R/generics.R
, R/preprocessing.R
, R/preprocessing5.R
FindSpatiallyVariableFeatures.Rd
Identify features whose variability in expression can be explained to some degree by spatial location.
FindSpatiallyVariableFeatures(object, ...)
# S3 method for default
FindSpatiallyVariableFeatures(
object,
spatial.location,
selection.method = c("markvariogram", "moransi"),
r.metric = 5,
x.cuts = NULL,
y.cuts = NULL,
verbose = TRUE,
...
)
# S3 method for Assay
FindSpatiallyVariableFeatures(
object,
slot = "scale.data",
spatial.location,
selection.method = c("markvariogram", "moransi"),
features = NULL,
r.metric = 5,
x.cuts = NULL,
y.cuts = NULL,
nfeatures = nfeatures,
verbose = TRUE,
...
)
# S3 method for Seurat
FindSpatiallyVariableFeatures(
object,
assay = NULL,
slot = "scale.data",
features = NULL,
image = NULL,
selection.method = c("markvariogram", "moransi"),
r.metric = 5,
x.cuts = NULL,
y.cuts = NULL,
nfeatures = 2000,
verbose = TRUE,
...
)
# S3 method for StdAssay
FindSpatiallyVariableFeatures(
object,
layer = "scale.data",
spatial.location,
selection.method = c("markvariogram", "moransi"),
features = NULL,
r.metric = 5,
x.cuts = NULL,
y.cuts = NULL,
nfeatures = nfeatures,
verbose = TRUE,
...
)
A Seurat object, assay, or expression matrix
Arguments passed to other methods
Coordinates for each cell/spot/bead
Method for selecting spatially variable features.
markvariogram
: See RunMarkVario
for details
moransi
: See RunMoransI
for details.
r value at which to report the "trans" value of the mark variogram
Number of divisions to make in the x direction, helps define the grid over which binning is performed
Number of divisions to make in the y direction, helps define the grid over which binning is performed
Print messages and progress
Slot in the Assay to pull data from
If provided, only compute on given features. Otherwise, compute for all features.
Number of features to mark as the top spatially variable.
Assay to pull the features (marks) from
Name of image to pull the coordinates from
Layer in the Assay5 to pull data from