SlimR (version 1.0.7)

Celltype_annotation_PanglaoDB: 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"
)

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

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")

See Also

Other Other_Functions_Provided_By_SlimR: Celltype_annotation_Cellmarker2(), Celltype_annotation_Excel(), Celltype_annotation_Seurat()