Create phylogenetic tree

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 LymphoSeq2 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" (the default) sequences should be compared.

layout

A character vector indicating the tree layout. Options include "rectangular" (the default), "slanted", "fan", "circular", "radial" and "unrooted".

label

A Boolean value

• TRUE (the default): use sequencing duplicate_count to label the tree

• FALSE : do not show duplicate_count

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")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
nucleotide_table <- LymphoSeq2::productiveSeq(
  study_table = study_table,
  aggregate = "junction"
)
LymphoSeq2::phyloTree(
  study_table = nucleotide_table, repertoire_ids = "IGH_MVQ92552A_BL",
  type = "junction", layout = "rectangular"
)
#> Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
#> of ggplot2 3.3.4.
#> ℹ The deprecated feature was likely used in the LymphoSeq2 package.
#>   Please report the issue at
#>   <https://github.com/shashidhar22/LymphoSeq2/issues>.

LymphoSeq2::phyloTree(
  study_table = nucleotide_table, repertoire_ids = "IGH_MVQ92552A_BL",
  type = "junction_aa", layout = "circular"
)

# Add scale and title to figure
LymphoSeq2::phyloTree(
  study_table = nucleotide_table, 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
LymphoSeq2::phyloTree(
  study_table = nucleotide_table, repertoire_ids = "IGH_MVQ92552A_BL",
  type = "junction", layout = "rectangular", label = FALSE
) +
  ggplot2::theme(legend.position = "none")