SlimR (version 1.0.7)

Celltype_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"
)

Value

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

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")

See Also

Other Automated_Annotation_Workflow: Celltype_Calculate(), Celltype_Verification()

Examples

if (FALSE) {
sce <- Celltype_Annotation(seurat_obj = sce,
    cluster_col = "seurat_clusters",
    SlimR_anno_result = SlimR_anno_result,
    plot_UMAP = TRUE,
    annotation_col = "Cell_type_SlimR"
    )
    }