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- 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).
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.
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)