Celltype_Annotation: Annotate Seurat Object with SlimR Cell Type Predictions

In SlimR: Marker-Based Package for Single-Cell and Spatial-Transcriptomic Annotation

Annotate Seurat Object with SlimR Cell Type Predictions

Description

This function assigns SlimR predicted cell types to a Seurat object based on cluster annotations, and stores the results in the meta.data slot.

Usage

Celltype_Annotation(
  seurat_obj,
  cluster_col,
  SlimR_anno_result,
  plot_UMAP = TRUE,
  annotation_col = "Cell_type_SlimR"
)

Arguments

seurat_obj	A Seurat object containing cluster information in meta.data.
cluster_col	Character string indicating the column name in meta.data that contains cluster IDs.
SlimR_anno_result	List generated by function Celltype_Calculate() which containing a data.frame in $Prediction_results with: 1.cluster_col (Cluster identifiers (should match cluster_col in meta.data)) 2.Predicted_cell_type (Predicted cell types for each cluster).
plot_UMAP	logical(1); if TRUE, plot the UMAP with cell type annotations.
annotation_col	The location to write in 'meta.data' that contains the predicted cell type. (default = "Cell_type_SlimR")

Value

A Seurat object with updated meta.data containing the predicted cell types.

Note

If plot_UMAP = TRUE, this function will print a UMAP plot as a side effect.

See Also

Other Automated_Annotation_Workflow: Celltype_Calculate(), Celltype_Verification()

Examples

## Not run: 
sce <- Celltype_Annotation(seurat_obj = sce,
    cluster_col = "seurat_clusters",
    SlimR_anno_result = SlimR_anno_result,
    plot_UMAP = TRUE,
    annotation_col = "Cell_type_SlimR"
    )
    
## End(Not run)

SlimR documentation built on Aug. 19, 2025, 1:13 a.m.