plot_manhattan: Manhattan plot

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

Manhattan plot

Description

Manhattan plot with p-values from the t-Student test and peptide position.

Usage

plot_manhattan(
  p_dat,
  skip_amino = 0,
  plot_title = NULL,
  separate_times = TRUE,
  times = NULL,
  confidence_level = NULL,
  show_confidence_limit = TRUE,
  show_peptide_position = FALSE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

p_dat	data produced by the create_p_diff_uptake_dataset function.
skip_amino	integer, indicator how many amino acids from the N-terminus should be omitted
plot_title	title for the plot. If not provided, it is constructed in a form: "Differences between state_1 and state_2"
separate_times	logical, indicates if the data should be seen on the same plot, or on separate plots for each time point of measurement.
times	vector of time points of measurements to be included in the plot.
confidence_level	confidence level for the test, from range [0, 1].
show_confidence_limit	logical, indicates if the hybrid testing confidence intervals are shown.
show_peptide_position	logical, indicates if the peptide length and position in the sequence is shown. Otherwise, the peptides are represented by their ID.
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 manhattan plot presents the P-values from t-student test, to see the regions of the protein with statistically significant changes between two biological states. 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 P-value from t-Student 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).

See Also

read_hdx create_p_diff_uptake_dataset

Examples

p_dat <- create_p_diff_uptake_dataset(alpha_dat)
plot_manhattan(p_dat)
plot_manhattan(p_dat, separate_times = FALSE)
plot_manhattan(p_dat, show_peptide_position = TRUE, separate_times = FALSE)
plot_manhattan(p_dat, separate_times = FALSE, show_confidence_limit = FALSE)
 

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