plot_differential_uptake_curve: Plot differential uptake curve

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

Plot differential uptake curve

Description

Differential uptake curve for one peptide between two biological states.

Usage

plot_differential_uptake_curve(
  diff_uptake_dat = NULL,
  diff_p_uptake_dat = NULL,
  sequence = NULL,
  theoretical = FALSE,
  fractional = FALSE,
  uncertainty_type = "ribbon",
  log_x = TRUE,
  show_houde_interval = FALSE,
  show_tstud_confidence = FALSE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

diff_uptake_dat	produced by calculate_diff_uptake or create_diff_uptake_dataset function
diff_p_uptake_dat	differential uptake data alongside the P-value as calculated by create_p_diff_uptake_dataset
sequence	sequence of chosen peptide
theoretical	logical, determines if plot shows theoretical values
fractional	logical, determines if plot shows fractional values
uncertainty_type	type of presenting uncertainty, possible values: "ribbon", "bars" or "bars + line"
log_x	logical, determines if x axis shows logarithmic values
show_houde_interval	logical, determines if houde interval is shown
show_tstud_confidence	logical, determines if t-Student test validity is shown
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

This plot shows the differential deuterium uptake between two biological states for selected peptides in different time points. The possibility to plot multiple differences (between state and mutant) for the peptide will be added soon.

Value

a ggplot object.

See Also

read_hdx create_diff_uptake_dataset calculate_diff_uptake

Examples

diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
plot_differential_uptake_curve(diff_uptake_dat = diff_uptake_dat, sequence = "GDLKSPAGL")

diff_p_uptake_dat <- create_p_diff_uptake_dataset(alpha_dat)
plot_differential_uptake_curve(diff_p_uptake_dat = diff_p_uptake_dat, 
                               sequence = "GDLKSPAGL", show_houde_interval = TRUE)
plot_differential_uptake_curve(diff_p_uptake_dat = diff_p_uptake_dat, 
                               sequence = "GDLKSPAGL", show_houde_interval = TRUE, 
                               show_tstud_confidence = TRUE)
plot_differential_uptake_curve(diff_p_uptake_dat = diff_p_uptake_dat, 
                               sequence = "GDLKSPAGL", show_tstud_confidence = TRUE)

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