apply_CCN: Apply CCN (**BETA**)

In AllenInstitute/CCN: Generate the Standardized Common Cell type Nomenclature (CCN)

Apply CCN (**BETA**)

Description

This **BETA** function is a wrapper for most of the other functions in the CCN library. It takes as input whatever information is available (e.g., dend, nomenclature, cell_assignment, metadata) and uses this to try and output a standard nomenclature table and other CCN outputs. Please see the "Applying CCN to an existing taxonomy: one function" vignette for examples of how to use this function to apply the CCN in various contexts.

Usage

apply_CCN(
  dend = NULL,
  nomenclature = NULL,
  cell_assignment = NULL,
  metadata = NULL,
  first_label = setNames("All", 1),
  taxonomy_id = paste0("CCN", format(Sys.time(), "%Y%m%d"), 0),
  taxonomy_author = "Unspecified",
  taxonomy_citation = "",
  structure = "neocortex",
  ontology_tag = NULL,
  metadata_columns = c("subclass_label"),
  metadata_order = NULL,
  annotation_columns = rep("cell_set_preferred_alias", length(metadata_columns)),
  cluster_column = "cluster_label",
  append_metadata = FALSE,
  ccn_filename = "nomenclature.zip",
  duplicate_annotations = "cell_set_additional_aliases"
)

Arguments

dend	dendrogram of cell types to annotate. At least one of dend, nomenclature, cell_assignment, or metadata must be provided.
nomenclature	the nomenclature table output from 'build_nomenclature_table' or related/downstream functions.
cell_assignment	a named vector linking each unique cell id ('names(cell_assignment)') to their cell type assignments ('cell_assignment')
metadata	cell or cell type metadata table that includes the columns to annotate
first_label	a named vector used as prefix for cell_set_label
taxonomy_id	unique accession ID for the taxonomy also used to prefix the cell sets accessions. Defaults to 'CCN[YYYYMMDD]0'. If more than one is provided (not recommended), any IDs beyond the first in the character vector are saved in a "taxonomy_alias" column.
taxonomy_author	the name of a point person for this taxonomy
taxonomy_citation	permanent data identifier corresponding to the taxonomy (or default="" if none). Ideally the DOI for a relevant publication.
structure	the location in the brain (or body) from where the data in the taxonomy was collected
ontology_tag	a standard ontology term (e.g., from UBERON) for the 'structure', or "none" if unavailable. NULL (default) attempts to find one in UBERON using 'find_ontology_terms'.
metadata_columns	a character vector of column names corresponding to the metadata fields to add annotations. Only used if "metadata" is provided
metadata_order	optional character vector of column names indicating the order to include metadata. If supplied, must be the same length as "metadata_columns". Only used if "metadata" is provided
annotation_columns	character vector indicating which column to annotate for each metadata column supplied (default is is "cell_set_preferred_alias"). Only used if "metadata" is provided
cluster_column	column name in "metadata" that corresponds to values in the "cell_set_preferred_alias" column of "cell_set_information". Only used if "metadata" is provided
append_metadata	If TRUE, it will append info; if FALSE (default), it will skip cases where there is already an entry. Only used if "metadata" is provided
ccn_filename	file name for zip file with final CCN files containing the same information that is returned. Will output to current working directory unless full path is specified. Will not output anywhere if set to NULL.
duplicate_annotations	either NULL or a character indicating which column to append annotations if the annotation_columns column already has an entry. Only used if append=TRUE. Default "cell_set_additional_aliases"

Value

a list containing the three CCN standard outputs:

# Describe is optional and can go after and param or return

cell_set_information

Final nomenclature table where rows correspond to cell sets and columns correspond to standard CCN columns.

initial_dendrogram

A dendrogram updated with node numeric labels, if dend was provided. These are useful for post-hoc manual annotations but otherwise can be ignored.

final_dendrogram

A dendrogram updated with node labels and CCN annotations, if dend was provided. This is what is output in dend.json

mapping

A data frame where the first columns corresponds to each cell's unique ID (if cell_assignment or metadata is provided) and the remaining columns correspond to cell sets. Entries are either 0 = cell unassigned to cell set or 1 = cell assigned to cell set.

AllenInstitute/CCN documentation built on April 15, 2023, 10:48 p.m.