTML/Markdown documents or shiny app)

Details

The function plot_coverage generates sequence coverage plot based on experimental data for selected protein in selected biological states. Only non-duplicated peptides are shown on the plot, next to each other.

The aim of this plot is to see the dependence between position of the peptide on the protein sequence. Their position on y-axis does not contain any information.

Value

a ggplot object

See Also

read_hdx plot_position_frequency

Examples

plot_coverage(alpha_dat)
plot_coverage(alpha_dat, show_blanks = FALSE)

diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
plot_coverage(diff_uptake_dat)

HaDeX2 documentation built on Feb. 9, 2026, 5:07 p.m.