Centroids MethodsMethods for Centroids objects
# S3 method for Centroids
Cells(x, ...)# S3 method for Centroids
GetTissueCoordinates(object, full = TRUE, ...)
# S3 method for Centroids
Radius(object, ...)
# S3 method for Centroids
RenameCells(object, new.names = NULL, ...)
# S3 method for Centroids
Theta(object)
# S3 method for Centroids
is.finite(x)
# S3 method for Centroids
is.infinite(...)
# S3 method for Centroids
length(x)
# S3 method for Centroids
lengths(x, use.names = TRUE)
# S3 method for Centroids
subset(x, cells = NULL, ...)
# S4 method for Centroids,character,ANY,ANY
[(x, i, j, ..., drop = TRUE)
# S4 method for Centroids,numeric,ANY,ANY
[(x, i, j, ..., drop = TRUE)
# S4 method for Centroids
show(object)
GetTissueCoordinates: A data frame with three columns:
“x”: the x-coordinate
“y”: the y-coordinate
“cell”: the cell name
If full is TRUE, then each coordinate will indicate a vertex
for the cell polygon; otherwise, each coordinate will indicate a centroid
for the cell
Radius The radius of the centroids
RenameCells: object with the cells renamed to
new.names
Theta: The offset angle in degrees
is.finite: TRUE if the centroids are polygonal,
FALSE if circular
is.infinite: The opposite of is.finite
length: 0 if the centroids are circular, otherwise the
number of sides of the polygonal centroid
lengths: An rle object for the cells
subset, [: x subsetted to the cells specified
by cells/i
show: Invisibly returns NULL
A Centroids
object
Arguments passed to other methods
Expand the coordinates to the full polygon
vector of new cell names
Ignored
A vector of cells to keep; if NULL, defaults
to all cells
Ignored
GetTissueCoordinates: Get cell spatial coordinates
Radius: Get the centroid radius
RenameCells: Update cell names
Theta: Get the offset angle
is.finite, is.infinite: Test to see if the centroids
are circular or polygonal
length: Get the number of sides for the polygonal centroid
lengths: Generate a run-length encoding of the cells present
subset, [: Subset a Centroids object to
certain cells
show: Display an object summary to stdout
Centroids-class
Segmentation layer classes:
Centroids-class,
Molecules-class,
Molecules-methods,
Segmentation-class,
Segmentation-methods