View source: R/calc-diversity.R
calc_diversity | R Documentation |
Calculate repertoire diversity
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
)
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 |
Single cell object or data.frame with diversity metrics
plot_diversity()
# 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)
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