R/plot_amino_distribution.R

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

#' generate_amino_distribution
#' 
#' @description Generates amino distribution based on the 
#' protein sequence and shows if the amino acid is hydrophobic
#' or hydrophylic.
#' 
#' @param position_in_sequence custom format
#' @param hydro_properties data with hydrophobic properties
#' @param protein chosen protein
#' @param charge_colors vector of desired colors
#' @inheritParams plot_butterfly
#' 
#' @details The data for this function is not packaged yet.
#' 
#' @return a \code{\link[ggplot2]{ggplot}} object.
#' 
#' @importFrom dplyr n
#' @importFrom ggplot2 scale_fill_manual
#' @export plot_amino_distribution

plot_amino_distribution <- function(position_in_sequence, 
                                    hydro_properties,
                                    protein,
                                    charge_colors,
                                    interactive = getOption("hadex_use_interactive_plots")){
  amino_groups <- c("G", "A", "V", "I", "L", "F", "P", "M", "S", "T", "Y", "W", "N", "Q", "C", "D", "E", "K", "R", "H")
  
  chosen_geom_col <- if (interactive) ggiraph::geom_col_interactive(
    aes(tooltip = glue(
      "Amino acid: {amino}
       Charge: {charge}
       Is hydrophobic? {is_hydrophobic}
       Count: {cnt}"
    ))
  ) else geom_col()
  
  position_in_sequence %>%
    mutate(affinity = ifelse(is_hydrophobic, "phobic", "philic")) %>% 
    filter(affinity %in% hydro_properties) %>%
    mutate(amino = factor(amino, levels = amino_groups)) %>%
    group_by(amino, charge, is_hydrophobic) %>%
    summarise(cnt = n()) %>%
    ggplot(aes(x = amino, y = cnt, fill = charge)) + 
    chosen_geom_col +
    scale_fill_manual("Charge", values = charge_colors) + 
    labs(title = paste0('Amino acid composition for ', protein),
         x = 'Amino acid',
         y = 'Count')
  
}