plot_peptide_mass_measurement: Plot peptide mass measurement

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

Plot peptide mass measurement

Description

Plot the mass measurements from replicates for peptide in specific time point.

Usage

plot_peptide_mass_measurement(
  dat,
  protein = dat[["Protein"]][1],
  state = dat[["State"]][1],
  sequence = dat[["Sequence"]][1],
  show_charge_values = TRUE,
  time_t = unique(dat[["Exposure"]])[3],
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

dat	data produced by read_hdx function
protein	chosen protein
state	biological state for chosen protein
sequence	sequence of chosen peptide
show_charge_values	logical, indicator if the data is shown for replicates or for charge values within the replicates
time_t	chosen time point
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 function shows the measurements of mass from different replicates for specific peptide in specific state in specific time point of measurement on the plot. Moreover, on the plot is shown the average mass from the replicates, used later in calculations. The ribbon next to the dotted average mass indicates the uncertainty.

Value

a [ggplot2::ggplot()] object.

See Also

read_hdx calculate_exp_masses_per_replicate calculate_exp_masses calculate_state_uptake calculate_diff_uptake

Examples

plot_peptide_mass_measurement(alpha_dat, sequence = "FGSDDEEESEEAKRLRE")
plot_peptide_mass_measurement(alpha_dat, sequence = "FGSDDEEESEEAKRLRE", show_charge_values = FALSE)

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