GWASTools: Tools for Genome Wide Association Studies

Documented in anomStatsPlot

#####
# Function to plot anomalies with stats
#####

#-------------------------------------------------------
# Accessory function

# input will be zoom type - zl for left breakpoint, zr for right breakpoint, zb for both
.zoom2 <- function(pos, 	# position vector over all snps in the netCDF
	left.index,   # left index for anomaly(ies) to be plotted
	right.index,
	xlim.all, 
	ztype, 	# zoom type zl=left, zr=right, zb=both
	z		# zoom factor or window size
	){
	mb <- 1000000
	leftx <- pos[left.index]/mb
	rightx <- pos[right.index]/mb
	dif <- rightx-leftx
	if(ztype=="zb") {left <- max(leftx-z*dif, xlim.all[1]); right <- min(rightx+z*dif, xlim.all[2])}
	if(ztype=="zl") {left <- max(leftx-z*dif, xlim.all[1]); right <- min(leftx+z*dif, xlim.all[2])}
	if(ztype=="zr") {left <- max(rightx-z*dif, xlim.all[1]); right <- min(rightx+z*dif, xlim.all[2])}			
	xlim <- c(left,right)
	return(xlim)
}	
#-------------------------------------------------------
# Main function

anomStatsPlot <- function(intenData, genoData,
	anom.stats, # data.frame with names c("anom.id","scanID", "chromosome", "left.index","right.index","method","nmark.all","nmark.elig","left.base","right.base",
		#	"nbase","non.anom.baf.med","non.anom.lrr.med","anom.baf.dev.med","anom.baf.dev.5","anom.lrr.med","nmark.baf","nmark.lrr") 
		#     this is produced by anom.seg.stats function
	snp.ineligible,	# vector of "int.id"s for intensity-only, failed snps, XTR and HLA regions
	plot.ineligible=FALSE,  # whether or not to include ineligible points in the plot
	centromere=NULL,	# if a data.frame of centromere positions is given here, they will be shown as a gray rectangle on the plot
				# centromere is a data.frame with variables "chromosome","left.base","right.base"
	brackets = c("none","bases","markers"),	# re plotting brackets around breakpoints - none, use base length, use number of markers (note that using markers give asymmetric brackets)
	brkpt.pct = 10,  # percent of anomaly length in bases (or number of markers) for width of brackets
	whole.chrom=FALSE,  # logical to plot the whole chromosome or not (over-rides win and zoom arguments)
	win=5,			# size of the window surrounding the anomaly to plot = a multiple of anomaly length
	win.calc=FALSE,		# calculate window size from anomaly length; over-rides win and gives window of fixed length given by win.fixed
	win.fixed = 1,		# number of megabases for window size when win.calc=TRUE
	zoom=c("both","left","right"), # indicates whether plot includes the whole anomaly ("both") or zooms on just the left or right breakpoint; "both" is default                      
	main = NULL,   
	info=NULL,		# character vector of extra information to include in the main title of the upper plot
        ideogram=TRUE,
        ideo.zoom=FALSE, ideo.rect=TRUE,
        mult.anom=FALSE,
	cex=0.5,		# cex value for points on the plots
        cex.leg=1.5,
        colors = c("default", "neon", "primary"),
        ...
){

	# v3 adds option to plot vertical lines to bracket each breakpoint, width of bracket being a percentage of the length or number of markers 
	# 	in the anomaly
	#     also uses new var names for 'anom' data.frame (from the new anom.seg.stats function)
	#	allow for missing value codes other than -1 for genotypes
	# v4 adds options to identify the centromere as a shaded rectangle and to make whole-chromosome plot
	# v5 adds option to add a second row of identifier information to the main title
	# v6 adds arguments 'zoom','win.calc','win.fixed'; fix use of to bl.ncdf.file and geno.ncdf.file; add plotting of terminal markers as orange vertical lines (among all markers, intensity-only or not)
	# v7 fix arg order and defaults; when plot.ineligible=T these will be plotted only on LRR, not on BAF
	# v8 add anom.id to plot title
	# v9 when plotting ineligible points for lrr, put them underneath the eligible

  colors <- match.arg(colors)

