Methods for FOV objects
# S3 method for FOV
Cells(x, boundary = NULL, ...)
# S3 method for FOV
Features(x, set = NULL, ...)
# S3 method for FOV
FetchData(object, vars, cells = NULL, simplify = TRUE, ...)
# S3 method for FOV
GetTissueCoordinates(object, which = NULL, ...)
# S3 method for FOV
Keys(object, ...)
# S3 method for FOV
RenameCells(object, new.names = NULL, ...)
# S3 method for FOV
$(x, i, ...)
# S3 method for FOV
[(x, i, j, ...)
# S3 method for FOV
[[(x, i, ...)
# S3 method for FOV
length(x)
# S3 method for FOV
names(x)
# S3 method for FOV
subset(x, cells = NULL, features = NULL, ...)
# S4 method for FOV,character,missing,Centroids
[[(x, i, j, ...) <- value
# S4 method for FOV,character,missing,Molecules
[[(x, i, j, ...) <- value
# S4 method for FOV,character,missing,NULL
[[(x, i, j, ...) <- value
# S4 method for FOV,character,missing,Segmentation
[[(x, i, j, ...) <- value
# S4 method for FOV
show(object)A FOV object
Name of segmentation boundary or molecule set to
extract cell or feature names for; pass NA to return all
cells or feature names
Arguments passed to other methods
A vector of variables to fetch; can be the name of a segmentation boundary, to get tissue coordinates, or molecule names, to get molecule coordinates
If only returning either boundary or molecule coordinates, return a single data frame instead of a list
Name of segmentation boundary or molecule set
vector of new cell names
For [[ and [[<-, the name of a segmentation or
“molecules”; for FetchData, subset. and [, a
vector of cells to keep
For subset and [, a vector of features to
keep; for [[<-, not used
For [[<-, a replacement
Molecules,
Centroids, or
Segmentation object;
otherwise NULL to remove the boundary stored at i
Cells: A vector of cell names
Features: A vector of spatially-resolved molecule names;
if no molecular information present, returns NULL
FetchData: If both molecule and boundary coordinates are
requested, then a two-length list:
“molecules”: A data frame with the molecule coordinates
requested. If molecules requested are keyed, the keys are preserved in the
data frame
“coordinates”: A data frame with coordinates from the
segmentation boundaries requested
If simplify is TRUE and only one data frame is generated, then
only the data frame is returned. Otherwise, a one-length list is returned
with the single data frame generated
GetTissueCoordinates: ...
Keys: A named vector of molecule set keys; names are the
names of the molecule sets and values are the keys for the respective
molecule set
RenameCells: object with the cells renamed to
new.names
$, [[: The segmentation boundary or spatially-resolved
molecule information stored at i
length: The number of segmentation layers
(Segmentation or
Centroids objects)
names: A vector of segmentation boundary and molecule set names
subset: x with just the cells and features specified
[[<-: Varies depending on the class of value:
If value is NULL, returns x with the boundary
i removed; also allows removing molecules; does not allow
removing the default segmentation
If value is a Molecules, returns x with
value stored in molecules; requires that i is
“molecules”
Otherwise, stores value as a segmentation boundary named i
show: Invisibly returns NULL
The following methods are defined for interacting with a
FOV object:
Cells: Get cell names
Features: Get spatially-resolved molecule names
FetchData: Fetch boundary and/or molecule coordinates from
a FOV object
GetTissueCoordinates: Get boundary or molecule
coordinates from a FOV object
Keys: Get the keys of molecule sets contained within a
FOV object
RenameCells: Update cell names
$, [[: Extract a segmentation boundary
length: Get the number of segmentation layers in a
FOV object
names: Get the names of segmentation layers and molecule sets
subset, [: Subset a FOV object
[[<-: Add or remove segmentation layers and molecule
information to/from a FOV object
show: Display an object summary to stdout