SeuratObject (version 5.0.2)

Idents: 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 Seurat
Idents(object, ...)
# S3 method for Seurat
Idents(object, cells = NULL, drop = FALSE, replace = FALSE, ...) <- value
# S3 method for Seurat
ReorderIdent(
  object,
  var,
  reverse = FALSE,
  afxn = mean,
  reorder.numeric = FALSE,
  ...
)
# S3 method for Seurat
RenameIdents(object, ...)
# S3 method for Seurat
SetIdent(object, cells = NULL, value, ...)
# S3 method for Seurat
StashIdent(object, save.name = "orig.ident", ...)
# S3 method for Seurat
droplevels(x, ...)
# S3 method for Seurat
levels(x)
# S3 method for Seurat
levels(x) <- value

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

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

replace

Replace identities for unset cells with NA

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

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)

if (FALSE) {
head(Idents(pbmc_small))
pbmc_small <- ReorderIdent(pbmc_small, var = 'PC_1')
head(Idents(pbmc_small))
}

# 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)