R/addArmlines.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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# Function that separates chromosome arms in genome-plots by dashed lines

## Required by:
## plotFreq (genomeFreq)

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



# Function used to separate chromosome arms by stapled lines in genome plot:
addArmlines <- function(chromosomes, xaxis, unit, ind = NULL, cex, op) {
  if (xaxis == "pos") {
    # Use cytoband data information to get stopping points of chromosome arms:
    marks <- getArmandChromStop(op$assembly, unit)
    armstop <- c(marks$pstop[1], cumsum(marks$chromstop)[1:length(marks$chromstop) - 1] + marks$pstop[2:length(marks$pstop)])
    scale.fac <- convert.unit(unit1 = op$plot.unit, unit2 = unit) # Scaling factor according to plot.unit
    arm.mark <- armstop * scale.fac
    # Separate arms by vertical lines in existing plot:
    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 = arm.mark[1:(length(arm.mark) - 1)], col = arg$chrom.col, lwd = arg$chrom.lwd, lty = 2)
  }
}