colGeometries: Column geometry getters and setters

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

Column geometry getters and setters

Description

colGeometries are geometries that correspond to columns of the gene count matrix, such as Visium spots or cells. Same as dimGeometry(x, MARGIN = 2L, ...), with convenience wrappers for getters and setters of special geometries:

spotPoly

Polygons of spots from technologies such as Visium, ST, and slide-seq, which do not correspond to cells. Centroids of the polygons are stored in spatialCoords of the underlying SpatialExperiment object.

ROIPoly

Polygons of regions of interest (ROIs) from technologies such as laser capture microdissection (LCM) and GeoMX DSP. These should correspond to columns of the gene count matrix.

cellSeg

Cell segmentation polygons. If the columns of the gene count matrix are single cells, then this is stored in colGeometries. Otherwise, this is stored in annotGeometries.

nucSeg

Similar to cellSeg, but for nuclei rather than whole cell.

Usage

colGeometry(x, type = 1L, sample_id = 1L, withDimnames = TRUE)

colGeometry(
  x,
  type = 1L,
  sample_id = 1L,
  withDimnames = TRUE,
  translate = TRUE
) <- value

colGeometries(x, withDimnames = TRUE)

colGeometries(x, withDimnames = TRUE, translate = TRUE) <- value

colGeometryNames(x)

colGeometryNames(x) <- value

spotPoly(x, sample_id = 1L, withDimnames = TRUE)

spotPoly(x, sample_id = 1L, withDimnames = TRUE, translate = TRUE) <- value

centroids(x, sample_id = 1L, withDimnames = TRUE)

centroids(x, sample_id = 1L, withDimnames = TRUE, translate = TRUE) <- value

ROIPoly(x, sample_id = 1L, withDimnames = TRUE)

ROIPoly(x, sample_id = 1L, withDimnames = TRUE, translate = TRUE) <- value

cellSeg(x, sample_id = 1L, withDimnames = TRUE)

cellSeg(x, sample_id = 1L, withDimnames = TRUE, translate = TRUE) <- value

nucSeg(x, sample_id = 1L, withDimnames = TRUE)

nucSeg(x, sample_id = 1L, withDimnames = TRUE, translate = TRUE) <- value

Arguments

x	A SpatialFeatureExperiment object.
type	An integer specifying the index or string specifying the name of the *Geometry to query or replace. If missing, then the first item in the *Geometries will be returned or replaced.
sample_id	Sample ID to get or set geometries.
withDimnames	Logical. If TRUE, then the dimnames (colnames or rownames) of the gene count matrix should correspond to row names of the sf data frames of interest.
translate	Logical. Only used if removeEmptySpace has been run of the SFE object. If that's the case, this argument indicates whether the new value to be assigned to the geometry is in the coordinates prior to removal of empty space so it should be translated to match the new coordinates after removing empty space. Default to TRUE.
value	Value to set. For dimGeometry, must be a sf data frame with the same number of rows as size in the dimension of interest, or an ordinary data frame that can be converted to such a sf data frame (see df2sf). For dimGeometries, must be a list of such sf or ordinary data frames.

See Also

[dimGeometries()], [rowGeometries()]

Examples

library(SFEData)
sfe <- McKellarMuscleData(dataset = "small")
cgs <- colGeometries(sfe)
spots <- spotPoly(sfe)

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