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

# 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)