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

## Not run: 
VDJ_phylogenetic_trees_plot(tree.dfs,color.by='clonotype_id', size.by='sequence_frequency')

## End(Not run)

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.