R: 'FOV' Methods

FOV-methods {SeuratObject} | R Documentation

## `FOV` Methods

### Description

Methods for `FOV` objects

### Usage

    ## S3 method for class 'FOV'
    Cells(x, boundary = NULL, ...)

    ## S3 method for class 'FOV'
    Features(x, set = NULL, ...)

    ## S3 method for class 'FOV'
    FetchData(object, vars, cells = NULL, simplify = TRUE, ...)

    ## S3 method for class 'FOV'
    GetTissueCoordinates(object, which = NULL, ...)

    ## S3 method for class 'FOV'
    Keys(object, ...)

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

    ## S3 method for class 'FOV'
    x$i, ...

    ## S3 method for class 'FOV'
    x[i, j, ...]

    ## S3 method for class 'FOV'
    x[[i, ...]]

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

    ## S3 method for class 'FOV'
    names(x)

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

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

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

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

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

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

### Arguments

`x, object` | A `FOV` object
`boundary, set` | Name of segmentation boundary or molecule set to extract cell or feature names for; pass `NA` to return all cells or feature names
`...` | Arguments passed to other methods
`vars` | A vector of variables to fetch; can be the name of a segmentation boundary, to get tissue coordinates, or molecule names, to get molecule coordinates
`simplify` | If only returning either boundary or molecule coordinates, return a single data frame instead of a list
`which` | Name of segmentation boundary or molecule set
`new.names` | vector of new cell names
`i, cells` | For `[[` and `[[<-`, the name of a segmentation or “molecules”; for `FetchData`, `subset`. and `[`, a vector of cells to keep
`j, features` | For `subset` and `[`, a vector of features to keep; for `[[<-`, not used
`value` | For `[[<-`, a replacement `Molecules`, `Centroids`, or `Segmentation` object; otherwise `NULL` to remove the boundary stored at `i`

### Details

The following methods are defined for interacting with a `FOV` object:

`Cells`: Get cell names

`Features`: Get spatially-resolved molecule names

`FetchData`: Fetch boundary and/or molecule coordinates from a `FOV` object

`GetTissueCoordinates`: Get boundary or molecule coordinates from a `FOV` object

`Keys`: Get the keys of molecule sets contained within a `FOV` object

`RenameCells`: Update cell names

`$`, `[[`: Extract a segmentation boundary

`length`: Get the number of segmentation layers in a `FOV` object

`names`: Get the names of segmentation layers and molecule sets

`subset`, `[`: Subset a `FOV` object

`[[<-`: Add or remove segmentation layers and molecule information to/from a `FOV` object

`show`: Display an object summary to stdout

### Value

`Cells`: A vector of cell names

`Features`: A vector of spatially-resolved molecule names; if no molecular information present, returns `NULL`

`FetchData`: If both molecule and boundary coordinates are requested, then a two-length list:

- “`molecules`”: A data frame with the molecule coordinates requested. If molecules requested are keyed, the keys are preserved in the data frame

- “`coordinates`”: A data frame with coordinates from the segmentation boundaries requested

If `simplify` is `TRUE` and only one data frame is generated, then only the data frame is returned. Otherwise, a one-length list is returned with the single data frame generated

`GetTissueCoordinates`: ...

`Keys`: A named vector of molecule set keys; names are the names of the molecule sets and values are the keys for the respective molecule set

`RenameCells`: `object` with the cells renamed to `new.names`

`$`, `[[`: The segmentation boundary or spatially-resolved molecule information stored at `i`

`length`: The number of segmentation layers (`Segmentation` or `Centroids` objects)

`names`: A vector of segmentation boundary and molecule set names

`subset`: `x` with just the cells and features specified

`[[<-`: Varies depending on the class of `value`:

- If `value` is `NULL`, returns `x` with the boundary `i` removed; also allows removing `molecules`; does not allow removing the default segmentation

- If `value` is a `Molecules`, returns `x` with `value` stored in `molecules`; requires that `i` is “molecules”

- Otherwise, stores `value` as a segmentation boundary named `i`

`show`: Invisibly returns `NULL`

### See Also

`FOV-class`

[Package SeuratObject version 4.1.0 Index]