R/coverage_lit_seq_plot.R

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

#' Displays the literature sequence with identified residues for a specific protein
#'
#' @description A plot of the literature sequence with identified fragment residues in green
#'
#' @param PeptideCoverage A "peptide_coverage" object generated by get_peptide_coverage. Required.
#'
#' @examples
#' \dontrun{
#'
#' # Make Peptide Coverage Object
#' PeptideCoverage <- get_peptide_coverage(ScanMetadata = BU_ScanMetadata, ProteinTable = ProteinTable, ProteinID = "SO_0225")
#'
#' # Make plot
#' coverage_lit_seq_plot(PeptideCoverage)
#'
#' }
#'
#' @export
coverage_lit_seq_plot <- function(PeptideCoverage) {

  ##################
  ## CHECK INPUTS ##
  ##################

  # Assert that PeptideCoverage is a "peptide_coverage" object
  if ("peptide_coverage" %in% class(PeptideCoverage) == FALSE) {
    stop("PeptideCoverage must be an object of the peptide_coverage class generated by get_peptide_coverage.")
  }

  ##############################
  ## GENERATE PLOT AESTHETICS ##
  ##############################

  # Pull literature sequence and residue count
  LitSeq <- PeptideCoverage$PeptidesByPosition[PeptideCoverage$PeptidesByPosition$`Scan Number` == 0, "Sequence"] %>% unlist()
  Residues <- PeptideCoverage$ResidueCount

  # Get size
  sizeTest <- nchar(LitSeq) / 60
  if (sizeTest <= 5) {
    size <- 10
  } else if (sizeTest <= 10) {
    size <- 8
  } else if (sizeTest <= 20) {
    size <- 6
  } else {
    size <- 4
  }

  # Make plotting data.table
  LitSeqDF <- data.table::data.table(
    "x" = rep_len(1:60, nchar(LitSeq)),
    "y" = (1:nchar(LitSeq) / -60) %>% floor(),
    "Residue" = LitSeq %>% strsplit("") %>% unlist(),
    "Ref" = ifelse(1:nchar(LitSeq) %in% Residues$Position, "In Scans", "Not in Scans")
  )

  ###############
  ## MAKE PLOT ##
  ###############

  return(

    ggplot2::ggplot(LitSeqDF, ggplot2::aes(x = x, y = y, label = Residue, color = Ref)) +
           ggplot2::geom_text(size = size) + ggplot2::theme_void() +
           ggplot2::theme(legend.title = ggplot2::element_blank()) +
           ggplot2::scale_color_manual(values = list("In Scans" = "forestgreen", "Not in Scans" = "black"))

  )

}