Pull_Cluster_Annotation {scCustomize} | R Documentation |
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)
[Package scCustomize version 2.1.2 Index]