Celltype_Verification_PerCell: Verify per-cell annotations with marker expression dotplot

In SlimR: Adaptive Machine Learning-Powered, Context-Matching Tool for Single-Cell and Spatial Transcriptomics Annotation

Verify per-cell annotations with marker expression dotplot

Description

This function verifies per-cell SlimR annotations by generating a dotplot showing marker gene expression across predicted cell types.

Usage

Celltype_Verification_PerCell(
  seurat_obj,
  SlimR_percell_result,
  assay = "RNA",
  gene_number = 5,
  colour_low = "white",
  colour_high = "navy",
  annotation_col = "Cell_type_PerCell_SlimR",
  min_cells = 10
)

Arguments

seurat_obj	A Seurat object with per-cell annotations.
SlimR_percell_result	A list from Celltype_Calculate_PerCell() containing Expression_list with marker genes per cell type.
assay	Assay to use. Default: "RNA".
gene_number	Number of top genes to show per cell type. Default: 5.
colour_low	Color for lowest expression. Default: "white".
colour_high	Color for highest expression. Default: "navy".
annotation_col	Column in meta.data with cell type annotations. Default: "Cell_type_PerCell_SlimR".
min_cells	Minimum number of cells required for a cell type to be included in the plot. Default: 10.

Value

A ggplot object showing marker gene expression dotplot.

See Also

Other Section_3_Automated_Annotation: Celltype_Annotation(), Celltype_Annotation_PerCell(), Celltype_Calculate(), Celltype_Calculate_PerCell(), Celltype_Verification(), Parameter_Calculate(), percell_workflow

Examples

## Not run: 
# After running Celltype_Calculate_PerCell and Celltype_Annotation_PerCell
dotplot <- Celltype_Verification_PerCell(
    seurat_obj = sce,
    SlimR_percell_result = result,
    gene_number = 5,
    annotation_col = "Cell_type_PerCell_SlimR"
)
print(dotplot)

## End(Not run)

SlimR documentation built on Feb. 5, 2026, 5:08 p.m.