R/image2-AnnotatedImagingExperiment.R

In Cardinal: A mass spectrometry imaging toolbox for statistical analysis

#### Image plotting for optical imaging experiments ####
## ---------------------------------------------

setMethod("image", c(x = "AnnotatedImagingExperiment"),
	function(x, i, frame = 1, ...)
{
	image(imageData(x), i=i, frame=frame, ...)
})

setMethod("image", c(x = "AnnotatedImageList"),
	function(x, i, frame = 1,
		strip = TRUE,
		layout = !add,
		native = TRUE,
		interpolate = TRUE,
		add = FALSE, ...)
{
	if ( !missing(i) )
		x <- x[i]
	data <- as(x, "SimpleList", strict=FALSE)
	fun <- function(y) {
		y <- getFrame(y, frame, type="render")
		if ( native ) {
			EBImage:::as.nativeRaster(y)
		} else {
			as.raster(y)
		}
	}
	rasters <- lapply(data, fun)
	offsets <- lapply(data, "coord")
	heights <- vapply(data, "height", numeric(1))
	widths <- vapply(data, "width", numeric(1))
	facet.raster(rasters, offsets=offsets,
		heights=heights, widths=widths, ...,
		strip=strip, layout=layout,
		interpolate=interpolate,
		add=add)
})