R/addChromlines.r

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

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## Author: Gro Nilsen, Knut Liestøl and Ole Christian Lingjærde.
## Maintainer: Gro Nilsen <gronilse@ifi.uio.no>
## License: Artistic 2.0
## Part of the copynumber package
## Reference: Nilsen and Liestøl et al. (2012), BMC Genomics
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## Input:
### chromosomes: a vector of chromosome numbers
### xaxis: what should be plotted along xaxis; pos or index
### unit: the unit used for positions, bp, kbp or mbp
### ind: only used when called by plotSegments; vector with start position and last stop position for segments
### cex: size used to plot chromosome numbers
### op: other plot parameters

## Output:
### adds chromosome lines to existing genome plot

## Required by:
### plotObs
### plotSegments
### plotFreq
### plotHeatmap
### plotWeightedFreq


## Requires:
### convert.unit
### getArmandChromStop
### separateChrom

# Function used to separate chromosomes by stapled lines in genome plot:
addChromlines <- function(chromosomes, xaxis, unit, ind = NULL, cex, op) {
  if (xaxis == "pos") {
    # Use cytoband data information to get stopping points of chromosomes:
    chromstop <- getArmandChromStop(op$assembly, unit)$chromstop
    scale.fac <- convert.unit(unit1 = op$plot.unit, unit2 = unit) # Scaling factor according to plot.unit
    chrom.mark <- c(1, cumsum(chromstop)) * scale.fac
    # Drop chrom24 if no observations for this chrom in data/segments:
    if (any(chromosomes == 24)) {
      chromosomes <- 1:24
    } else {
      chromosomes <- 1:23
      chrom.mark <- chrom.mark[-length(chrom.mark)]
    }
  } else {
    chrom.mark <- separateChrom(chromosomes)
    if (!is.null(ind)) {
      # Segments are used to decide where to separate chromosomes; get index start where chromosome number changes and last index
      chrom.mark <- ind[chrom.mark]
    }
    chrom.mark <- chrom.mark - 0.5
  }
  # Separate chromosomes by vertical lines in existing plot:
  nChrom <- length(unique(chromosomes))
  arg <- list(chrom.lwd = 1, chrom.lty = 2, chrom.col = "darkgrey", chrom.side = 3, chrom.cex = cex, chrom.line = c(0, 0.3))

  if (!is.null(op)) {
    arg <- modifyList(arg, op)
  }
  abline(v = chrom.mark[2:(length(chrom.mark) - 1)], col = arg$chrom.col, lwd = arg$chrom.lwd, lty = arg$chrom.lty)

  at <- (chrom.mark[1:nChrom] - 1) + (chrom.mark[2:(nChrom + 1)] - chrom.mark[1:nChrom]) / 2
  chrom.names <- unique(chromosomes)
  # Plot half at bottom, half at top:
  bot <- seq(1, length(chrom.mark), 2)
  top <- seq(2, length(chrom.mark), 2)
  mtext(chrom.names[bot], side = 1, line = arg$chrom.line[1], at = at[bot], cex = arg$chrom.cex)
  mtext(chrom.names[top], side = 3, line = arg$chrom.line[2], at = at[top], cex = arg$chrom.cex)
} # endaddChromlines