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