plotNovel - Visualize evidence of novel V alleles


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


v_call = "v_call",
j_call = "j_call",
seq = "sequence_alignment",
junction = "junction",
junction_length = "junction_length",
ncol = 1,
multiplot = TRUE


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


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.


# 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",