plot_coverage_heatmap: Coverage heatmap

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

Coverage heatmap

Description

Coverage heatmap with color indicating specific value

Usage

plot_coverage_heatmap(
  x_dat,
  protein = x_dat[["Protein"]][1],
  state = NULL,
  value = NULL,
  time_t = NULL,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

x_dat	data created using calculate_ or create_ function
protein	selected protein
state	selected biological state
value	value to be presented
time_t	chosen time point
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

Plots standard protein coverage but colored with desired value.

Value

a ggplot object

See Also

read_hdx plot_coverage

Examples

uptake_dat <- create_uptake_dataset(alpha_dat, states = "Alpha_KSCN")
plot_coverage_heatmap(uptake_dat)
plot_coverage_heatmap(x_dat = uptake_dat, value = "frac_deut_uptake", time_t = 0.167)
plot_coverage_heatmap(uptake_dat, value = "err_frac_deut_uptake", time_t = 0.167)

diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
plot_coverage_heatmap(diff_uptake_dat)
plot_coverage_heatmap(diff_uptake_dat, value = "diff_frac_deut_uptake")
plot_coverage_heatmap(diff_uptake_dat, value = "diff_frac_deut_uptake", time_t = 0.167)
plot_coverage_heatmap(diff_uptake_dat, value = "err_diff_frac_deut_uptake", time_t = 0.167)

auc_dat <- calculate_auc(create_uptake_dataset(alpha_dat))
plot_coverage_heatmap(auc_dat, value = "auc")

bex_dat <- calculate_back_exchange(alpha_dat, state = "Alpha_KSCN")
plot_coverage_heatmap(bex_dat, value = "back_exchange")

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