plot_volcano: Volcano plot

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

Volcano plot

Description

Volcano plot for differential deuterium uptake between two biological states

Usage

plot_volcano(
  p_dat,
  state_1 = "",
  state_2 = "",
  adjust_axes = TRUE,
  show_confidence_limits = FALSE,
  confidence_level = 0.98,
  color_times = TRUE,
  show_insignificant_grey = FALSE,
  hide_insignificant = FALSE,
  fractional = FALSE,
  theoretical = FALSE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

p_dat	data produced by the create_p_diff_uptake_dataset function
state_1	selected biological state for given protein
state_2	selected biological state for given protein
adjust_axes	logical, indicator if the X-axis is symmetrical in relation to 0
show_confidence_limits	logical, indicates if the hybrid test confidence levels are shown
confidence_level	confidence level for the test, from range [0, 1]. It should be the same as used to prepare p_dat
color_times	logical, indicator if different time points are distinguishable by color
show_insignificant_grey	logical, indicator if the values not passing the test are shown in grey
hide_insignificant	logical, indicator if the values not passing the test are hidden
fractional	logical, indicator if values are shown in fractional form
theoretical	logical, indicator if values are calculated using theoretical controls
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_volcano generates the volcano plot based on supplied p_dat. On X-axis there is differential deuterium uptake in selected form. On Y-axis there is the P-value from t-Student test between two biological states. Based on selected confidence level, the confidence limits are calculated to indicate statistically significant values - shown as red dotted lines. The values that are in upper left and right corners pass the hybrid test.

Value

a 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).

Houde, D., Berkowitz, S.A., and Engen, J.R. (2011). The Utility of Hydrogen/Deuterium Exchange Mass Spectrometry in Biopharmaceutical Comparability Studies. J Pharm Sci 100, 2071–2086.

See Also

create_p_diff_uptake_dataset

Examples

p_dat <- create_p_diff_uptake_dataset(alpha_dat)
plot_volcano(p_dat, show_confidence_limits = TRUE)

plot_volcano(p_dat, show_confidence_limits = TRUE, show_insignificant_grey = TRUE)
plot_volcano(p_dat, show_confidence_limits = TRUE, hide_insignificant = TRUE)

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