Differential plot

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

Usage

plot_differential(
  diff_uptake_dat = NULL,
  diff_p_uptake_dat = NULL,
  skip_amino = 0,
  time_t = NULL,
  theoretical = FALSE,
  fractional = FALSE,
  show_houde_interval = FALSE,
  hide_houde_insignificant = FALSE,
  show_tstud_confidence = FALSE,
  hide_tstud_insignificant = FALSE,
  confidence_level = 0.98,
  all_times = FALSE,
  line_size = 1.5,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

diff_uptake_dat: produced by create_diff_uptake_dataset function.
diff_p_uptake_dat: produced by create_p_diff_uptake_dataset function.
skip_amino: integer, indicator how many aminos from the N-terminus should be omitted
time_t: time point of measurement, if only one should be displayed on the plot.
theoretical: logical, determines if values are theoretical.
fractional: logical, determines if values are fractional.
show_houde_interval: logical, determines if houde interval is shown.
hide_houde_insignificant: logical, determines if statistically insignificant values using Houde test are hidden on the plot.
show_tstud_confidence: logical, determines if t-Student test validity is shown.
hide_tstud_insignificant: logical, determines if statistically insignificant values using t-Student test are hidden on the plot.
confidence_level: confidence level for the test, from range [0, 1].
all_times: logical, determines if all the time points from the supplied data should be displayed on the plots next to each other.
line_size: line size of the lines displayed on the plot.
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 presents provided data in a form of differential (Woods) plot. The plot shows difference in exchange for two biological states, selected in generation of dataset at one time point of measurement. 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 difference in chosen form. Error bars represents the combined and propagated uncertainty. For Woods Plot there is available Houde test and t-Student test to see the statistically significant peptides. Selecting both of them simultaneously results in hybrid testing, as described in Weis et al. The statistically significant values are in color (red if the difference is positive, blue if negative), and the insignificant values are grey.

References

Hageman, T. S. & Weis, D. D. Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach. Anal Chem 91, 8008–8016 (2019).

Examples

diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat, state_1 = "Alpha_KSCN", state_2 = "ALPHA_Gamma")
plot_differential(diff_uptake_dat = diff_uptake_dat, time_t = 0.167) 

plot_differential(diff_uptake_dat = diff_uptake_dat, time_t = 0.167, show_houde_interval = T) #' 

plot_differential(diff_uptake_dat = diff_uptake_dat, time_t = 0.167, skip_amino = 0) 

plot_differential(diff_uptake_dat = diff_uptake_dat, time_t = 0.167, line_size = 1) 

plot_differential(diff_uptake_dat = diff_uptake_dat, all_times = T)

plot_differential(diff_uptake_dat = diff_uptake_dat, all_times = T, show_houde_interval = T)

plot_differential(diff_uptake_dat = diff_uptake_dat, all_times = T, show_houde_interval = T, hide_houde_insignificant = T)


diff_p_uptake_dat <- create_p_diff_uptake_dataset(alpha_dat, state_1 = "Alpha_KSCN", state_2 = "ALPHA_Gamma")
plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, all_times = T, show_tstud_confidence = T)

plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, all_times = F, time_t = 0.167, show_tstud_confidence = T, show_houde_interval = T)

plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, show_tstud_confidence = T, show_houde_interval = T, all_times = F)

plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, show_tstud_confidence = T, show_houde_interval = T, all_times = F, hide_houde_insignificant = T)

plot_differential(diff_p_uptake_dat = diff_p_uptake_dat, show_tstud_confidence = T, show_houde_interval = T, all_times = F, hide_houde_insignificant = T, hide_tstud_insignificant = T)