R/updateFreqParameters.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
####################################################################


# Function to set default ylim and at.y for plotFreq

## Input:
### freq.del: vector with deletion frequencies
### freq.amp: vector with amplification frequencies
### op: list with plot parameters

## Output:
### op: list wiht updated plot parameters

## Required by:
### plotFreq (genomeFreq and chromosomeFreq)
### plotWeightedFreq (weightedGenomeFreq and weightedChromosomeFreq)

## Requires: none


updateFreqParameters <- function(freq.del, freq.amp, op) {
  # Y-limits; symmetric:
  max.freq <- max(c(freq.del, freq.amp))

  # Define tickmarks on y-axis
  if (max.freq > 30) {
    at.y <- seq(0, 100, by = 25)
  } else if (max.freq > 10) {
    at.y <- seq(0, 100, by = 10)
  } else {
    at.y <- seq(0, 100, by = 5)
  }
  if (is.null(op$at.y)) {
    op$at.y <- c(at.y)
  }
  # Make sure ylim includes the first tickmark above max.freq
  q <- min(op$at.y[op$at.y >= max.freq])
  ylim <- c(-q, q)

  if (is.null(op$ylim)) {
    op$ylim <- ylim
  }

  return(op)
}