plot_differential_chiclet: Chiclet differential deuterium uptake plot

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

Chiclet differential deuterium uptake plot

Description

Chiclet plot of differential deuterium uptake values between two biological states in time.

Usage

plot_differential_chiclet(
  diff_uptake_dat = NULL,
  diff_p_uptake_dat = NULL,
  theoretical = FALSE,
  fractional = FALSE,
  show_houde_interval = FALSE,
  show_tstud_confidence = FALSE,
  confidence_level = 0.98,
  show_uncertainty = FALSE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

diff_uptake_dat	data 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
theoretical	logical, determines if values are theoretical
fractional	logical, determines if values are fractional
show_houde_interval	logical, determines if houde interval is shown
show_tstud_confidence	logical, determines if t-Student test validity is shown
confidence_level	confidence level for the test, from range [0, 1] Important if selected show_confidence_limit
show_uncertainty	logical, determines if the uncertainty 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

Function plot_differential_chiclet generates chiclet differential plot based on provided data and parameters. On X-axis there is a peptide ID. On Y-axis are time points of measurement. Each tile for a peptide in time has a color value representing the deuterium uptake difference between chosen states, in a form based on provided criteria (e.q. fractional). Each tile has a plus sign, which size represent the uncertainty of measurement for chosen value.

Value

a [ggplot2::ggplot()] object.

See Also

create_diff_uptake_dataset calculate_diff_uptake

Examples

diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
plot_differential_chiclet(diff_uptake_dat)
plot_differential_chiclet(diff_uptake_dat, show_houde_interval = TRUE)

diff_p_uptake_dat <- create_p_diff_uptake_dataset(alpha_dat)
plot_differential_chiclet(diff_p_uptake_dat = diff_p_uptake_dat, 
                          show_tstud_confidence = TRUE)
plot_differential_chiclet(diff_p_uptake_dat = diff_p_uptake_dat, 
                          show_tstud_confidence = TRUE, show_houde_interval = TRUE) 

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