Celltype_Verification: Perform cell type verification and generate the validation...

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

Perform cell type verification and generate the validation dotplot

Description

This function performs verification of predicted cell types by selecting high log2FC and high expression proportion genes and generates and generate the validation dotplot.

Usage

Celltype_Verification(
  seurat_obj,
  SlimR_anno_result,
  assay = "RNA",
  gene_number = 5,
  colour_low = "white",
  colour_high = "navy",
  annotation_col = "Cell_type_SlimR"
)

Arguments

seurat_obj	A Seurat object containing single-cell data.
SlimR_anno_result	A list containing SlimR annotation results with: Expression_list - List of expression matrices for each cell type. Prediction_results - Data frame with cluster annotations.
assay	Enter the assay used by the Seurat object, such as "RNA". Default parameters use "assay = 'RNA'".
gene_number	Integer specifying number of top genes to select per cell type.
colour_low	Color for lowest expression level. (default = "white")
colour_high	Color for highest expression level. (default = "black")
annotation_col	Character string specifying the column in meta.data to use for grouping.

Value

A ggplot object showing expression of top variable genes.

See Also

Other Automated_Annotation_Workflow: Celltype_Annotation(), Celltype_Calculate()

Examples

## Not run: 
Celltype_Verification(seurat_obj = sce,
    SlimR_anno_result = SlimR_anno_result,
    assay = "RNA",
    gene_number = 5,
    colour_low = "white",
    colour_high = "navy",
    annotation_col = "Cell_type_SlimR"
    )
    
## End(Not run)

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