Run cell cycle scoring

Estimate cell cycle state with Seurat gene-set scoring, scran::cyclone(), or tricycle.

Usage

RunCellCycle(
  object,
  method = c("Seurat", "cyclone", "tricycle"),
  assay = NULL,
  layer = "counts",
  species = "Homo_sapiens",
  name = "CellCycle",
  phase_col = NULL,
  overwrite = FALSE,
  verbose = TRUE,
  srt = NULL,
  ...
)

Arguments

object

A Seurat object.

method

Cell cycle estimation method. One of "Seurat", "cyclone", or "tricycle".

assay

Assay to use. NULL uses the default assay.

layer

Data layer used by cyclone and tricycle.

species

Latin names for animals, i.e., "Homo_sapiens", "Mus_musculus"

name

Prefix for metadata columns and tricycle reduction names.

phase_col

Optional metadata column used to store the final phase call, for example "Phase". Default is NULL, which avoids writing a compatibility phase column.

overwrite

Whether to overwrite existing output columns.

verbose

Whether to print the message. Default is TRUE.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

...

Arguments passed to other functions.

Value

A Seurat object with cell cycle metadata and, for tricycle, a tricycle embedding reduction.

Examples

data(pancreas_sub)
srt <- pancreas_sub[, 1:80]

if (FALSE) { # \dontrun{
srt <- RunCellCycle(
  srt,
  method = "cyclone",
  species = "Mus_musculus",
  name = "Cyclone"
)

srt <- RunCellCycle(
  srt,
  method = "tricycle",
  species = "Mus_musculus",
  name = "Tricycle"
)
CellDimPlot(
  srt,
  reduction = "Tricycle_tricycleEmbedding",
  group.by = "Cyclone_cyclone_Phase"
)
FeatureDimPlot(
  srt,
  reduction = "Tricycle_tricycleEmbedding",
  features = "Tricycle_tricyclePosition"
)
} # }