Nothing
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)
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