R: 'Segmentation' Methods

Segmentation-methods {SeuratObject} | R Documentation

## `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 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
`cells` | A vector of cells to keep; if `NULL`, defaults to all cells
`i` | A vector of cells to keep; if `NULL`, defaults to all cells
`j` | Ignored
`drop` | Ignored

### 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

`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`

`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`

[Package SeuratObject version 4.1.0 Index]