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Split SFE object with categorical vector or geometry

Source: R/split.R
splitByCol.Rd

The split methods for SFE split an SFE object into multiple SFE objects by geometries (all cells/spots intersecting with each geometry will become a separate SFE object). The splitSamples function splits the SFE object by sample_id so each sample will become a separate SFE object. The splitContiguity function splits the SFE object by contiguity of an annotGeometry, which by default is "tissueBoundary". The splitComponent function splits the SFE object by graph component, so if there are disconnected components in the graph, then each component will become a new SFE object.

Usage

# S4 method for class 'SpatialFeatureExperiment,sf'
splitByCol(x, f, sample_id = "all", colGeometryName = 1L, cover = FALSE)

# S4 method for class 'SpatialFeatureExperiment,sfc'
splitByCol(x, f, sample_id = 1L, colGeometryName = 1L, cover = FALSE)

# S4 method for class 'SpatialFeatureExperiment,list'
splitByCol(x, f, sample_id = "all", colGeometryName = 1L, cover = FALSE)

splitSamples(x)

splitContiguity(
  x,
  colGeometryName = 1L,
  annotGeometryName = "tissueBoundary",
  min_area = 0,
  cover = FALSE
)

Arguments

x

An SFE object

f

It can be a sf data frame or sfc to split by geometry. Each row of the sf data frame or each element in the sfc will correspond to a new SFE object. The sf data frame must have a column sample_id when splitting multiple samples. Can also be a list of sfc whose names correspond to sample_ids to split.

sample_id

Which samples to split.

colGeometryName

Which colGeometry to use to determine which cells or spots should belong to which new SFE object when splitting by sf or sfc. Default to the first one.

cover

Logical, whether the geometries in x must be entirely covered by y if op = st_intersection or whether x must be entirely outside y if op = st_difference. Only relevant when keep_whole != "none".

annotGeometryName

Name of annotGeometry to use to split by contiguity.

min_area

Minimum area in the same unit as the geometry coordinates (squared) for each piece to be considered a separate piece when splitting by contiguity. Only pieces that are large enough are considered.

Value

A list of SFE objects.

Examples

# example code