Segmentation-methods: 'Segmentation' Methods

In SeuratObject: Data Structures for Single Cell Data

Segmentation Methods

Description

Methods for Segmentation objects

Usage

## S3 method for class 'Segmentation'
Cells(x, ...)

## S3 method for class 'Segmentation'
GetTissueCoordinates(object, full = TRUE, ...)

## S3 method for class 'Segmentation'
RenameCells(object, new.names = NULL, ...)

## S3 method for class 'Segmentation'
lengths(x, use.names = TRUE)

## S3 method for class 'Segmentation'
subset(x, cells = NULL, ...)

## S4 replacement method for signature 'Segmentation,character,missing,ANY'
x[[i, j, ...]] <- value

## S4 replacement method for signature 'Segmentation,character,missing,NULL'
x[[i, j, ...]] <- value

## S4 method for signature 'Segmentation,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'Segmentation'
coordinates(obj, full = TRUE, ...)

## S4 method for signature 'Segmentation'
show(object)

Arguments

x, object, obj	A Segmentation object
...	Arguments passed to other methods
full	Expand the coordinates to the full polygon
new.names	vector of new cell names
use.names	Ignored
i, cells	A vector of cells to keep; if NULL, defaults to all cells
j, drop	Ignored
value	The value to assign to the slot specified by i in the Segmentation object.

Details

Cells: Get cell names

GetTissueCoordinates, coordinates: Get tissue coordinates

RenameCells: Update cell names

lengths: Generate a run-length encoding of the cells present

subset, [: Subset a Segmentation object to certain cells

[[<-: Attach or remove sf object to/from a Segmentation object

show: Display an object summary to stdout

Value

Cells: A vector of cell names

GetTissueCoordinates, coordinates: A data frame with three columns:

• “x”: the x-coordinate

• “y”: the y-coordinate

• “cell” or “ID”: the cell name

If full is TRUE, then each coordinate will indicate a vertex for the cell polygon; otherwise, each coordinate will indicate a centroid for the cell. Note: GetTissueCoordinates ....

RenameCells: object with the cells renamed to new.names

lengths: An rle object for the cells

subset, [: x subsetted to the cells specified by cells/i

[[<-:

• If value is an sf object, returns x with value stored in sf; requires that i is “sf.data”.

• If value is NULL, returns x with sf removed.

show: Invisibly returns NULL

Progress Updates with progressr

The following methods use progressr to render status updates and progress bars:

• RenameCells

To enable progress updates, wrap the function call in with_progress or run handlers(global = TRUE) before running this function. For more details about progressr, please read vignette("progressr-intro")

Parallelization with future

The following methods use future to enable parallelization:

• RenameCells

Parallelization strategies can be set using plan. Common plans include “sequential” for non-parallelized processing or “multisession” for parallel evaluation using multiple R sessions; for other plans, see the “Implemented evaluation strategies” section of ?future::plan. For a more thorough introduction to future, see vignette("future-1-overview")

See Also

Segmentation-class

Segmentation layer classes: Centroids-class, Centroids-methods, Molecules-class, Molecules-methods, Segmentation-class, Segmentation-validity

SeuratObject documentation built on Aug. 28, 2025, 1:10 a.m.