PositionDataFrame-class {Cardinal} | R Documentation |
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.
PositionDataFrame(coord, run, ..., row.names = NULL, check.names = TRUE)
coord |
A |
run |
A |
... |
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 |
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).
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
## 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)