SlimR (version 1.0.7)

Celltype_Annotation_Combined: 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"
)

Value

The cell annotation picture is saved in "save_path".

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")

See Also

Other Semi_Automated_Annotation_Workflow: Celltype_Annotation_Features(), Celltype_Annotation_Heatmap()

Examples

if (FALSE) {
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"
    )
    }