Rename_Clusters: Rename Clusters

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Rename Clusters

Description

Wrapper function to rename active cluster identity in Seurat or Liger Object with new idents.

Usage

Rename_Clusters(object, ...)

## S3 method for class 'liger'
Rename_Clusters(
  object,
  new_idents,
  old_ident_name = NULL,
  new_ident_name = NULL,
  overwrite = FALSE,
  ...
)

## S3 method for class 'Seurat'
Rename_Clusters(
  object,
  new_idents,
  old_ident_name = NULL,
  new_ident_name = NULL,
  meta_col_name = deprecated(),
  overwrite = FALSE,
  ...
)

Arguments

object	Object of class Seurat or liger.
...	Arguments passed to other methods
new_idents	vector of new cluster names. Must be equal to the length of current default identity of Object. Will accept named vector (with old idents as names) or will name the new_idents vector internally.
old_ident_name	optional, name to use for storing current object idents in object meta data slot.
new_ident_name	optional, name to use for storing new object idents in object meta data slot.
overwrite	logical, whether to overwrite columns in object meta data slot. if they have same names as old_ident_name and/or new_ident_name.
meta_col_name	. See old_ident_name.

Value

An object of the same class as object with updated default identities.

Examples

## Not run: 
# Liger version
obj <- Rename_Clusters(object = obj_name, new_idents = new_idents_vec,
old_ident_name = "LIGER_Idents_Round01", new_ident_name = "LIGER_Idents_Round02")

## End(Not run)

## Not run: 
obj <- Rename_Clusters(seurat_object = obj_name, new_idents = new_idents_vec,
old_ident_name = "Seurat_Idents_Round01", new_ident_name = "Round01_Res0.6_Idents")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.