phyloTree {LymphoSeq} | R Documentation

## Create phylogenetic tree

### 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")

[Package LymphoSeq version 1.8.0 Index]