R/ChromosomeExplorer.LAYERS.R

In HenrikBengtsson/aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

setMethodS3("writeAxesLayers", "ChromosomeExplorer", function(this, ...) {
  model <- getModel(this)

  path <- getPath(this)
  path <- filePath(getParent(path), "axes,chrLayer")
  path <- Arguments$getWritablePath(path)
  plotAxesLayers(model, path=path, imageFormat="png", transparent=TRUE, ...)

  invisible(path)
}, private=TRUE)


setMethodS3("writeGridHorizontalLayers", "ChromosomeExplorer", function(this, ...) {
  model <- getModel(this)

  path <- getPath(this)
  path <- filePath(getParent(path), "gridH,chrLayer")
  path <- Arguments$getWritablePath(path)
  plotGridHorizontalLayers(model, path=path, imageFormat="png", transparent=TRUE, ...)

  invisible(path)
}, private=TRUE)



setMethodS3("writeCytobandLayers", "ChromosomeExplorer", function(this, ...) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Get the model
  model <- getModel(this)

  path <- getPath(this)
  path <- filePath(getParent(path), "cytoband,chrLayer")
  path <- Arguments$getWritablePath(path)
  plotCytobandLayers(model, path=path, imageFormat="png", transparent=TRUE, ...)

  invisible(path)
}, private=TRUE)


setMethodS3("getSampleLayerName", "Explorer", function(this, name, class="sampleLayer", ...) {
  layer <- c(getSampleLayerPrefix(this), name, class)
  layer <- paste(layer, collapse=",")
  layer
}, private=TRUE)


setMethodS3("writeRawCopyNumberLayers", "ChromosomeExplorer", function(this, ...) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Get the model
  model <- getModel(this)

  path <- getPath(this)
  layer <- getSampleLayerName(this, "rawCNs")
  path <- filePath(getParent(path), layer)

  path <- Arguments$getWritablePath(path)
  plotRawCopyNumbers(model, path=path, imageFormat="png", transparent=TRUE, ...)

  invisible(path)
}, private=TRUE)


setMethodS3("writeCopyNumberRegionLayers", "ChromosomeExplorer", function(this, ...) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Get the model
  model <- getModel(this)

  # Not supported?
  if (!inherits(model, "CopyNumberSegmentationModel"))
    return(NULL)

  path <- getPath(this)
  tags <- getAsteriskTags(model, collapse=",")
  path <- filePath(getParent(path), sprintf("%s,sampleLayer", tags))

  path <- Arguments$getWritablePath(path)
  plotCopyNumberRegionLayers(model, path=path, imageFormat="png", transparent=TRUE, ...)

  invisible(path)
}, private=TRUE)