phyloTree: Create phylogenetic tree

In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors

Create phylogenetic tree

Description

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

Usage

phyloTree(
  study_table,
  repertoire_ids,
  type = "junction",
  layout = "rectangular",
  label = TRUE
)

Arguments

study_table	A tibble of unproductive junction sequences or productive junction sequences generated by the LymphoSeq function productiveSeq. v_family, d_family, j_family, and duplicate_count are required columns.
repertoire_ids	A character vector indicating the name of the repertoire_id in the study table.
type	A character vector indicating whether "junction_aa" or "junction" 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 duplicate_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 duplicate_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 = "LymphoSeq2")

stable <- readImmunoSeq(path = file_path)

ntable <- productiveSeq(study_table = stable, aggregate = "junction")

phyloTree(study_table = ntable, repertoire_ids = "IGH_MVQ92552A_BL", type = "junction", 
         layout = "rectangular")

phyloTree(study_table = ntable, repertoire_ids = "IGH_MVQ92552A_BL", type = "junction_aa", 
         layout = "circular")
         
# Add scale and title to figure
phyloTree(study_table = ntable, repertoire_ids = "IGH_MVQ92552A_BL", type = "junction_aa", 
         layout = "rectangular") +
         ggtree::theme_tree2() +
         ggplot2::theme(legend.position = "right", legend.key = ggplot2::element_rect(colour = "white")) +
         ggplot2::ggtitle("Title")
         
# Hide legend and leaf labels
phyloTree(study_table = ntable, repertoire_ids = "IGH_MVQ92552A_BL", type = "junction", 
         layout = "rectangular", label = FALSE) +
         ggplot2::theme(legend.position="none")

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.