pairing_tables {CellaRepertorium} | R Documentation

## Generate a list of tables representing clusters paired in cells

### Description

A contingency table of every combination of `cluster_idx` up to `table_order` is generated. Combinations that are found in at least `min_expansion` number of cells are reported. All cells that have these combinations are returned, as well as cells that only have `orphan_level` of matching `cluster_idx`.

### Usage

    pairing_tables(
      ccdb,
      ranking_key = "grp_rank",
      table_order = 2,
      min_expansion = 2,
      orphan_level = 1,
      cluster_keys = character(),
      cluster_whitelist = NULL,
      cluster_blacklist = NULL
    )

### Arguments

`ccdb` | `ContigCellDB`
`ranking_key` | field in `ccdb$contig_tbl` giving the ranking of each contig per cell. Probably generated by a call to `rank_prevalence_ccdb()` or `rank_chain_ccdb()`.
`table_order` | Integer larger than 1. What order of cluster_idx will be paired, eg, order = 2 means that the first and second highest ranked contigs will be sought and paired in each cell
`min_expansion` | the minimal number of times a pairing needs to occur for it to be reported
`orphan_level` | Integer in interval [1, `table_order`]. Given that at least `min_expansion` cells are found that have `table_order` chains identical, how many `cluster_idx` pairs will we match on to select other cells. Example: `ophan_level=1` means that cells that share just a single chain with an expanded pair will be reported.
`cluster_keys` | optional `character` naming additional columns in `ccdb$cluster_tbl` to be reported in the pairing
`cluster_whitelist` | a table of pairings or clusters that should always be reported. Here the clusters must be named "cluster_idx.1", "cluster_idx.2" (if order-2 pairs are being selected) rather than with 'ccdb$cluster_pk“
`cluster_blacklist` | a table of pairings or clusters that will never be reported. Must be named as per `cluster_whitelist`.

### Details

For example, if `table_order=2` and `min_expansion=2` then heavy/light or alpha/beta pairs found two or more times will be returned (as well as alpha-alpha pairs, etc, if those are present). If `orphan_level=1` then all cells that share just a single chain with an expanded clone will be returned.

The `cluster_idx.1_fct` and `cluster_idx.2_fct` fields in `cell_tbl`, `idx1_tbl`, `idx2_tbl` are cast to factors and ordered such that pairings will tend to occur along the diagonal when they are cross-tabulated. This facilitates plotting.

### Value

list of tables. The `cell_tbl` is keyed by the `cell_identifiers`, with fields "cluster_idx.1", "cluster_idx.2", etc, IDing the contigs present in each cell. "cluster_idx.1_fct" and "cluster_idx.2_fct" cast these fields to factors and are reordered to maximize the number of pairs along the diagonal. The `idx1_tbl` and `idx2_tbl` report information (passed in about the `cluster_idx` by `feature_tbl`.) The `cluster_pair_tbl` reports all pairings found of contigs, and the number of times observed.

### See Also

`rank_prevalence_ccdb()`

### Examples

    library(dplyr)
    tbl = tibble(clust_idx = gl(3, 2), cell_idx = rep(1:3, times = 2), contig_idx = 1:6)
    ccdb = ContigCellDB(tbl, contig_pk = c('cell_idx', 'contig_idx'),
    cell_pk = 'cell_idx', cluster_pk = 'clust_idx')
    # add `grp_rank` to ccdb$contig_tbl indicating how frequent a cluster is
    ccdb = rank_prevalence_ccdb(ccdb, tie_break_keys = character())
    # using `grp_rank` to determine pairing
    # no pairs found twice
    pt1 = pairing_tables(ccdb)
    # all pairs found, found once.
    pt2 = pairing_tables(ccdb, min_expansion = 1)
    pt2$cell_tbl
    tbl2 = bind_rows(tbl, tbl %>% mutate(cell_idx = rep(4:6, times = 2)))
    ccdb2 = ContigCellDB(tbl2, contig_pk = c('cell_idx', 'contig_idx'), cell_pk = 'cell_idx',
    cluster_pk = 'clust_idx') %>% rank_prevalence_ccdb(tie_break_keys = character())
    #all pairs found twice
    pt3 = pairing_tables(ccdb2, min_expansion = 1)
    pt3$cell_tbl
    ccdb2$contig_tbl = ccdb2$contig_tbl %>%
        mutate(umis = 1, reads = 1, chain = rep(c('TRA', 'TRB'), times = 6))
    ccdb2 = rank_chain_ccdb(ccdb2, tie_break_keys = character())
    pt4 = pairing_tables(ccdb2, min_expansion = 1, table_order = 2)

[Package CellaRepertorium version 1.2.0 Index]