FindSpatiallyVariableFeatures: Find spatially variable features

In satijalab/seurat: Tools for Single Cell Genomics

Find spatially variable features

Description

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,
  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,
  ...
)

## S3 method for class '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,
  ...
)

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. markvariogram: See RunMarkVario for details moransi: See RunMoransI for details.
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
layer	Layer in the Assay5 to pull data from

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.