R/updatePlotParameters.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 that updates pcfPlot parameters
# Updates or sets main, ylimits, xlimits, tickmarks, mgp, and margin

# Input:
### seg.lim: segmentation limits
### xmax: maximum on xaxis
### type: plot type
### xaxis: index or positions along xaxis?
### op: list with set plot parameters
### data.lim: data limits
### sampleID: the sampleID to be plotted
### k: the chromosome number to be plotted


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

### Required by:
### plotObs
### plotSegments

### Requires:
### get.xticks
### get.yticks


updatePlotParameters <- function(seg.lim, xmax, type, xaxis, op, data.lim, sampleID, k) {
  # Set MAIN TITLE for this plot depending on type of plot:
  if (is.null(op$main)) {
    if (type %in% c("genome", "chromosome")) {
      op$main <- sampleID
    } else {
      # type = sample or aspcf
      op$main <- paste("Chromosome", k, sep = " ")
    }
  } # endif

  # YLIM;if not specified by user:
  # leave out the q/2 % most extreme observations in both directions (either based on entire genome or within chromosome), make sure h is included in plot
  # and that segment-limits are taken into account:
  if (is.null(op$ylim)) {
    op$ylim[1] <- min(data.lim[1], op$h, seg.lim[1]) # y-min
    op$ylim[2] <- max(data.lim[2], op$h, seg.lim[2]) # y-max
  }

  # set XLIM parameters:
  if (is.null(op$xlim)) {
    op$xlim <- c(0, xmax)
  }


  # TICK MARKS on x and y axis:
  if (is.null(op$at.x)) {
    if (type == "genome") {
      n.ticks <- 10
    } else {
      n.ticks <- 6
    }
    if (xaxis == "pos") {
      op$at.x <- get.xticks(op$xlim[1], op$xlim[2], unit = op$plot.unit, ideal.n = n.ticks)
    } else {
      # xaxis = index:
      op$at.x <- get.xticks(op$xlim[1], op$xlim[2], unit = "mbp", ideal.n = n.ticks)
    }
  }
  if (is.null(op$at.y)) {
    op$at.y <- get.yticks(op$ylim[1], op$ylim[2])
  }

  # MGP; placement of labels and axis annotation:
  if (is.null(op$mgp)) {
    op$mgp <- c(1.3, 0.05, 0) * op$f
    mgp.y <- c(2, 0.5, 0) * op$f
  } else {
    mgp.y <- op$mgp
  }
  op$mgp.y <- mgp.y


  # Default is no xlab, if specified by user the BOTTOM MARGIN must be increased:
  if (op$xlab != "") {
    op$mar[1] <- op$mar[1] + 1
  }

  return(op)
} # end updatePlotParameters