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.
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",
...
)Saves cell type annotation PNGs in save_path. Returns invisibly.
A valid Seurat object with cluster annotations in meta.data.
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().
Type of marker database to use. Be one of:
"Cellmarker2", "PanglaoDB", "Seurat", or "Excel".
Species of the dataset: "Human" or "Mouse" for gene name standardization.
Column name in meta.data defining clusters (default: "seurat_clusters").
Assay layer in the Seurat object (default: "RNA").
Directory to save output PNGs. Must be explicitly specified.
Minimum number of counts for Cellmarker2 annotations (default: 1).
Optional. Change the row name for the input mertics, not recommended unless necessary. (NULL is used as default parameter; used in "Seurat"/"Excel").
Color for lowest expression level. (default = "white")
Color for highest expression level. (default = "black")
Color for lowest mertic level. (default = "white")
Color for highest mertic level. (default = "black")
Additional parameters passed to the specific annotation function.
Other Semi_Automated_Annotation_Workflow:
Celltype_Annotation_Combined(),
Celltype_Annotation_Heatmap()