  # check that intenData has BAF/LRR
  if (!hasBAlleleFreq(intenData)) stop("BAlleleFreq not found in intenData")
  if (!hasLogRRatio(intenData)) stop("LogRRatio not found in intenData")
  
  # check that dimensions of intenData and genoData are equal
  intenSnpID <- getSnpID(intenData)
  genoSnpID <- getSnpID(genoData)
  if (!all(intenSnpID == genoSnpID)) stop("snp dimensions of intenData and genoData differ")
  intenScanID <- getScanID(intenData)
  genoScanID <- getScanID(genoData)
  if (!all(intenScanID == genoScanID)) stop("scan dimensions of intenData and genoData differ")
  
  intid <- intenSnpID
  sid <- intenScanID
  indices <- 1:length(intid)
  chrom <- getChromosome(intenData)
  pos <- getPosition(intenData)

  # character chromosome for ideogram
  chrom.ids <- anom.stats$chromosome
  anom.stats$chrom.char <- chrom.ids
  anom.stats$chrom.char[chrom.ids == XchromCode(intenData)] <- "X"
  anom.stats$chrom.char[chrom.ids == YchromCode(intenData)] <- "Y"
  
  # check centromere
  if(!is.null(centromere)){
    if(!class(centromere)=="data.frame") stop("centromere must be a data.frame")
    if(!all(is.element(c("chrom","left.base","right.base"), names(centromere)))) stop("names of centromere must include chrom, left.base, right.base")
    centromere$chrom[is.element(centromere$chrom, "X")] <- XchromCode(intenData)
    centromere$chrom[is.element(centromere$chrom, "Y")] <- YchromCode(intenData)
    centromere$chrom[is.element(centromere$chrom, "XY")] <- XYchromCode(intenData)
    centromere$chrom <- as.integer(centromere$chrom)
    centromere <- centromere[, c("chrom","left.base","right.base")]
    if(!all(unlist(lapply(centromere, class))=="integer")) stop("required centromere variables must be of class integer")
    if(!all(is.element(c(autosomeCode(intenData), XchromCode(intenData)),centromere$chrom))) stop("centromere positions must be given for chroms 1-22 and X")
  }
  cent.col <- "lightblue1"
  term.col <- "orange"
  
  # zoom
  zoom <- match.arg(zoom)

  # check anom.stats
  if(class(anom.stats)!="data.frame") stop("anom.stats should be a data.frame")
  anames <- c("anom.id","scanID", "chromosome", "left.index","right.index","method","nmark.all","nmark.elig","left.base","right.base",
              "nbase","non.anom.baf.med","non.anom.lrr.med","anom.baf.dev.med","anom.baf.dev.5","anom.lrr.med","nmark.baf","nmark.lrr")
  if(!all(is.element(anames,names(anom.stats)))) stop("anom.stats does not have required variable names")
  if(!all(is.element(c(anom.stats$left.index,anom.stats$right.index),indices))) stop("left and/or right are not within range of snp indices")
  
  # check snp.ineligible
  if(!all(is.element(snp.ineligible,intid))) stop("snp.ineligible are not snpIDs")

  # check win
  if(!is.null(win)) if(!(is.numeric(win) & length(win==1) & win>0)) stop("win must be null or a positive number")
  if(!win.calc){
    if(is.null(win)) stop("specify win when win.calc=FALSE")
  } 
	
  # check brackets and brkpt.pct
  brackets <- match.arg(brackets)
  if(!(brkpt.pct>0 & brkpt.pct<50)) stop("brkpt.pct must be >0 and <50")

  # check info
  if (!is.null(main)) {
    if (length(main) == 1 & nrow(anom.stats) > 1) {
      main <- rep(main, nrow(anom.stats))
    } else {
      stopifnot(length(main) == nrow(anom.stats))
    }
  }
  if(!is.null(info)) {
    if(!(length(info)==nrow(anom.stats) & is.character(info))) stop("info should be a character vector of length equal to rows of anom.stats")
  }

