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State deuterium uptake comparison

plot_state_comparison.Rd

Comparison plot of deuterium uptake values in time point for biological states.

Usage

plot_state_comparison(
  uptake_dat,
  skip_amino = 0,
  theoretical = FALSE,
  fractional = FALSE,
  line_size = 1.5,
  all_times = FALSE,
  time_t = NULL,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

uptake_dat

data produced by calculate_state_uptake function

skip_amino

integer, indicator how many aminos from the N-terminus should be omitted

theoretical

logical, indicator if values are calculated using theoretical controls

fractional

logical, indicator if values are shown in fractional form

line_size

line size for the plot

all_times

logical, indicator is all all time should be ploted next to each other

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)

Value

a ggplot object

Details

The function plot_state_comparison generates a comparison plot, presenting deuterium uptake values of peptides from selected protein in selected biological states at one time point of measurement at once. 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 in selected form. Error bars represents the combined and propagated uncertainty.

See also

read_hdx calculate_state_uptake

Examples

uptake_dat <- calculate_state_uptake(alpha_dat)
plot_state_comparison(uptake_dat)


plot_state_comparison(uptake_dat, all_times = TRUE)

plot_state_comparison(uptake_dat, fractional = TRUE, all_times = TRUE)