calc_diversity: Calculate repertoire diversity

In rnabioco/AVIDtools: A collection of single-cell V(D)J tools

Calculate repertoire diversity

Description

Calculate repertoire diversity

Usage

calc_diversity(
  input,
  data_col,
  cluster_col = NULL,
  method = abdiv::simpson,
  downsample = FALSE,
  n_boots = 0,
  chain = NULL,
  chain_col = global$chain_col,
  prefix = paste0(data_col, "_"),
  return_df = FALSE,
  sep = global$sep
)

Arguments

input	Single cell object or data.frame containing V(D)J data. If a data.frame is provided, the cell barcodes should be stored as row names.
data_col	meta.data column containing values to use for calculating diversity, e.g. 'clonotype_id'
cluster_col	meta.data column containing cluster IDs to use for grouping cells when calculating diversity. If cluster_col is omitted, diversity index will be calculated using all cells.
method	Method to use for calculating diversity. A named list can also be passed to use multiple methods. The names should specify names for the output columns.
downsample	Downsample clusters to the same size when calculating diversity metrics
n_boots	Number of bootstrap replicates for calculating standard error, if n_boots is 0 this will be skipped.
chain	Chain to use for calculating diversity. To calculate diversity for a single chain, the column passed to the data_col argument must contain per-chain data such as CDR3 sequences. Set to NULL to include all chains.
chain_col	meta.data column containing chains for each cell
prefix	Prefix to add to new columns
return_df	Return results as a data.frame. If FALSE, results will be added to the input object.
sep	Separator used for storing per-chain V(D)J data for each cell

Value

Single cell object or data.frame with diversity metrics

See Also

plot_diversity()

Examples

# Calculate diversity for each cell cluster
res <- calc_diversity(
  vdj_sce,
  data_col    = "clonotype_id",
  cluster_col = "orig.ident",
  method      = abdiv::simpson
)

head(slot(res, "colData"), 1)

rnabioco/AVIDtools documentation built on Oct. 28, 2023, 10:23 a.m.