  # logical for ineligible
  ne <- is.element(intid, snp.ineligible)
	
  # bases per megabase
  mb <- 1000000
  
  # colors for breakpoints of each anomaly
  bcols <- rep(c("black", "darkgreen", "cyan", "magenta", "orange", "brown", "turquoise", "salmon", "gray", "purple"),10)

  # plot multiple anomalies per chromosome?
  if (mult.anom) {
    # add sample-chrom to anom
    anom.stats$sc <- paste(anom.stats$scanID, anom.stats$chromosome)
    anom.stats <- anom.stats[order(anom.stats$scanID, anom.stats$chromosome, anom.stats$left.index),]
    sc <- unique(anom.stats$sc)
    nplot <- length(sc)

  } else {
    nplot <- nrow(anom.stats)
  }

  # layout
  if (ideogram) {
    layout(matrix(c(1,2,3), nrow=3, ncol=1), heights=c(0.4, 0.4, 0.2))
  } else {
    layout(matrix(c(1,2), nrow=2, ncol=1), heights=c(0.5, 0.5))
  }
  
  for(i in 1:nplot) {
    if (!mult.anom) {
      # data frame for this anomaly
      dat <- anom.stats[i,]
      
      this.scanID <- anom.stats$scanID[i]
      this.chr <- anom.stats$chromosome[i]
      this.chr.char <- anom.stats$chrom.char[i]
      this.sex <- anom.stats$sex[i]
      this.anomID <- anom.stats$anom.id[i]
      this.method <- anom.stats$method[i]
      this.main <- main[i]
      this.info <- info[i]
     
      # get left and right index and anomaly length in Mb
      left <- anom.stats$left.index[i]
      right <- anom.stats$right.index[i]
      this.len <- anom.stats$nbase[i]/mb
    } else {
      # data frame of all anomalies for this plot
      dat <- anom.stats[anom.stats$sc == sc[i],]
      
      this.scanID <- dat$scanID[1]
      this.chr <- dat$chromosome[1]
      this.chr.char <- dat$chrom.char[1]
      this.sex <- dat$sex[1]
      this.anomID <- paste(dat$anom.id, collapse=",")
      this.method <- paste(dat$method, collapse=",")
      this.main <- main[anom.stats$sc == sc[i]][1]
      this.info <- paste(info[anom.stats$sc == sc[i]], collapse=",")
           
      # get left and right extremes of all anomalies on the chrom 
      left <- min(dat$left.index)
      right <- max(dat$right.index)
      this.len <- (pos[right] - pos[left])/mb
    }
    nanom <- nrow(dat)
    
    sind <- which(is.element(sid, this.scanID))
    chr <- chrom == this.chr
    baf <- getBAlleleFreq(intenData, snp=c(1,-1), scan=c(sind,1))
    lrr <- getLogRRatio(intenData, snp=c(1,-1), scan=c(sind,1))
    geno <- getGenotype(genoData, snp=c(1,-1), scan=c(sind,1))

    # calculate window size if indicated
    if(win.calc){
      win <- win.fixed / this.len		
    }

    # color-coding for genotype calls
    cols <- .colorByGeno(colors)
    gcol <- rep(NA, length(geno))
    gcol[geno %in% 2] <- cols["AA"]
    gcol[geno %in% 1] <- cols["AB"]
    gcol[geno %in% 0] <- cols["BB"]
    gcol[is.na(geno)] <- cols["NA"]
    gcol[ne] <- "pink"
    # color-coding for lrr
    lcol <- rep("gray", length(lrr))
    lcol[ne] <- "pink"
		
