Pull_Cluster_Annotation: Pull cluster information from annotation csv file.

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Pull cluster information from annotation csv file.

Description

shortcut filter and pull function compatible with annotation files created by Create_Cluster_Annotation_File by default but also any other csv file.

Usage

Pull_Cluster_Annotation(
  annotation = NULL,
  cluster_name_col = "cluster",
  cell_type_col = "cell_type"
)

Arguments

annotation	name of the data.frame/tibble or path to CSV file containing cluster annotation.
cluster_name_col	name of column containing cluster names/numbers (default is "cluster").
cell_type_col	name of column contain the cell type annotation (default is "cell_type").

Value

a list of named vectors for every cell type in the cell_type_col column of the annotation table and vectors new cluster names (for use with Rename_Clusters function or manual identity renaming).

Examples

## Not run: 
# If pulling from a data.frame/tibble
cluster_annotation <- Pull_Cluster_Annotation(annotation = annotation_df,
cluster_name_col = "cluster", cell_type_col = "cell_type")

# If pulling from csv file
cluster_annotation <- Pull_Cluster_Annotation(annotation = "file_path/file_name.csv",
cluster_name_col = "cluster", cell_type_col = "cell_type")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.