R: 'Centroids' Methods

Centroids-methods {SeuratObject}

R Documentation

`Centroids` Methods

Description

Methods for Centroids objects

Usage

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

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

## S3 method for class 'Centroids'
Radius(object)

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

## S3 method for class 'Centroids'
Theta(object)

## S3 method for class 'Centroids'
is.finite(x)

## S3 method for class 'Centroids'
is.infinite(...)

## S3 method for class 'Centroids'
length(x)

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

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

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

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

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

Arguments

`x, object`	A `Centroids` 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

Details

GetTissueCoordinates: Get cell spatial coordinates

Radius: Get the centroid radius

RenameCells: Update cell names

Theta: Get the offset angle

is.finite, is.infinite: Test to see if the centroids are circular or polygonal

length: Get the number of sides for the polygonal centroid

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

subset, [: Subset a Centroids object to certain cells

show: Display an object summary to stdout

Value

GetTissueCoordinates: A data frame with three columns:

“x”: the x-coordinate
“y”: the y-coordinate
“cell”: 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

Radius The radius of the centroids

RenameCells: object with the cells renamed to new.names

Theta: The offset angle in degrees

is.finite: TRUE if the centroids are polygonal, FALSE if circular

is.infinite: The opposite of is.finite

length: 0 if the centroids are circular, otherwise the number of sides of the polygonal centroid

lengths: An rle object for the cells

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

show: Invisibly returns NULL