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`

### See Also

`Centroids-class`

[Package SeuratObject version 4.1.0 Index]