R: Get, set, and manipulate an object's identity classes

Idents {SeuratObject} | R Documentation

## Get, set, and manipulate an object's identity classes

### Description

Get, set, and manipulate an object's identity classes

### Usage

    Idents(object, ...)

    Idents(object, ...) <- value

    RenameIdents(object, ...)

    ReorderIdent(object, var, ...)

    SetIdent(object, ...)

    StashIdent(object, save.name, ...)

    ## S3 method for class 'Seurat'
    Idents(object, ...)

    ## S3 replacement method for class 'Seurat'
    Idents(object, cells = NULL, drop = FALSE, ...) <- value

    ## S3 method for class 'Seurat'
    ReorderIdent(
      object,
      var,
      reverse = FALSE,
      afxn = mean,
      reorder.numeric = FALSE,
      ...
    )

    ## S3 method for class 'Seurat'
    RenameIdents(object, ...)

    ## S3 method for class 'Seurat'
    SetIdent(object, cells = NULL, value, ...)

    ## S3 method for class 'Seurat'
    StashIdent(object, save.name = "orig.ident", ...)

    ## S3 method for class 'Seurat'
    droplevels(x, ...)

    ## S3 method for class 'Seurat'
    levels(x)

    ## S3 replacement method for class 'Seurat'
    levels(x) <- value

### Arguments

`...` | Arguments passed to other methods; for `RenameIdents`: named arguments as `old.ident = new.ident`; for `ReorderIdent`: arguments passed on to `FetchData`
`value` | The name of the identities to pull from object metadata or the identities themselves
`var` | Feature or variable to order on
`save.name` | Store current identity information under this name
`cells` | Set cell identities for specific cells
`drop` | Drop unused levels
`reverse` | Reverse ordering
`afxn` | Function to evaluate each identity class based on; default is `mean`
`reorder.numeric` | Rename all identity classes to be increasing numbers starting from 1 (default is FALSE)
`x, object` | An object

### Value

`Idents`: The cell identities

`Idents<-`: `object` with the cell identities changed

`RenameIdents`: An object with selected identity classes renamed

`ReorderIdent`: An object with

`SetIdent`: An object with new identity classes set

`StashIdent`: An object with the identities stashed

### Examples

    # Get cell identity classes
    Idents(pbmc_small)

    # Set cell identity classes
    # Can be used to set identities for specific cells to a new level
    Idents(pbmc_small, cells = 1:4) <- 'a'
    head(Idents(pbmc_small))

    # Can also set idents from a value in object metadata
    colnames(pbmc_small[[]])
    Idents(pbmc_small) <- 'RNA_snn_res.1'
    levels(pbmc_small)

    # Rename cell identity classes
    # Can provide an arbitrary amount of idents to rename
    levels(pbmc_small)
    pbmc_small <- RenameIdents(pbmc_small, '0' = 'A', '2' = 'C')
    levels(pbmc_small)

    ## Not run:
    head(Idents(pbmc_small))
    pbmc_small <- ReorderIdent(pbmc_small, var = 'PC_1')
    head(Idents(pbmc_small))

    ## End(Not run)

    # Set cell identity classes using SetIdent
    cells.use <- WhichCells(pbmc_small, idents = '1')
    pbmc_small <- SetIdent(pbmc_small, cells = cells.use, value = 'B')

    head(pbmc_small[[]])
    pbmc_small <- StashIdent(pbmc_small, save.name = 'idents')
    head(pbmc_small[[]])

    # Get the levels of identity classes of a Seurat object
    levels(x = pbmc_small)

    # Reorder identity classes
    levels(x = pbmc_small)
    levels(x = pbmc_small) <- c('C', 'A', 'B')
    levels(x = pbmc_small)

[Package SeuratObject version 4.1.0 Index]