Celltype_annotation_Cellmarker2: Uses "marker_list" from Cellmarker2 for cell annotation

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

Uses "marker_list" from Cellmarker2 for cell annotation

Description

Uses "marker_list" from Cellmarker2 for cell annotation

Usage

Celltype_annotation_Cellmarker2(
  seurat_obj,
  gene_list,
  species,
  cluster_col = "seurat_clusters",
  assay = "RNA",
  save_path = NULL,
  min_counts = 1,
  colour_low = "white",
  colour_high = "navy",
  colour_low_mertic = "white",
  colour_high_mertic = "navy"
)

Arguments

seurat_obj	Enter the Seurat object with annotation columns such as "seurat_cluster" in meta.data to be annotated.
gene_list	Enter the standard "Marker_list" generated by the Cellmarker2 database for the SlimR package, generated by the "Markers_filter_Cellmarker2 ()" function.
species	This parameter selects the species "Human" or "Mouse" for standard gene format correction of markers entered by "Marker_list".
cluster_col	Enter annotation columns such as "seurat_cluster" in meta.data of the Seurat object to be annotated. Default parameters use "cluster_col = 'seurat_clusters'".
assay	Enter the assay used by the Seurat object, such as "RNA". Default parameters use "assay = "RNA"".
save_path	The output path of the cell annotation picture. Example parameters use "save_path = './SlimR/Celltype_annotation_Cellmarker2/'".
min_counts	The minimum number of counts of genes in "Marker_list" entered. This number represents the number of the same gene in the same species and the same location in the Cellmarker2 database used for annotation of this cell type. Default parameters use "min_counts = 1".
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")

Value

The cell annotation picture is saved in "save_path".

See Also

Other Other_Functions_Provided_By_SlimR: Celltype_annotation_Excel(), Celltype_annotation_PanglaoDB(), Celltype_annotation_Seurat()

Examples

## Not run: 
Celltype_annotation_Cellmarker2(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",
    )
    
## End(Not run)

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