highline: highlineR plotting

In PoonLab/highlineR: A Novel Visualization Tool to Assess Diversity in NGS Data

Description

highline generates Highlighter-style visualizations from one or more sequence alignments. These plots use colour marks to annotate the differences of each sequence in the alignment from a reference sequence.

Usage

highline(file, datatype='fasta', seqtype='nucleotide', unique=FALSE, 
         rf=1, mode='mismatch', sort_by='similarity', quiet=TRUE)

Arguments

file	a character vector containing one or more relative or absolute paths to the files containing sequence alignment(s).
datatype	specifies the file format - one of 'fasta', 'fastq' or 'csv'.
seqtype	specifies the type of sequence - 'nucleotide' or 'amino acid'
unique	if FALSE, gather identical sequences into unique variants

PoonLab/highlineR documentation built on Aug. 2, 2019, 4:32 p.m.