plot_replicate_mass_uptake: Replicate mass uptake curve

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

Replicate mass uptake curve

Description

Plot the mass uptake curve for selected peptide to see the difference between replicates.

Usage

plot_replicate_mass_uptake(
  dat,
  protein = dat[["Protein"]][1],
  state = dat[["State"]][1],
  sequence = dat[["Sequence"]][1],
  aggregated = FALSE,
  log_x = TRUE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

dat	data imported by the read_hdx function
protein	selected protein
state	selected biological state for given protein
sequence	selected peptide sequence for given protein in given biological state
aggregated	logical, indicator if presented data is aggregated on replicate level
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_replicate_mass_uptake generates a plot showing the mass uptake for selected protein in replicates of the experiments. The values can be presented in two ways: as aggregated values for each replicate, or before aggregation - measured values for charge values within a replicate. The mass uptake is generated by subtracting the MHP mass of a peptide from measured mass and the mass uptake is presented in Daltons.

Value

a ggplot object.

See Also

read_hdx calculate_exp_masses_per_replicate

Examples

plot_replicate_mass_uptake(alpha_dat)
plot_replicate_mass_uptake(alpha_dat, aggregated = TRUE)

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