Rename clusters for the Seurat object

Usage

RenameClusters(
  srt,
  group.by,
  nameslist = list(),
  name = "newclusters",
  keep_levels = FALSE
)

Arguments

srt: A Seurat object.
group.by: The old group used to rename cells.
nameslist: A named list of new cluster value.
name: The name of the new cluster stored in the Seurat object.
keep_levels: If the old group is a factor, keep the order of the levels.

Examples

data("pancreas_sub")
levels(pancreas_sub@meta.data[["SubCellType"]])
#> [1] "Ductal"        "Ngn3 low EP"   "Ngn3 high EP"  "Pre-endocrine" "Beta"          "Alpha"         "Delta"        
#> [8] "Epsilon"      

# Rename all clusters
pancreas_sub <- RenameClusters(pancreas_sub, group.by = "SubCellType", nameslist = letters[1:8])
CellDimPlot(pancreas_sub, "newclusters")
#> Warning: No shared levels found between `names(values)` of the manual scale and the data's fill values.


# Rename specified clusters
pancreas_sub <- RenameClusters(pancreas_sub,
  group.by = "SubCellType",
  nameslist = list("a" = "Alpha", "b" = "Beta")
)
CellDimPlot(pancreas_sub, "newclusters")
#> Warning: No shared levels found between `names(values)` of the manual scale and the data's fill values.


# Merge and rename clusters
pancreas_sub <- RenameClusters(pancreas_sub,
  group.by = "SubCellType",
  nameslist = list("EndocrineClusters" = c("Alpha", "Beta", "Epsilon", "Delta")),
  name = "Merged", keep_levels = TRUE
)
CellDimPlot(pancreas_sub, "Merged")
#> Warning: No shared levels found between `names(values)` of the manual scale and the data's fill values.