plotTree: Plot a neighbor join tree object

In quick2063706271/Cov2Comparator: Analyzing SARS covid-2 genome across different geographic regions

Description

A function that creates a neighbor join tree from multiple sequence alignment

Usage

plotTree(tree, name = "Phylogenetic Tree", showRegionName = TRUE, type)

Arguments

tree	A phylo object for plotting
name	A char indicating the name of plot
showRegionName	A boolean indicating if showing the region in the plot
type	A string indicating the type of tree including "phylogram", "cladogram", "fan", "unrooted", "radial"

Value

Plot a phylogenetic tree using this phylo object

References

Charif D, Lobry J. 2007. “SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis.” In Bastolla U, Porto M, Roman H, Vendruscolo M (eds.), Structural approaches to sequence evolution: Molecules, networks, populations, series Biological and Medical Physics, Biomedical Engineering, 207-232. Springer Verlag, New York.

Paradis E. & Schliep K. 2019. ape 5.0: an environment for modern phylogenetics and evolutionaryanalyses in R. Bioinformatics 35: 526-528.

U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015) msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997- 9999. DOI: 10.1093/bioinformatics/btv176.

Examples

# Example 1
# Create a basic msa and then plot a tree from it
library(msa)
library(Biostrings)
set1 <- Biostrings::DNAStringSet("ATCGATCG")
set2 <- Biostrings::DNAStringSet("ATTTTTTT")
set3 <- Biostrings::DNAStringSet("ATCGATTT")
setTotal <- union(set1, set2)
setTotal <- union(setTotal, set3)
align <- msa::msa(setTotal)
tree <- createTree(align)
plotTree(tree = tree,
         name = "Simple tree",
         showRegionName = TRUE)

quick2063706271/Cov2Comparator documentation built on Dec. 22, 2021, 10:59 a.m.