    # set xlim values for base position, leftp and rightp
    # terminal positions for the selected chromosome
    posc <- pos[chr]
    xlim.all <- c(posc[1], posc[length(posc)])/mb
    # anom length
    if(whole.chrom==TRUE) {
      xlim <- xlim.all	# set xlim to be the start and end of the chromosome
    } else {
     # zoom2 accessory function defined above
      if(zoom=="left")  xlim <- .zoom2(pos=pos, left.index=left, right.index=right, xlim.all=xlim.all, ztype="zl", z=win)
      if(zoom=="right") xlim <- .zoom2(pos=pos, left.index=left, right.index=right, xlim.all=xlim.all, ztype="zr", z=win)
      if(zoom=="both")  xlim <- .zoom2(pos=pos, left.index=left, right.index=right, xlim.all=xlim.all, ztype="zb", z=win)
    }

    # set lower limit on lrr to be -2 or the min within the anomaly, whichever is smaller
    mina <- rep(NA, nanom)
    for(a in 1:nanom) mina[a] <- min(lrr[dat$left.index[a]:dat$right.index[a]], na.rm=TRUE)
    lrr.min <- min(c(mina, -2))

    # select points to plot
    if(plot.ineligible==FALSE) {
      sel.lrr <- chr & !ne
    }  else {
      sel.lrr <- chr
    }
    sel.baf <- chr & !ne

    # brackets around breakpoints
    if (!mult.anom) {
      if(brackets=="bases"){
        br <- (brkpt.pct/100)*(anom.stats$nbase[i])
        left.lower <- pos[left]-br
        left.upper <- pos[left]+br
        right.lower <- pos[right]-br
        right.upper <- pos[right]+br
        bkt.pos <- c(left.lower/mb, left.upper/mb, right.lower/mb, right.upper/mb)
      }
      if(brackets=="markers"){
        br <- ceiling((brkpt.pct/100)*(anom.stats$nmark.elig[i])) # number of eligible markers to include in bracket
        elig <- !ne
        bre <- 0; j <- 0; while(bre<br) { j <- j+1; bre <- bre + elig[left-j]}
        left.lower <- pos[left-j]
        table(elig[(left-j):(left-1)])
        bre <- 0; j <- 0; while(bre<br) { j <- j+1; bre <- bre + elig[left+j-1]}  # includes the breakpoint marker
        left.upper <- pos[left+j-1]
        table(elig[left:(left+j-1)])
        bre <- 0; j <- 0; while(bre<br) { j <- j+1; bre <- bre + elig[right-j]}
        right.lower <- pos[right-j]
        table(elig[(right-j):(right-1)])
        bre <- 0; j <- 0; while(bre<br) { j <- j+1; bre <- bre + elig[right+j-1]} # includes the breakpoint marker
        right.upper <- pos[right+j-1]
        table(elig[right:(right+j-1)])
        bkt.pos <- c(left.lower/mb, left.upper/mb, right.lower/mb, right.upper/mb)
      }
    } else {
      brackets <- "none"
    }
    
    # get centromere start and end points
    if(!is.null(centromere)){
      # if >1 centromere position given, the first is used
      cent <- centromere[centromere$chrom == this.chr,][1,] 
      if(nrow(cent)>1) stop(paste("more than one row in centromere for chromosome",i))
    }
			
    # plot LRR
    par(mar=c(5,4,4,2)+0.1, mgp=c(2.5,0.75,0))
    if (is.null(main)) {
      if (!mult.anom) {
        mtxt <- paste("anom", this.anomID, "- scan", this.scanID, "-",
                      this.sex, "- chrom", this.chr, "-", this.method)
      } else {
        # split into two lines, as mult anoms and methods can get long
        mtxt <- paste("anom", this.anomID, "- scan", this.scanID, "-",
                      this.sex, "\nchrom", this.chr, "-", this.method)
      }
    } else {
      mtxt <- this.main
    }
    if(brackets!="none") mtxt <- paste(mtxt, "- gray brackets =", brkpt.pct, "% of", brackets)
    if(!is.null(info)) mtxt <- paste(mtxt, "\n", this.info)
    plot(pos[sel.lrr]/mb, lrr[sel.lrr], xlab="position (Mb)", ylab="LRR", type="n",
         ylim=c(lrr.min,2), xlim=xlim, main=mtxt, ...) 
    if(!is.null(centromere)){
      rect(cent$left.base/mb,lrr.min,cent$right.base/mb,2, col=cent.col, border=cent.col)
    }
    abline(v=xlim.all, col=term.col)  # terminal markers
    abline(h=0, col="gray")
    # plot lrr values
    if(plot.ineligible) points(pos[chr & ne]/mb, lrr[chr & ne], col="pink", cex=cex)
    points(pos[chr & !ne]/mb, lrr[chr & !ne], col="darkgray", cex=cex)

