plot_aggregated_uptake_structure: Plot aggregated uptake on the 3D structure

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

Plot aggregated uptake on the 3D structure

Description

Function plots the aggregated data (either one state deuterium uptake or differential deuterium uptake) on the 3d structure.

Usage

plot_aggregated_uptake_structure(
  aggregated_dat,
  differential = FALSE,
  fractional = TRUE,
  theoretical = FALSE,
  time_t,
  pdb_file_path
)

Arguments

aggregated_dat	aggregated data, either for single uptake or differential
differential	indicator if the aggregated_dat contains differential results
fractional	indicator if fractional values are used
theoretical	indicator if theoretical values are used
time_t	time point from aggregated_dat to be shown on the structure
pdb_file_path	file path to the pdb file

Value

a r3dmol object.

Examples

library(shiny)
# disabled due to its long time and producing 3rdmol object

diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
diff_aggregated_dat <- create_aggregated_diff_uptake_dataset(diff_uptake_dat)
pdb_file_path <- system.file(package = "HaDeX2", "HaDeX/data/Model_eEF1Balpha.pdb")

plot_aggregated_uptake_structure(diff_aggregated_dat,
                                differential = TRUE,
                                 time_t = 1,
                                 pdb_file_path = pdb_file_path)

kin_dat <- create_uptake_dataset(alpha_dat, states = "Alpha_KSCN" )
aggregated_dat <- create_aggregated_uptake_dataset(kin_dat)
plot_aggregated_uptake_structure(aggregated_dat,
                                 differential = FALSE,
                                 time_t = 1,
                                 pdb_file_path = pdb_file_path) 

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