plot_uptake_curve: Deuterium uptake curve

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

Deuterium uptake curve

Description

Plot deuterium uptake curve for selected peptides

Usage

plot_uptake_curve(
  uc_dat,
  theoretical = FALSE,
  fractional = FALSE,
  uncertainty_type = "ribbon",
  log_x = TRUE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

uc_dat	data produced by calculate_kinetics or calculate_peptide_kinetics or create_kinetic_dataset functions
theoretical	logical, indicator if values are calculated using theoretical controls
fractional	logical, indicator if values are shown in fractional form
uncertainty_type	type of uncertainty presentation, possible values: "ribbon", "bars" or "bars + line"
log_x	logical, indicator if the X axis values are transformed to log10
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_uptake_curve generates the deuterium uptake curve for selected peptides from selected protein. On X-axis there are time points of measurements. On Y-axis there is deuterium uptake in selected form. The combined and propagated uncertainty can be presented as ribbons or error bars.

Value

a ggplot object.

See Also

read_hdx calculate_kinetics calculate_peptide_kinetics create_kinetic_dataset

Examples

uc_dat <- calculate_kinetics(alpha_dat, protein = "db_eEF1Ba",
                             sequence = "GFGDLKSPAGL", 
                             state = "Alpha_KSCN",
                             start = 1, end = 11,
                             time_0 = 0, time_100 = 1440)
plot_uptake_curve(uc_dat = uc_dat, 
                  theoretical = FALSE, 
                  fractional = TRUE)
                

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