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# Runtricycle()

> Estimate cell cycle position from scRNA-seq data using tricycle

`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

```r theme={null}
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

<ParamField path="object" type="Seurat" required>
  A Seurat object.
</ParamField>

<ParamField path="assay" type="character" default="NULL">
  Assay to use. Defaults to the active default assay.
</ParamField>

<ParamField path="slot" type="character" default="data">
  Slot to use. Should be normalized log-expression (`"data"`).
</ParamField>

<ParamField path="reduction.name" type="character" default="tricycleEmbedding">
  Name for the resulting 2D projection stored as a DimReduc.
</ParamField>

<ParamField path="reduction.key" type="character" default="tricycleEmbedding_">
  Prefix for embedding column names.
</ParamField>

<ParamField path="gname" type="character vector" default="NULL">
  Gene names used to subset the data. If `NULL`, all genes are used.
</ParamField>

<ParamField path="gname.type" type="character" default="ENSEMBL">
  Type of gene identifiers used. One of `"ENSEMBL"` or `"SYMBOL"`.
</ParamField>

<ParamField path="species" type="character" default="mouse">
  Species for the reference projection. One of `"mouse"` or `"human"`.
</ParamField>

<ParamField path="AnnotationDb" type="AnnotationDb" default="NULL">
  An annotation database object (e.g., from `org.Mm.eg.db`) for gene name conversion. Required when `gname.type = "SYMBOL"`.
</ParamField>

<ParamField path="center.pc1" type="numeric" default="0">
  Value to subtract from PC1 of the projection (centering adjustment).
</ParamField>

<ParamField path="center.pc2" type="numeric" default="0">
  Value to subtract from PC2 of the projection (centering adjustment).
</ParamField>

## 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 range        | Cell cycle phase |
| -------------- | ---------------- |
| \~1.5 – 2π / 0 | G1               |
| \~0 – 0.5π     | S                |
| \~0.5π – π     | G2/M             |
| \~π – 1.5π     | M/G1             |

## Examples

```r theme={null}
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

* [tricycle method guide](/methods/tricycle)