Code usage"

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

knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(dev = "png", dev.args = list(type = "cairo-png"))

Convention

Purpose of groups of functions in the package:

• calculate_* - calculates one specific value. e.q. deuterium uptake values for specific time point.
• create_* - creates a dataset for set of values e.q. multiple time points.
• plot_ - plots a visualization of provided data, accepts calculate_ and create_* outputs.
• show_ - subsets the dataset to show specific values, accepts calculate_ and create_* outputs.

Variables:

• deut_uptake - deuterium uptake [Da]
• frac_deut_uptake - fractional deuterium uptake [%]
• theo_deut_uptake - theoretical deuterium uptake [Da]
• theo_frac_deut_uptake - theoretical fractional deuterium uptake [%]
• diff_deut_uptake - differential deuterium uptake [Da]
• frac_diff_deut_uptake - theoretical differential fractional deuterium uptake [%]
• theo_diff_deut_uptake - differential deuterium uptake [Da]
• theo_frac_diff_deut_uptake - theoretical differential fractional deuterium uptake [%]

Example of use

library(HaDeX2)
library(magrittr)

Read data file

dat <- read_hdx(system.file(package = "HaDeX2", "HaDeX/data/alpha.csv"))

Different forms of visualization

Create data frame with uptake values for state in all time points:

uptake_dat <- create_state_uptake_dataset(dat)

Butterfly:

plot_butterfly(uptake_dat)

Chiclet:

plot_chiclet(uptake_dat)

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