VDJ_phylogenetic_trees_plot: Phylogenetic tree plotting

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Phylogenetic tree plotting

Description

Function to plot phylogenetic trees obtained from VDJ_phylogenetic_trees

!Requires the ggtree package to be loaded! Plots trees from function VDJ_phylogenetic_trees

Usage

VDJ_phylogenetic_trees_plot(
  tree.dfs,
  color.by,
  size.by,
  shape.by,
  specific.leaf.colors,
  specific.leaf.shapes
)

Arguments

tree.dfs	nested list of tidytree dataframes obtained from VDJ_phylogenetic_trees with output.format='tree.df.list'. tree.dfs[[1]][[2]] represent a tree dataframe for the first sample, second clonotype.
color.by	string - VDJ or tree df column name which will be used to color the tree nodes.
size.by	string or NULL - VDJ or tree df column name which determines the node size. If NULL, node sizes will be equal.
shape.by	string or NULL - VDJ or tree df column name which determines the node shape. If NULL, node sizes will be equal.
specific.leaf.colors	named list or NULL - if NULL, colors will be automatically selected for each node according to its color.by value.
specific.leaf.shapes	named list or NULL - if NULL, shapes will be automatically selected for each node according to its shape.by value.

Value

nested list of ggtree plot objects for each sample and each clonotype.

Examples

try({
tree.dfs <- VDJ_phylogenetic_trees(VDJ=Platypus::small_vgm[[1]], sequence.type='VDJ.VJ',
trimmed=TRUE, as.nucleotide=TRUE, include.germline=TRUE,
additional.feature.columns=NULL, tree.level='intraclonal',
output.format='tree.df.list')
VDJ_phylogenetic_trees_plot(tree.dfs,color.by='clonotype_id', size.by='sequence_frequency')
})

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.