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


plotNovel(data, novel_row, v_call = "V_CALL", j_call = "J_CALL",
seq = "SEQUENCE_IMGT", junction = "JUNCTION",
junction_length = "JUNCTION_LENGTH", ncol = 1)


a data.frame in Change-O format. See findNovelAlleles for details.
a 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_IMGT.
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


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 sequece as a function of the sequence-wide mutation. Sequences that pass the novel allele test are colored red, while sequences that don’t pass the test are colored yellow. The second panel shows the nucleotide usage at the positions as a function of sequence-wide 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.


# Plot the evidence for the first (and only) novel allele in the example data
novel <- selectNovel(SampleNovel)
plotNovel(SampleDb, novel[1, ])