Celltype_Annotation_Features: Annotate cell types using features plot with different marker...

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

Annotate cell types using features plot with different marker databases

Description

This function dynamically selects the appropriate annotation method based on the gene_list_type parameter. It supports marker databases from Cellmarker2, PanglaoDB, Seurat (via FindAllMarkers), or Excel files.

Usage

Celltype_Annotation_Features(
  seurat_obj,
  gene_list,
  gene_list_type = "Default",
  species = NULL,
  cluster_col = "seurat_clusters",
  assay = "RNA",
  save_path = NULL,
  min_counts = 1,
  metric_names = NULL,
  colour_low = "white",
  colour_high = "navy",
  colour_low_mertic = "white",
  colour_high_mertic = "navy",
  ...
)

Arguments

seurat_obj	A valid Seurat object with cluster annotations in meta.data.
gene_list	A list of data frames containing marker genes and metrics. Format depends on gene_list_type: - Cellmarker2: Generated by Markers_filter_Cellmarker2(). - PanglaoDB: Generated by Markers_filter_PanglaoDB(). - Seurat: Generated by read_seurat_markers(). - Excel: Generated by read_excel_markers().
gene_list_type	Type of marker database to use. Be one of: "Cellmarker2", "PanglaoDB", "Seurat", or "Excel".
species	Species of the dataset: "Human" or "Mouse" for gene name standardization.
cluster_col	Column name in meta.data defining clusters (default: "seurat_clusters").
assay	Assay layer in the Seurat object (default: "RNA").
save_path	Directory to save output PNGs. Must be explicitly specified.
min_counts	Minimum number of counts for Cellmarker2 annotations (default: 1).
metric_names	Optional. Change the row name for the input mertics, not recommended unless necessary. (NULL is used as default parameter; used in "Seurat"/"Excel").
colour_low	Color for lowest expression level. (default = "white")
colour_high	Color for highest expression level. (default = "black")
colour_low_mertic	Color for lowest mertic level. (default = "white")
colour_high_mertic	Color for highest mertic level. (default = "black")
...	Additional parameters passed to the specific annotation function.

Value

Saves cell type annotation PNGs in save_path. Returns invisibly.

See Also

Other Semi_Automated_Annotation_Workflow: Celltype_Annotation_Combined(), Celltype_Annotation_Heatmap()

Examples

## Not run: 
# Example for Cellmarker2
Celltype_Annotation_Features(seurat_obj = sce,
    gene_list = Markers_list_Cellmarker2,
    species = "Human",
    cluster_col = "seurat_clusters",
    assay = "RNA",
    save_path = file.path(tempdir(),"SlimR_Celltype_annotation_Cellmarker2"),
    colour_low = "white",
    colour_high = "navy",
    colour_low_mertic = "white",
    colour_high_mertic = "navy",
    )

# Example for PanglaoDB
Celltype_Annotation_Features(seurat_obj = sce,
    gene_list = Markers_list_panglaoDB,
    species = "Human",
    cluster_col = "seurat_clusters",
    assay = "RNA",
    save_path = file.path(tempdir(),"SlimR_Celltype_annotation_PanglaoDB")
    colour_low = "white",
    colour_high = "navy",
    colour_low_mertic = "white",
    colour_high_mertic = "navy",
    )

# Example for Seurat marker list
Celltype_Annotation_Features(seurat_obj = sce,
    gene_list = Markers_list_Seurat,
    species = "Human",
    cluster_col = "seurat_clusters",
    assay = "RNA",
    save_path = file.path(tempdir(),"SlimR_Celltype_annotation_Seurat")
    colour_low = "white",
    colour_high = "navy",
    colour_low_mertic = "white",
    colour_high_mertic = "navy",
    )

# Example for Excel marker list
Celltype_Annotation_Features(seurat_obj = sce,
    gene_list = Markers_list_Excel,
    species = "Human",
    cluster_col = "seurat_clusters",
    assay = "RNA",
    save_path = file.path(tempdir(),"SlimR_Celltype_annotation_Excel")
    colour_low = "white",
    colour_high = "navy",
    colour_low_mertic = "white",
    colour_high_mertic = "navy",
    )

## End(Not run)

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