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Chiclet differential deuterium uptake plot

plot_differential_chiclet.Rd

Chiclet plot of differential deuterium uptake values between two biological states in time.

Usage

plot_differential_chiclet(
  diff_uptake_dat = NULL,
  diff_p_uptake_dat = NULL,
  theoretical = FALSE,
  fractional = FALSE,
  show_houde_interval = FALSE,
  show_tstud_confidence = FALSE,
  confidence_level = 0.98,
  show_uncertainty = FALSE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

diff_uptake_dat

data produced by create_diff_uptake_dataset function.

diff_p_uptake_dat

...

theoretical

logical, determines if values are theoretical.

fractional

logical, determines if values are fractional.

show_houde_interval

logical, determines if houde interval is shown.

show_tstud_confidence

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

confidence_level

confidence level for the test, from range [0, 1]. Important if selected show_confidence_limit.

show_uncertainty

logical, determines if the uncertainty 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

Function plot_differential_chiclet generates chiclet differential plot based on provided data and parameters. On X-axis there is a peptide ID. On Y-axis are time points of measurement. Each tile for a peptide in time has a color value representing the deuterium uptake difference between chosen states, in a form based on provided criteria (e.q. fractional). Each tile has a plus sign, which size represent the uncertainty of measurement for chosen value.

See also

create_diff_uptake_dataset

Examples

diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
plot_differential_chiclet(diff_uptake_dat)

plot_differential_chiclet(diff_uptake_dat, show_houde_interval = TRUE)


diff_p_uptake_dat <- create_p_diff_uptake_dataset(alpha_dat)
plot_differential_chiclet(diff_p_uptake_dat = diff_p_uptake_dat, 
                          show_tstud_confidence = TRUE)

plot_differential_chiclet(diff_p_uptake_dat = diff_p_uptake_dat, 
                          show_tstud_confidence = TRUE, show_houde_interval = TRUE)