SlimR (version 1.1.1)

Celltype_Verification_PerCell: 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
)

Value

A ggplot object showing marker gene expression dotplot.

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.

See Also

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

Examples

if (FALSE) {
# 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)
}