R/get_yticks.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 calculate pretty ticks along y-axis in plot:

## Input:
### min: minimum observed y-value
### max: maximum observed y-value

## Output:
### ticks: tickmarks to be used along yaxis

## Required by:
### plotGamma
### updatePlotParameters

## Requires:
### none

get.yticks <- function(min, max) {
  ideal.n <- 5
  by <- c(0.05, 0.1, 0.2, 0.5, 1, 2, 5, 10, 50, 100, 500, 1000, 2000, 5000, 10000)
  use.min <- rep(NA, length(by))
  use.max <- rep(NA, length(by))
  n.tick <- rep(NA, length(by))

  for (i in 1:length(by)) {
    use.max[i] <- max
    if (max %% by[i] != 0) {
      use.max[i] <- max + (by[i] - max %% by[i])
    }
    use.min[i] <- min
    if (min %% by[i] != 0) {
      use.min[i] <- min - min %% by[i]
    }
    seq <- seq(use.min[i], use.max[i], by = by[i])
    n.tick[i] <- length(seq)
  } # endfor

  diff <- sapply(n.tick, "-", ideal.n)
  best <- which.min(abs(diff))

  ticks <- seq(use.min[best], use.max[best], by = by[best])
  return(ticks)
} # endfunction