cell_assignment_from_dendrogram: Assign cells to cell sets from dendrogram

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

Assign cells to cell sets from dendrogram

Description

Automatically link each cell to each cell set that is available in the dendrogram to produce a table of the probabilities of each cell mapping to each cell type. In this case we define hard probabilities (0 = unassigned to cell set; 1 = assigned to cell set) but this could be adapted to reflect real probabilities calculated elsewhere.

Usage

cell_assignment_from_dendrogram(
  dend,
  samples,
  cell_id,
  mapping = data.frame(sample_name = samples),
  continue = TRUE
)

Arguments

dend	dendrogram of annotated cell types
samples	a character vector of unique sample (e.g., cell or nucleus) names
cell_id	a character vector of cell_set_accession_ids that corresponds to each sample
mapping	do not set this parameter
continue	do not set this parameter

Value

A data frame where the first columns corresponds to the cell sample_name and the remaining columns correspond to cell sets from the dendrogram. 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.