plot_differential: Differential plot

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

Differential plot

Description

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

Usage

plot_differential(
  diff_uptake_dat = NULL,
  diff_p_uptake_dat = NULL,
  skip_amino = 0,
  time_t = NULL,
  theoretical = FALSE,
  fractional = FALSE,
  show_houde_interval = FALSE,
  hide_houde_insignificant = FALSE,
  show_tstud_confidence = FALSE,
  hide_tstud_insignificant = FALSE,
  confidence_level = 0.98,
  all_times = FALSE,
  line_size = 1.5,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

diff_uptake_dat	produced by calculate_diff_uptake or create_diff_uptake_dataset function.
diff_p_uptake_dat	produced by create_p_diff_uptake_dataset function.
skip_amino	integer, indicator how many amino acids from the N-terminus should be omitted
time_t	time point of measurement, if only one should be displayed on the plot.
theoretical	logical, determines if values are theoretical.
fractional	logical, determines if values are fractional.
show_houde_interval	logical, determines if houde interval is shown.
hide_houde_insignificant	logical, determines if statistically insignificant values using Houde test are hidden on the plot.
show_tstud_confidence	logical, determines if t-Student test validity is shown.
hide_tstud_insignificant	logical, determines if statistically insignificant values using t-Student test are hidden on the plot.
confidence_level	confidence level for the test, from range [0, 1].
all_times	logical, determines if all the time points from the supplied data should be displayed on the plots next to each other.
line_size	line size of the lines displayed on the plot.
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 presents provided data in a form of differential (Woods) plot. The plot shows difference in exchange for two biological states, selected in generation of dataset at one time point of measurement. On X-axis there is a position in a sequence, with length of a segment of each peptide representing its length. On Y-axis there is deuterium uptake difference in chosen form. Error bars represents the combined and propagated uncertainty. For Woods Plot there is available Houde test and t-Student test to see the statistically significant peptides. Selecting both of them simultaneously results in hybrid testing, as described in Weis et al. The statistically significant values are in color (red if the difference is positive, blue if negative), and the insignificant values are grey.

Value

a [ggplot2::ggplot()] object.

References

Hageman, T. S. & Weis, D. D. Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach. Anal Chem 91, 8008–8016 (2019).

See Also

create_diff_uptake_dataset calculate_diff_uptake show_diff_uptake_data

Examples

# disabled due to long execution time 

diff_uptake_dat <- calculate_diff_uptake(alpha_dat,  
                                         states = c("ALPHA_Gamma", "Alpha_KSCN"), time_t = 0.167)
plot_differential(diff_uptake_dat = diff_uptake_dat, time_t = 0.167) 
plot_differential(diff_uptake_dat = diff_uptake_dat, time_t = 0.167, show_houde_interval = TRUE) 
plot_differential(diff_uptake_dat = diff_uptake_dat, time_t = 0.167, skip_amino = 0) 
plot_differential(diff_uptake_dat = diff_uptake_dat, time_t = 0.167, line_size = 1) 
plot_differential(diff_uptake_dat = diff_uptake_dat, all_times = TRUE)
plot_differential(diff_uptake_dat = diff_uptake_dat, all_times = TRUE, show_houde_interval = TRUE)
plot_differential(diff_uptake_dat = diff_uptake_dat, all_times = TRUE, show_houde_interval = TRUE, 
                 hide_houde_insignificant = TRUE)

diff_p_uptake_dat <- create_p_diff_uptake_dataset(alpha_dat, state_1 = "Alpha_KSCN", 
                                                  state_2 = "ALPHA_Gamma")
plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, all_times = TRUE, 
                  show_tstud_confidence = TRUE)
plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, all_times = FALSE, 
                  time_t = 0.167, show_tstud_confidence = TRUE, show_houde_interval = TRUE)
plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, show_tstud_confidence = TRUE, 
                  show_houde_interval = TRUE, all_times = FALSE)
plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, show_tstud_confidence = TRUE, 
                  show_houde_interval = TRUE, all_times = FALSE, hide_houde_insignificant = TRUE)
plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, show_tstud_confidence = TRUE, 
                  show_houde_interval = TRUE, all_times = FALSE, hide_houde_insignificant = TRUE, 
                  hide_tstud_insignificant = TRUE)

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