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Find spatially variable features

Source: 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.

Usage

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,
  layer = "scale.data",
  slot = deprecated(),
  spatial.location,
  selection.method = c("markvariogram", "moransi"),
  features = NULL,
  r.metric = 5,
  x.cuts = NULL,
  y.cuts = NULL,
  nfeatures = 2000,
  verbose = TRUE,
  ...
)

# S3 method for class 'Seurat'
FindSpatiallyVariableFeatures(
  object,
  assay = NULL,
  layer = "scale.data",
  slot = NULL,
  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 class 'StdAssay'
FindSpatiallyVariableFeatures(
  object,
  layer = "scale.data",
  slot = deprecated(),
  spatial.location,
  selection.method = c("markvariogram", "moransi"),
  features = NULL,
  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

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

layer

The layer in the specified assay to pull data from.

slot

Deprecated, use `layer`.

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