R/pvca.plot.R

In msuprun/bbeaR: an R package and framework for epitope-specific antibody profiling

pvca.plot<-function (pvcaObj, cex.percentage = 1, fname = NULL, ht = 4, 
                     wd = 5, title = fname,ylim=c(0,1), order=labels) 
{
  require(stringr)
  require(ggplot2)
  title <- mgsub(c("/", ".", "PVCA"), rep("", 3), fixed = TRUE, 
                 fname)
  labels <- gsub(":", " x ", pvcaObj$label)
  db <- data.frame(perc = t(pvcaObj$dat), labels = factor(labels, 
                                                          levels = order))
  p <- ggplot(db, aes(x = labels, y = perc)) + geom_bar(stat = "identity", 
                                                        fill = "blue") + theme_bw() + scale_y_continuous(limits = c(0, 
                                                                                                                    1.1)) + geom_text(aes(x = labels, y = perc + 0.05, label = paste0(as.character(round(100 * 
                                                                                                                                                                                                           perc, 1)), "%"))) + labs(x = "Effects", y = "Weighted average proportion variance", 
                                                                                                                                                                                                                                    title = paste("PVCA ", title)) + scale_x_discrete(labels = function(x) str_wrap(x, 
                                                                                                                                                                                                                                                                                                                    width = 8)) + coord_cartesian(ylim=ylim)
  if (!is.null(fname)) {
    ggsave(file = paste0(fname, ".pdf"), height = ht, width = wd, 
           plot = p)
  }
  return(p)
}