R/getx.r

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

####################################################################
## 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
####################################################################

# Returns the values to be plotted along xaxis depending on the choice of xaxis (index or pos), and the type of plot
# If type=genome and xaxis=pos, global positions are calculated.
# Positions are scaled according to plotunit

### input:
### xaxis: index or pos
### type: plot type; genome, chromosome, sample or aspcf
### chromosomes: vector of same length as pos giving the corresponding chromosome numbers
### pos: vector giving probe positions
### unit: unit used to represent positons   (bp,kbp, or mbp)
### op: a list containing other plot parameters

### Output:
### x: a vector containg the numbers to be plotted along xaxis of plot


## Required by:
### adjustPos
### plotObs

## Requires:
### getGlobPos
### convert.unit


getx <- function(xaxis, type, chromosomes, pos, unit, op) {
  if (xaxis == "pos") {
    x <- pos
    if (type == "genome") {
      # Convert to global position:
      global.pos <- getGlobPos(chromosomes, pos, pos.unit = unit, cyto.data = op$assembly)
      x <- global.pos
    }

    # Want to scale the x-axis to fit the desired unit given in plot.unit (default is mega base pairs)
    scale.fac <- convert.unit(unit1 = op$plot.unit, unit2 = unit)
    x <- x * scale.fac
  } else {
    # xaxis=="index"
    x <- 1:length(pos)
  } # endif

  return(x)
} # endgetx