R: Visualize evidence of novel V alleles

plotNovel {tigger} | R Documentation

## Visualize evidence of novel V alleles

### Description

`plotNovel` is be used to visualize the evidence of any novel V alleles found using findNovelAlleles. It can also be used to visualize the results for alleles that did

### Usage

    plotNovel(
      data,
      novel_row,
      v_call = "v_call",
      j_call = "j_call",
      seq = "sequence_alignment",
      junction = "junction",
      junction_length = "junction_length",
      ncol = 1,
      multiplot = TRUE
    )

### Arguments

`data` | `data.frame` containing repertoire data. See findNovelAlleles for details.
`novel_row` | single row from a data frame as output by findNovelAlleles that contains a polymorphism-containing germline allele.
`v_call` | name of the column in `data` with V allele calls. Default is `v_call`.
`j_call` | name of the column in `data` with J allele calls. Default is `j_call`.
`seq` | name of the column in `data` with the aligned, IMGT-numbered, V(D)J nucleotide sequence. Default is `sequence_alignment`.
`junction` | Junction region nucleotide sequence, which includes the CDR3 and the two flanking conserved codons. Default is `junction`.
`junction_length` | number of junction nucleotides in the junction sequence. Default is `junction_length`.
`ncol` | number of columns to use when laying out the plots.
`multiplot` | whether to return one single plot (`TRUE`) or a list with the three individual plots (`FALSE`).

### Details

The first panel in the plot shows, for all sequences which align to a particular germline allele, the mutation frequency at each postion along the aligned sequence as a function of the sequence-wide mutation count. Each line is a position. Positions that contain polymorphisms (rather than somatic hypermutations) will exhibit a high apparent mutation frequency for a range of sequence-wide mutation counts. The positions are color coded as follows:

- red: the position(s) pass(ess) the novel allele test

- yellow: the position(s) pass(ess) the y-intercept test but not other tests

- blue: the position(s) didn't pass the y-intercept test and was(were) not further considered

The second panel shows the nucleotide usage at each of the polymorphic positions as a function of sequence-wide mutation count. If no polymorphisms were identified, the panel will show the mutation count.

To avoid cases where a clonal expansion might lead to a false positive, TIgGER examines the combinations of J gene and junction length among sequences which perfectly match the proposed germline allele. Clonally related sequences usually share the same V gene, J gene and junction length. Requiring the novel allele to be found in different combinations of J gene and junction lengths is a proxy for requiring it to be found in different clonal lineages.

### Examples

    # Plot the evidence for the first (and only) novel allele in the example data
    novel <- selectNovel(SampleNovel)
    plotNovel(AIRRDb, novel[1, ], v_call="v_call", j_call="j_call",
              seq="sequence_alignment", junction="junction", junction_length="junction_length",
              multiplot=TRUE)

[Package tigger version 1.0.0 Index]