Create an interactive phylogenetic tree — heat

Create an interactive phylogenetic tree using the javascript heat-tree package

Usage

heat_tree(
  tree = NULL,
  metadata = NULL,
  aesthetics = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL,
  ...
)

Arguments

tree: One or more trees to plot. Can be a raw newick-formatted string, a phylo object, or a list of such inputs. If a list is provided, its names will be used to name trees.
metadata: Metadata associated with tree. Can be a data.frame or tibble with a column containing IDs matching the tree labels. The ID column is detected automatically. If there are multiple trees (a list), then a list of tables of equal length is required. If a list is provided, its names will be used to name metadata tables.
aesthetics: A named character vector defining which metadata columns are initially used to color/size tree parts. If there are multiple trees (a list), then a list of equal length is required.
width: Width of the widget (CSS units or number).
height: Height of the widget (CSS units or number).
elementId: Optional element ID for the widget.
...: Options passed to options parameter of the underlying HeatTree.heatTree() javascript function to modify the initial state of the widget.

Value

An htmlwidget object of class heat_tree that renders an interactive phylogenetic tree visualization. The object contains:

x: A list with tree data and options passed to JavaScript
width, height: Dimensions of the widget
elementId: Optional DOM element ID

The widget can be displayed in R Markdown, Quarto, or using and IDE like RStudio.

Examples

# Create an empty tree viewer for loading data interactively
heat_tree()


# Create a tree viewer with example data included with the package
data(weisberg_2020_metadata)
data(weisberg_2020_mlsa)
heat_tree(
  tree = weisberg_2020_mlsa,
  metadata = weisberg_2020_metadata,
  aesthetics = c(tipLabelColor = 'host_type')
)