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,
...
)

## Arguments

object 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