ImageList-class: ImageList: Abstract image data list
In Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Description Usage Arguments Details Author(s) See Also Examples

The ImageList virtual class provides an formal abstraction for the imageData slot of ImagingExperiment objects. It is analogous to the Assays classes from the SummarizedExperiment package.

The ImageArrayList virtual class specializes the ImageList abstraction by assuming the array-like data elements all have conformable dimensions.

The SimpleImageList and SimpleImageArrayList subclasses are the default implementations.

The MSContinuousImagingSpectraList and MSProcessedImagingSpectraList classes are subclasses of SimpleImageArrayList that make certain assumptions about how the underlying data elements are stored (i.e., either dense or sparse). They are intended to be used with mass spectrometry imaging data.

# Create a SimpleImageList
ImageList(data)

# Create a SimpleImageArrayList
ImageArrayList(data)

# ImageArrayList class for 'continuous' (dense) MS imaging data
MSContinuousImagingSpectraList(data)

# ImageArrayList class for 'processed' (sparse) MS imaging data
MSProcessedImagingSpectraList(data)

data

A SimpleList or list of array-like data elements, or an array-like object.

ImageList and ImageArrayList objects have list-like semantics where the elements are array-like (i.e., have dim), where ImageArrayList makes the additional assumption that the array-like elements have identical dims for at least the first two dimensions.

The ImageList class includes:

(1) The ImageList() and ImageArrayList() constructor functions.
(2) Lossless back-and-forth coercion from/to SimpleList. The coercion method need not and should not check the validity of the returned object.
(3) length, names, names<-, and `[[`, `[[<-` methods for ImageList, as well as `[`, `[<-`, rbind, and cbind methods for ImageArrayList.

See the documentation for the Assays class in the SummarizedExperiment package for additional details, as the implementation is quite similar, with the main difference being that all assumptions about the dimensions of the array-like data elements is contained in the ImageArrayList subclass. This is intended to allow subclasses of the ImageList class to handle images stored as arrays with non-conformable dimensions.

These classes are intended to eventually replace the ImageData classes.

Kylie A. Bemis

SimpleList

## create an ImageList object
data0 <- matrix(1:9, nrow=3)
data1 <- matrix(10:18, nrow=3)
data2 <- matrix(19:27, nrow=3)
idata <- ImageArrayList(list(d0=data0, d1=data1, d2=data2))

# subset all arrays at once
idataS <- idata[1:2,1:2]
all.equal(idataS[["d0"]], data0[1:2,1:2])

# combine over "column" dimension
idataB <- cbind(idata, idata)
all.equal(idataB[["d0"]], cbind(data0, data0))