plotNovel - 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", ncol = 1)

Arguments

data
a data.frame in Change-O format. See findNovelAlleles for details.
novel_row
a 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”.
ncol
number of columns to use when laying out the plots

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 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.

Examples

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

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