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).
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.
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)