splitByCol: Split SFE object with categorical vector or geometry

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Split SFE object with categorical vector or geometry

Description

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".

Usage

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

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

## S4 method for signature '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

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.