longreadvqs (version 0.1.4)

snvcompare: Plotting single nucleotide variant (SNV) frequency in read alignment across different samples

Description

Compares single nucleotide variant (SNV) profile between noise-minimized down-sampled read samples using cowplot's "plot_grid" function. The resulting plot may help evaluating the optimal cut-off percentage of low frequency nucleotide base used in "vqsassess", "vqscustompct", or "vqssub" functions.

Value

Comparative plot of SNV frequency in read alignment across different samples

Arguments

samplelist

List of samples, i.e., name of resulting objects from "vqsassess" or "vqscustompct" functions, for example list(BC1, BC2, BC3).

ncol

Number of columns for multiple plots (see cowplot's "plot_grid" function)

Examples

## Locate input FASTA files-----------------------------------------------------------------------
sample1filepath <- system.file("extdata", "s1.fasta", package = "longreadvqs")
sample2filepath <- system.file("extdata", "s2.fasta", package = "longreadvqs")

## Prepare data for viral quasispecies comparison between two samples-----------------------------
sample1 <- vqsassess(sample1filepath, pct = 10, label = "sample1")
sample2 <- vqsassess(sample2filepath, pct = 10, label = "sample2")

## Compare SNV profile between two listed samples-------------------------------------------------
snvcompare(samplelist = list(sample1, sample2), ncol = 1)