Plot Composite Map

plot-compost-map.R

PlotCompositeMap <- function(bins.file, par1 = "par1", par2 = "par2", 
  col1 = "sky blue", colh = "black", col2 = "orange", plot.file = "composite-map.png", 
  plot = FALSE, save = TRUE, chr.text.size = 7, chr.text.angle = 0, ggtitle = "Composite Genotype Map", 
  ...) {
  library(ggplot2)
  library(plyr)
  library(reshape)
  
  bins <- read.table(bins.file, header = T, sep = "\t")
  
  bins.binary <- colwise(as.character)(bins)
  bins.binary[bins.binary == par1] <- 0
  bins.binary[bins.binary == par2] <- 1
  bins.binary[bins.binary == "HET"] <- 1
  
  distances <- dist(t(bins.binary[, 5:ncol(bins.binary)]), method = "binary")
  hc <- hclust(distances)
  order <- hc$order
  bins.sorted <- bins[, c(1:4, order + 4)]
  
  bins.m <- melt(bins.sorted, id = c("chr", "bin.mid", "bin.start", "bin.end"), 
    variable_name = "BIL")
  bins.m$value <- factor(bins.m$value, levels = c(par2, "HET", par1))
  bins.m$bil.idx <- as.integer(bins.m$BIL)
  
  composite.map <- ggplot(bins.m) +
    geom_rect(aes(xmin = bin.start, xmax = bin.end,  ymin = bil.idx,
      ymax = bil.idx + 1, fill = value, color = value)) +
    facet_grid(. ~ chr, scales = "free_x", space = "free_x") +
    scale_colour_manual(values = c(col2, colh, col1)) +
    scale_fill_manual(values = c(col2, colh, col1)) +
    theme(strip.text.x = element_text(size = chr.text.size,
      angle = chr.text.angle), axis.text = element_blank(),
      panel.grid = element_blank(), axis.ticks = element_blank()) +
    labs(colour = "Genotype", fill = "Genotype") +
    ggtitle(ggtitle)
  
  if (plot) 
    print(composite.map)
  
  if (save) 
    ggsave(filename = plot.file, plot = composite.map, ...)
}

bins.file <- "/Users/mfc/Dropbox/lab/tomato/bils/re-seq/hmm-results/boundaries-fixed/bin-genotypes.BILs.2014-12-07.imputed-NAs.merged-like"

PlotCompositeMap(bins.file, par1 = "M82", par2 = "PEN", col1 = "magenta", col2 = "green")