Celltype_annotation_PanglaoDB: Uses "marker_list" from PanglaoDB for cell annotation

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

Uses "marker_list" from PanglaoDB for cell annotation

Description

Uses "marker_list" from PanglaoDB for cell annotation

Usage

Celltype_annotation_PanglaoDB(
  seurat_obj,
  gene_list,
  species,
  cluster_col = "seurat_clusters",
  assay = "RNA",
  save_path = NULL,
  metric_names = NULL,
  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 PanglaoDB database for the SlimR package, generated by the "Markers_filter_PanglaoDB ()" 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_PanglaoDB/'".
metric_names	Warning: Do not enter information. This parameter is used to check if "Marker_list" conforms to the PanglaoDB database output.
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_Cellmarker2(), Celltype_annotation_Excel(), Celltype_annotation_Seurat()

Examples

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

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