README.md

In phac-nml-phrsd/angedist: Antigenic Genetic Distance

angedist

Antigenic Genetic Distance

Warning: this repo is a work in progress

Pipeline

Installation

devtools::install_github('phac-nml-phrsd/angedist')

Simple examples

There are a few FASTA files attached to the angedist package. Let's use them in simple examples

To import a FASTA file, use the function import_seqs().

library(angedist)

path1 = system.file("extdata", "example1.fasta", package = "angedist")

seqs = import_seqs(path1,
                   prms = list(seq.source = 'GISAID',
                               pathogen = 'H3N2',
                               seq.type = 'AA'))

Given that we are working with influenza sequences, we can filter out low-quality sequences using clean_seq_influenza_A()

seqs.cleaned = clean_seq_influenza_A(seqs, verbose = TRUE)

TO DO DOCUMENT THE CODE BELOW

seqs.aligned = import_seqs('H3N2_cleaned_align.fasta',
                           prms = list(seq.source = 'GISAID',
                                       pathogen = 'H3N2',
                                       seq.type = 'AA'))

m = dist_matrix(sobj = seqs.aligned,
                sites = NULL,
                ncores = 4,
                dist.type = 'hamming')

metavars = list(sname = seqs.aligned$strain.name,
                datec = seqs.aligned$date.collection)

mdsobj = mds(m, dim.mds = 2, metavars=metavars)
mdsobj2 = mds(m, dim.mds = 2, metavars=NULL)

# highlight sequence from Aichi
mdsobj$df$highlight = grepl('Aichi', mdsobj$df$sname)
mdsobj$df$highlight.label = ifelse(mdsobj$df$highlight,'Aichi','')

g = plot_mds(mdsobj = mdsobj, color_varname = 'datec',
             highlight = TRUE, highlight.label = TRUE)
g2 = plot_mds(mdsobj = mdsobj)

plot(g)
plot(g2)

phac-nml-phrsd/angedist documentation built on Nov. 27, 2022, 7:23 p.m.