phyloTree: Create phylogenetic tree

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

Create a phylogenetic tree using neighbor joining tree estimation for amino acid or nucleotide CDR3 sequences in a list of data frames.

Usage

phyloTree(list, sample, type = "nucleotide", layout = "rectangular",
  label = TRUE)

Arguments

list	A list data frames of unproductive nucleotide sequences or productive nucleotide sequences generated by the LymphoSeq function productiveSeq. vFamilyName, dFamilyName, jFamilyName, and count are required columns.
sample	A character vector indicating the name of the sample in the productive sequence list.
type	A character vector indicating whether "aminoAcid" or "nucleotide" sequences should be compared.
layout	A character vector indicating the tree layout. Options include "rectangular", "slanted", "fan", "circular", "radial" and "unrooted".
label	A Boolean indicating if the sequencing count should be shown next to the leaves.

Value

Returns a phylogenetic tree where each leaf represents a sequence color coded by the V, D, and J gene usage. The number next to each leaf refers to the sequence count. A triangle shaped leaf indicates the dominant sequence. Refer to the ggtree Bioconductor package documentation for details on how to manipulate the tree.

Examples

file.path <- system.file("extdata", "IGH_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

productive.nt <- productiveSeq(file.list = file.list, aggregate = "nucleotide")

phyloTree(list = productive.nt, sample = "IGH_MVQ92552A_BL", type = "nucleotide", 
         layout = "rectangular")

phyloTree(list = productive.nt, sample = "IGH_MVQ92552A_BL", type = "aminoAcid", 
         layout = "circular")
         
# Add scale and title to figure
library(ggtree)
library(ggplot2)
phyloTree(list = productive.nt, sample = "IGH_MVQ92552A_BL", type = "aminoAcid", 
         layout = "rectangular") +
         ggtree::theme_tree2() +
         ggplot2::theme(legend.position = "right", legend.key = element_rect(colour = "white")) +
         ggplot2::ggtitle("Title")
         
# Hide legend and leaf labels
phyloTree(list = productive.nt, sample = "IGH_MVQ92552A_BL", type = "nucleotide", 
         layout = "rectangular", label = FALSE) +
         ggplot2::theme(legend.position="none")
         

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.