PositionDataFrame-class: PositionDataFrame: data frame with spatial position metadata
In Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Description Usage Arguments Details Methods Author(s) See Also Examples

An PositionDataFrame is an extension of the XDataFrame class with special slot-columns for spatial coordinates. It is designed specifically with biological imaging experiments in mind, so it also has an additional slot-column for tracking the experimental run.

1	PositionDataFrame(coord, run, ..., row.names = NULL, check.names = TRUE)

`coord`	A `data.frame`-like object containing columns which are spatial coordinates. This will be coerced to a `DataFrame`.
`run`	A `factor` with levels for each experimental run.
`...`	Named arguments that will become columns of the object.
`row.names`	Row names to be assigned to the object; no row names are assigned if this is `NULL`.
`check.names`	Should the column names be checked for syntactic validity?

PositionDataFrame is designed for spatial data, specifically for biological imaging data. It includes a slot-column for the experimental run. In most 2D imaging experiments, each distinct image is considered a distinct run. No additional assumptions are made about the spatial structure of the data, and non-gridded spatial coordinates are allowed.

This class is intended to eventually replace the IAnnotatedDataFrame class, and implements similar concepts but with a more robust and modern infrastructure.

run(object), run(object) <- value:: Get or set the experimental run slot-column.
runNames(object), runNames(object) <- value:: Get or set the experimental run levels.
coord(object), coord(object) <- value:: Get or set the spatial position slot-columns.
coordLabels(object), coordLabels(object) <- value:: Get or set the names of the spatial position slot-columns.
gridded(object), gridded(object) <- value:: Get or set whether the spatial positions are gridded or not. Typically, this should not be set manually.
resolution(object), resolution(object) <- value:: Get or set the spatial resolution of the spatial positions. Typically, this should not be set manually.
dims(object):: Get the gridded dimensions of the spatial positions (i.e., as if projected to an image raster).
is3D(object):: Check if the data is 3D or not.
as.list(x, ..., slots = TRUE):: Coerce the object to a list, where the slot-columns are included by default. Use slots=FALSE to exclude the slot-columns.

Kylie A. Bemis

XDataFrame

## Create an PositionDataFrame object
coord <- expand.grid(x=1:3, y=1:3)
values <- seq_len(nrow(coord))
pdata <- PositionDataFrame(coord=coord, values=values)

## Check the spatial properties
gridded(pdata)
resolution(pdata)
dims(pdata)