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Plot differential uptake curve

plot_differential_uptake_curve.Rd

Differential uptake curve for one peptide between two biological states.

Usage

plot_differential_uptake_curve(
  diff_uptake_dat = NULL,
  diff_p_uptake_dat = NULL,
  sequence = NULL,
  theoretical = FALSE,
  fractional = FALSE,
  uncertainty_type = "ribbon",
  log_x = TRUE,
  show_houde_interval = FALSE,
  show_tstud_confidence = FALSE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

diff_uptake_dat

produced by create_diff_uptake_dataset function

diff_p_uptake_dat

...

sequence

sequence of chosen peptide.

theoretical

logical, determines if plot shows theoretical values.

fractional

logical, determines if plot shows fractional values.

uncertainty_type

type of presenting uncertainty, possible values: "ribbon", "bars" or "bars + line".

log_x

logical, determines if x axis shows logarithmic values.

show_houde_interval

logical, determines if houde interval is shown.

show_tstud_confidence

logical, determines if t-Student test validity is shown.

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

This plot shows the differential deuterium uptake between two biological states for selected peptides in different time points. The possibility to plot multiple differences (between state and mutant) for the peptide will be added soon.

See also

read_hdx create_diff_uptake_dataset

Examples

diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
plot_differential_uptake_curve(diff_uptake_dat = diff_uptake_dat, sequence = "GDLKSPAGL")


diff_p_uptake_dat <- create_p_diff_uptake_dataset(alpha_dat)
plot_differential_uptake_curve(diff_p_uptake_dat = diff_p_uptake_dat, 
                               sequence = "GDLKSPAGL", show_houde_interval = TRUE)

plot_differential_uptake_curve(diff_p_uptake_dat = diff_p_uptake_dat, 
                               sequence = "GDLKSPAGL", show_houde_interval = TRUE, 
                               show_tstud_confidence = TRUE)

plot_differential_uptake_curve(diff_p_uptake_dat = diff_p_uptake_dat, 
                               sequence = "GDLKSPAGL", show_tstud_confidence = TRUE)