R/plotOverlapOverview.R

In MDegener/SpliceSelector: Filtering of Results from common Alternative Splicing Software

#' Plotting function for overlap between genomic and exon coordinates
#'
#' Creates two barplots for an overview of how supplied coordinates match to the exon annotation file
#'
#' @param overlap output of the "getOverlap" function
#' @param plotPrefix prefix for plot filename
#' @param outDir output directory
#'
#' @return None
#'
#' @export

plotOverlapOverview <- function(overlap, plotPrefix, outDir){

  # get number of exon matches per input coordinates
  exonMatches <- overlap %>%
    dplyr::filter(overlap != "none") %>%
    dplyr::group_by(query.index) %>%
    dplyr::count(annotation.exon_id) %>%
    dplyr::summarise(sum(n))

  # get unique matches of input coordinates to an exon
  uniqueMatches <- sum( exonMatches[, 2] == 1)

  matchCounts <- c(overlap$query.index %>% unique() %>% length(),
                   overlap[which(overlap$overlap != "none"), ] %>% nrow(),
                   uniqueMatches,
                   overlap[which(overlap$overlap == "none"), ] %>% nrow())

  # plot overview on how coordinates are matched to exons
  jpeg(paste0(outDir,"/", plotPrefix, "_matchCounts.jpeg"),
              width = 1000, height = 1000, pointsize = 24)

  plot <- barplot(height = matchCounts,
                  names = c("Input", "All Matches", "Unique", "No Match"),
                  ylab = "Count",
                  ylim = c(0, 1.1*max(matchCounts)))

  text(x = plot, y = matchCounts, label = matchCounts, pos = 3, cex = 1)
  dev.off()

  # get counts for all overlap types
  overlapCounts <- c(overlap[which(overlap$overlap == "equal"), ] %>% nrow(),
                     overlap[which(overlap$overlap == "within"), ] %>% nrow(),
                     overlap[which(overlap$overlap == "spans one"), ] %>% nrow(),
                     overlap[which(overlap$overlap == "spans multiple"), ] %>% nrow(),
                     overlap[which(overlap$overlap == "other"), ] %>% nrow())

  # plot counts for every type of overlap
  jpeg(paste0(outDir,"/", plotPrefix, "_overlapCounts.jpeg"),
       width = 1200, height = 1000, pointsize = 24)

  plot <- barplot(height = overlapCounts,
                  names = c("Equal", "Within", "Spans One", "Spans Multiple", "Other"),
                  xlab = "Type of Overlap",
                  ylab = "Count",
                  ylim = c(0, 1.1*max(overlapCounts)))

  text(x = plot, y = overlapCounts, label = overlapCounts, pos = 3, cex = 1)
  dev.off()
}