make_novel_base_grobs

Create plots showing base usage at selected locations in sequences based on novel alleles

Multiple tools are now available for inferring the personalised
germ line set from an adaptive immune receptor repertoire.
Output from these tools is converted to
a single format and supplemented with rich data such as usage and
characterisation of 'novel' germ line alleles. This data can be
particularly useful when considering the validity of novel inferences. Use
of the analysis provided is described in <doi:10.3389/fimmu.2019.00435>.

William Lees

ogrdbstats

Analysis of Adaptive Immune Receptor Repertoire Germ Line
Statistics

make_novel_base_grobs function

<dl><dt>inferred_seqs</dt>
<dd>named list of novel gene sequences</dd>
<dt>input_sequences</dt>
<dd>the input_sequences data frame</dd>
<dt>segment</dt>
<dd>one of V, D, J</dd>
<dt>all_inferred</dt>
<dd>true if user has requested all alleles in reference set plotted - will suppress some warnings</dd></dl>

Arguments

Create plots showing base usage at selected locations in sequences based on novel alleles — make_novel_base_grobs

<dl>

<dt>inferred_seqs</dt>
<dd>named list of novel gene sequences</dd>


<dt>input_sequences</dt>
<dd>the input_sequences data frame</dd>


<dt>segment</dt>
<dd>one of V, D, J</dd>


<dt>all_inferred</dt>
<dd>true if user has requested all alleles in reference set plotted - will suppress some warnings</dd>

</dl>

cdr3_dist	cdr3 length distribution plots
whole	whole-length usage plots
end	3' end usage plots
conc	3' end consensus composition plots
triplet	3' end triplet usage plots

make_novel_base_grobs: Create plots showing base usage at selected locations in sequences based on novel alleles

Description

Usage

Value

Arguments

Examples