Phylogenetic tree plotting

Function to plot phylogenetic trees obtained from VDJ_phylogenetic_trees

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

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

if (FALSE) {
VDJ_phylogenetic_trees_plot(tree.dfs,color.by='clonotype_id', size.by='sequence_frequency')
}