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Code usage

usage.Rmd

Convention

Purpose of groups of functions in the package:

  • calculate_* - calculates one specific value. e.q. deuterium uptake values for specific time point.
  • create_* - creates a dataset for set of values e.q. multiple time points.
  • plot_* - plots a visualization of provided data, accepts calculate_* and create_* outputs.
  • show_* - subsets the dataset to show specific values, accepts calculate_* and create_* outputs.

Variables:

  • deut_uptake - deuterium uptake [Da]
  • frac_deut_uptake - fractional deuterium uptake [%]
  • theo_deut_uptake - theoretical deuterium uptake [Da]
  • theo_frac_deut_uptake - theoretical fractional deuterium uptake [%]
  • diff_deut_uptake - differential deuterium uptake [Da]
  • frac_diff_deut_uptake - theoretical differential fractional deuterium uptake [%]
  • theo_diff_deut_uptake - differential deuterium uptake [Da]
  • theo_frac_diff_deut_uptake - theoretical differential fractional deuterium uptake [%]

Example of use

Read data file 

dat <- read_hdx(system.file(package = "HaDeX2", "HaDeX/data/alpha.csv"))

Different forms of visualization

Create data frame with uptake values for state in all time points:

uptake_dat <- create_state_uptake_dataset(dat)

Butterfly:

plot_butterfly(uptake_dat)

Chiclet:

plot_chiclet(uptake_dat)
## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## ℹ The deprecated feature was likely used in the HaDeX2 package.
##   Please report the issue to the authors.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.