R/AffymetrixCdfFile.PLOT.R

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

setMethodS3("stextChipType", "AffymetrixCdfFile", function(this, ...) {
  stextChipType(..., chipType=getChipType(this))
}, private=TRUE)



setMethodS3("getImage", "AffymetrixCdfFile", function(this, xrange=c(0,Inf), yrange=xrange, zrange=c(0,sqrt(2^16)), field=c("isPm"), levels=NULL, zoom=1, ..., verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
  # Argument 'field':
#  field <- match.arg(field)
  
  # Argument 'zoom':
  zoom <- Arguments$getDouble(zoom, range=c(0,Inf))

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
  # Read data
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
  verbose && enter(verbose, "Getting CDF image")

  verbose && enter(verbose, "Reading CDF image")
  fields <- unique(c("cell", field))
  data <- readDataFrame(this, fields=fields, ..., verbose=less(verbose,1))
  verbose && str(verbose, data)
  z <- vector(mode=mode(data[[field]]), 1)
  z <- matrix(z, nrow=nbrOfRows(this), ncol=nbrOfColumns(this))
  z[indexByRow(dim(z), data[,"cell"])] <- data[[field]]
  # Not needed anymore
  data <- NULL
  verbose && summary(verbose, as.vector(z))
  verbose && printf(verbose, "RAM: %s\n", hsize(object.size(z), digits = 2L, standard = "IEC"))
  verbose && exit(verbose)

  verbose && enter(verbose, "Transforming data")
  dim <- dim(z)
  mode <- mode(z)
  if (mode == "character") {
    if (is.null(levels)) {
      z <- factor(z)
    } else {
      z <- factor(z, levels=levels)
    }
    z <- as.integer(z)
  }
  dim(z) <- dim
  verbose && str(verbose, z)
  verbose && exit(verbose)

  verbose && enter(verbose, "Creating Image")
  verbose && cat(verbose, "Arguments:")
  args <- list(z=z, scale=zoom, lim=zrange, ...)
  verbose && str(verbose, args)
  # Not needed anymore
  args <- NULL
  img <- getImage(z, scale=zoom, lim=zrange, ..., verbose=less(verbose, 1))
  verbose && print(verbose, img)
  verbose && exit(verbose)

  verbose && exit(verbose)

  # Return the 'field'
  attr(img, "field") <- field

  img
})