Annotate

The key functions for annotations are annotate and annotate_immundata. Functions annotate_receptors(), annotate_barcodes() and annotate_chains() are light-weight wrappers around annotate_immundata(). Annotations assign passed values to specified receptors, e.g., gene expression or pattern matched values.

Run this code before running examples below:

R

library(immundata)

inp_files <- paste0(system.file("extdata/single_cell", "", package = "immundata"), "/*.csv.gz")
md_file <- system.file("extdata/single_cell", "metadata.tsv", package = "immundata")
md_table <- read_metadata(md_file)
cells_file <- system.file("extdata/single_cell", "cells.tsv.gz", package = "immundata")
cells <- readr::read_tsv(cells_file)

schema <- make_receptor_schema(features = c("cdr3", "v_call"), chains = c("TRB"))

idata <- read_repertoires(
    path              = inp_files, 
    schema            = schema, 
    metadata.         = md_table, 
    barcode_col       = "barcode", 
    locus_col         = "locus", 
    umi_col           = "umis", 
    preprocess        = make_default_preprocessing("10x"), 
    repertoire_schema = "Tissue")

Annotate by any column

R

idata2 <- annotate(idata = idata, annotations = cells[c("barcode", "ident")], by = c(imd_barcode = "barcode"), keep_repertoires = FALSE)
idata2 <- idata2 |> filter(!is.na(ident))
idata2 <- idata2 |> agg_repertoires(schema = "ident")

print(idata2)

Annotate by receptor identifiers

R

idata2 <- annotate_receptors(idata = idata, annotations = tibble::tibble(receptor = c(1,2,3), important_data = c("A", "B", "C")), annot_col = "receptor")

idata2 |> filter(important_data %in% c("A", "B"))

Annotate by barcodes

R

idata2 <- annotate_barcodes(idata = idata, annotations = cells[c("barcode", "ident")],  annot_col = "barcode", keep_repertoires = FALSE)
idata2 <- idata2 |> filter(!is.na(ident))
idata2 <- idata2 |> agg_repertoires(schema = "ident")

print(idata2)