Celltype_Annotation_Combined: Uses "marker_list" to generate combined plot for cell...

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

Uses "marker_list" to generate combined plot for cell annotation

Description

Uses "marker_list" to generate combined plot for cell annotation

Usage

Celltype_Annotation_Combined(
  seurat_obj,
  gene_list,
  species,
  cluster_col = "seurat_clusters",
  assay = "RNA",
  save_path = NULL,
  colour_low = "white",
  colour_high = "navy"
)

Arguments

seurat_obj	Enter the Seurat object with annotation columns such as "seurat_cluster" in meta.data to be annotated.
gene_list	A list of cells and corresponding gene controls, the name of the list is cell type, and the first column of the list corresponds to markers. Lists can be generated using functions such as "Markers_filter_Cellmarker2 ()", "Markers_filter_PanglaoDB ()", "read_excel_markers ()", "read_seurat_markers ()", etc.
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_Bar/'".
colour_low	Color for lowest expression level. (default = "white")
colour_high	Color for highest expression level. (default = "black")

Value

The cell annotation picture is saved in "save_path".

See Also

Other Semi_Automated_Annotation_Workflow: Celltype_Annotation_Features(), Celltype_Annotation_Heatmap()

Examples

## Not run: 
Celltype_Annotation_Combined(seurat_obj = sce,
    gene_list = Markers_list,
    species = "Human",
    cluster_col = "seurat_clusters",
    assay = "RNA",
    save_path = file.path(tempdir(),"SlimR_Celltype_Annotation_Combined"),
    colour_low = "white",
    colour_high = "navy"
    )
    
## End(Not run)

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