plotNovel {tigger}

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",
  pos_range_max = NULL,
  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.

pos_range_max

Name of the column in data with the ending positions of the V alignment in the germline (usually v_germline_end).

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)