R/connectSeg.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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# Connect segments by vertical plotting. For sample and chromosome plots (sep.arm will be != NULL), segments are not connected across different arms.

## Input:
### sep.arm: vector giving index at which chromosome arms changes
### nSeg: number of segments
### use.stop: segment stopping positions
### seg.mean: mean value of segments
### col: segment color
### lwd: segment line width
### lty: segment line type


## Required by:
### plotGamma
### plotSegments

## Requires:
## none


connectSeg <- function(sep.arm, nSeg, use.stop, seg.mean, col, lwd, lty) {
  if (!is.null(sep.arm) && nSeg > 2) {
    # No connection across arms in the case of sample- or chromosomePlot, and across not adjecent chromosomes in the case of genomePlot
    segments(x0 = use.stop[-c((sep.arm - 1), nSeg)], y0 = seg.mean[-c((sep.arm - 1), nSeg)], x1 = use.stop[-c((sep.arm - 1), nSeg)], y1 = seg.mean[-c(1, sep.arm)], col = col, lwd = lwd, lty = lty)
  } else {
    if (is.null(sep.arm) && nSeg > 1) {
      segments(x0 = use.stop[1:(nSeg - 1)], y0 = seg.mean[1:(nSeg - 1)], x1 = use.stop[1:(nSeg - 1)], y1 = seg.mean[2:nSeg], col = col, lwd = lwd, lty = lty)
    }
  }
} # end connectSeg