vqscompare {longreadvqs}

Comparing viral quasispecies profile and operational taxonomic unit (OTU) classified by k-means clustering between samples

Description

Pools error-minimized down-sampled read samples and compares their diversity by 1) viral quasispecies profile (haplotype and metrics from QSutils package), 2) operational taxonomic unit (OTU) classified by k-means clustering of single nucleotide variant (SNV) distance, and 3) visualization of different comparative method, i.e., haplotype, OTU, phylogenetic tree, MDS plot.

Arguments

samplelist

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

lab_name

Name of variable or type of sample for instance "barcode", "sample", "dpi", or "isolate" (optional).

kmeans.n

Number of clusters or operational taxonomic units (OTUs) needed from k-means clustering on multidimensional scale (MDS) of all samples' pairwise SNV distance.

showhap.n

Number of largest haplotypes (default = 30) labeled in the top five OTUs' MDS plot (optional).

Value

list of 1) "hapdiv": comparative table of viral quasispecies diversity metrics between listed samples calculated by QSutils package, 2) "otudiv": comparative table of OTU diversity metrics between listed samples calculated from consensus sequence of each OTU (similar to "otucompare" function's output), 3) "sumsnv_hap": frequency and SNV profile (by position in the alignment) of haplotypes that are not singleton (number of reads > 1), 4) "sumsnv_otu": frequency and SNV profile of all haplotypes grouped into different operational taxonomic unit (OTU), 5) "fullseq": complete read sequence of haplotypes that are not singleton, 6) "fulldata": complete read sequence of all haplotypes in every sample with frequency and OTU classification, 7) "summaryplot": visualization of viral quasispecies comparison between samples including 7.1) "happlot": proportion of haplotypes (top left), 7.2) "otuplot": proportion of OTUs (bottom left), and 7.3) multidimensional scale (MDS) plots (right) of k-means OTU ("top5otumds": 5 largest groups with major haplotypes labeled and "allotumds": all groups)

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-----------------------------
set.seed(123)
sample1 <- vqsassess(sample1filepath, pct = 5, samsize = 50, label = "sample1")
sample2 <- vqsassess(sample2filepath, pct = 5, samsize = 50, label = "sample2")

## Compare viral quasispecies and OTU (4 clusters) diversity between two samples------------------
out <- vqscompare(samplelist = list(sample1, sample2),
           lab_name = "Sample", kmeans.n = 4, showhap.n = 5)
out$summaryplot