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

In mojaveazure/seurat-object: Data Structures for Single Cell Data

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, replace = 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
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

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)

mojaveazure/seurat-object documentation built on Dec. 13, 2024, 9:23 a.m.