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Runtricycle() projects cells onto a reference cell cycle embedding to estimate each cell’s position in the cell cycle as a continuous angle θ (theta) between 0 and 2π.

​
Syntax

Runtricycle(
  object,
  assay = NULL,
  slot = "data",
  reduction.name = "tricycleEmbedding",
  reduction.key = "tricycleEmbedding_",
  gname = NULL,
  gname.type = c("ENSEMBL", "SYMBOL"),
  species = c("mouse", "human"),
  AnnotationDb = NULL,
  center.pc1 = 0,
  center.pc2 = 0
)

​
Parameters

​
object
Seurat
required
A Seurat object.
​
assay
character
default:"NULL"
Assay to use. Defaults to the active default assay.
​
slot
character
default:"data"
Slot to use. Should be normalized log-expression ("data").
​
reduction.name
character
default:"tricycleEmbedding"
Name for the resulting 2D projection stored as a DimReduc.
​
reduction.key
character
default:"tricycleEmbedding_"
Prefix for embedding column names.
​
gname
character vector
default:"NULL"
Gene names used to subset the data. If NULL, all genes are used.
​
gname.type
character
default:"ENSEMBL"
Type of gene identifiers used. One of "ENSEMBL" or "SYMBOL".
​
species
character
default:"mouse"
Species for the reference projection. One of "mouse" or "human".
​
AnnotationDb
AnnotationDb
default:"NULL"
An annotation database object (e.g., from org.Mm.eg.db) for gene name conversion. Required when gname.type = "SYMBOL".
​
center.pc1
numeric
default:"0"
Value to subtract from PC1 of the projection (centering adjustment).
​
center.pc2
numeric
default:"0"
Value to subtract from PC2 of the projection (centering adjustment).

​
Returns

A Seurat object with:
  • A new metadata column tricyclePosition containing the estimated cell cycle angle θ (0 to 2π)
  • A new DimReduc under reduction.name containing the 2D cell cycle embedding

​
Interpreting tricyclePosition

θ rangeCell cycle phase
~1.5 – 2π / 0G1
~0 – 0.5πS
~0.5π – πG2/M
~π – 1.5πM/G1

​
Examples

library(SeuratWrappers)
BiocManager::install("tricycle")

# Run tricycle (ENSEMBL gene IDs)
object <- Runtricycle(
  object = seurat_obj,
  slot = "data",
  species = "human",
  gname.type = "ENSEMBL"
)

# Visualize cell cycle position on UMAP
FeaturePlot(object, features = "tricyclePosition", reduction = "umap")

# View the tricycle embedding
DimPlot(object, reduction = "tricycleEmbedding")

​
See Also

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