phyloTree {LymphoSeq} | R Documentation |
Create a phylogenetic tree using neighbor joining tree estimation for amino acid or nucleotide CDR3 sequences in a list of data frames.
phyloTree(list, sample, type = "nucleotide", layout = "rectangular", label = TRUE)
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. |
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.
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")