R/colorSetup.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 range of colors for heatplot:


## Input:
### upper.lim, lower.lim: limits for aberration calling
### op: list with other plot parameters

## Output:
### colors: a vector giving a range of color nuances
### intervals: vector giving intervals between lower.lim and upper.lim corresponding to different color nuances

## Required by:
### plotHeatmap

## Requires:
### none

colorSetup <- function(upper.lim, lower.lim, op) {
  # Colors:
  if (is.na(op$n.col)) {
    op$n.col <- 50
  }
  # Range of colours in shades:
  range <- upper.lim - lower.lim
  n.col1 <- ceiling(op$n.col * abs(lower.lim) / range)
  n.col2 <- ceiling(op$n.col * upper.lim / range)
  col.down <- colorRampPalette(op$colors[1:2], space = "rgb")(n.col1)
  col.up <- colorRampPalette(op$colors[2:3], space = "rgb")(n.col2)
  colors <- c(col.down, col.up)

  # Divide into sequence according to values of limits:
  lim.seq1 <- seq(lower.lim, 0, length.out = n.col1 - 1)
  lim.seq2 <- seq(0, upper.lim, length.out = n.col2 - 1)
  lim.seq <- c(-Inf, unique(c(lim.seq1, lim.seq2)), Inf)
  n.seq <- length(lim.seq)

  # Get matrix with intervals:
  low <- lim.seq[1:(n.seq - 1)]
  high <- lim.seq[2:n.seq]
  intervals <- matrix(c(low, high), ncol = 2, nrow = n.seq - 1, byrow = FALSE)

  return(list(colors = colors, intervals = intervals))
}