    for (a in 1:nanom) {
      # get breakpoints
      aleft <- dat$left.index[a]
      aright <- dat$right.index[a]
      #check base positions
      chk <- pos[aleft]==dat$left.base[a] & pos[aright]==dat$right.base[a]
      if(!all(chk)) stop(paste("left.base and/or right.base for anom",dat$anom.id[a],"not correct"))
      # plot breakpoints
      abline(v=c(pos[aleft]/mb,pos[aright]/mb), col=bcols[a])
      if(brackets!="none") abline(v=bkt.pos, col="gray")
      # Add anom stats
      abline(h=dat$non.anom.lrr.med[a], col="red")
      tmp <- dat$anom.lrr.med[a]
      segments(pos[aleft]/mb, tmp, pos[aright]/mb, tmp, col="red", lty=2)
    }
              
    # plot BAF
    mtxt <- paste0(cols["AAname"], "=AA, ",
                   cols["ABname"], "=AB, ",
                   cols["BBname"], "=BB, ",
                   "pink=ineligible, ",
                   cols["NAname"], "=other missing\n",
                  "horiz solid red = non-anom median, horiz dashed red = anom median")
    plot(pos[sel.baf]/mb, baf[sel.baf], xlab="position (Mb)", ylab="BAF", type="n",
         ylim=c(0,1), xlim=xlim, main=mtxt, ...) 
    if(!is.null(centromere)){
      rect(cent$left.base/mb,0,cent$right.base/mb,1, col=cent.col, border=cent.col)
    }
    abline(v=xlim.all, col=term.col)    # terminal markers
    # plot baf values
    points(pos[sel.baf]/mb, baf[sel.baf], col=gcol[sel.baf], cex=cex)

    for (a in 1:nanom) {
      # get breakpoints
      aleft <- dat$left.index[a]
      aright <- dat$right.index[a]
      # plot breakpoints
      abline(v=c(pos[aleft]/mb,pos[aright]/mb), col=bcols[a])
      abline(h=c(0.5,1/3,2/3,0,1), col="pink")
      if(brackets!="none") abline(v=bkt.pos, col="gray")
      # Add anom stats
      abline(h=dat$non.anom.baf.med[a], col="red")
      tmp <- dat$non.anom.baf.med[a] + dat$anom.baf.dev.med[a] 
      segments(pos[aleft]/mb, tmp, pos[aright]/mb, tmp, col="red", lty=2)
      tmp <- dat$non.anom.baf.med[a] - dat$anom.baf.dev.med[a] 
      segments(pos[aleft]/mb, tmp, pos[aright]/mb, tmp, col="red", lty=2)
    }

    # plot ideogram
    if (ideogram) {
      par(mar=c(1,4,1,2)+0.1)
      if (ideo.zoom) {
        ideo.x <- xlim*mb
      } else {
        ideo.x <- c(0, lengthChromosome(this.chr.char, "bases"))
      }
      plot(ideo.x, c(-2,2),
           type="n", xaxt="n", yaxt="n", xlab="", ylab="", bty="n")
      paintCytobands(this.chr.char, units="bases", width=1, cex.leg=cex.leg)
      if (ideo.rect) rect(xlim[1]*mb, -1.2, xlim[2]*mb, 0.2, border="red", lwd=2)
    }
	
  }  # end loop over anomalies

} # end function definition