R/PlotDistro.R

In palmid: RdRP Analysis Suite

# PlotDistro
#' Plot a value relative to a background distribution from a palmprint
#'   data.frame.
#' @param pp A palmprint.df row to use for the plot "value"
#' @param pp.bg A multiple palmprint.df  for the plot background "distribution"
#' @param plotValue Which numeric column to use for pp and pp.bg. One of
#'   "score", "pssm_total_score", "pp_length", "v1_length", "v2_length"
#' @param distrocol Color to use for distribution ["skyblue"]
#' @param set.ylab Label for y-axis ["palmDB density"]
#' @return A ggplot2 object
#' @keywords palmid fev
#' @examples
#'
#' data("waxsys.palmprint")
#' data("palmdb")
#'
#' PlotDistro( pp = waxsys.palmprint, pp.bg = palmdb, "score", "black")
#' PlotDistro( pp = waxsys.palmprint, pp.bg = palmdb, "pp_length", "skyblue")
#'
#' @import viridisLite
#' @import dplyr ggplot2
#' @export
PlotDistro <- function(pp, pp.bg, plotValue, distrocol = "skyblue", set.ylab = "palmDB density") {
  # Bind variables locally
  bg <- NULL
  ## debug
  # pp = ps
  # plotValue = "score"
  # distrocol = "skyblue"
  # set.ylab = "test"
  # set.xlim = c(0,75)

  # check that an acceptable plotValue is used
  accepted_plot_value <- c("score", "pssm_total_score",
                           "pp_length", "v1_length", "v2_length")

  if ( !(plotValue %in% accepted_plot_value) ) {
    stop("plotValue must be set to an appropriate value.")
  }


  # Specific plot values
  if (plotValue == "score") {
    set.xlab <- "RdRP Score"
    set.xlim <- c(0,75)
  } else if (plotValue == "pssm_total_score") {
    set.xlab <- "PSSM Score"
    set.xlim <- c(0,NA)
  } else if (plotValue == "pp_length") {
    set.xlab <- "Palmprint Length (aa)"
    set.xlim <- c(50, 200)
  } else if (plotValue == "v1_length") {
    set.xlab <- "V1-region Length"
    set.xlim <- c(0,NA)
  } else if (plotValue == "v2_length") {
    set.xlab <- "V2-region Length"
    set.xlim <- c(0,NA)
  } else {
    set.xlab <- ""
    set.xlim <- c(0,NA)
  }

  #palmprint color
  pp.col <- "darkgoldenrod1"

  # Input palmprint value
  pp.value <- pp[, plotValue]

  # Background distribution of palmprints
  pp.bg.value <- data.frame( bg = pp.bg[, plotValue] )

  # Ditribution Plot
  distPlot <- ggplot() +
    # background distribution
    geom_density(data = pp.bg.value, aes( bg ),
                 color = distrocol, fill = distrocol, alpha = 0.8) +
    geom_vline( xintercept = pp.value, size = 1, color = pp.col) +
    geom_text( data = data.frame(pp.value),
               x = Inf, y = Inf,
               hjust = "inward", vjust = "inward",
               color = pp.col, size = 6, label = pp.value) +
    xlim(set.xlim) +
    theme_bw() +
    xlab(set.xlab) + ylab(set.ylab)
  #distPlot

  return(distPlot)
}