toytree
latest
The toytree ethos
Try it now
Installation
Conda install (recommended)
Pip install
Dependencies:
Quick Guide
Load and draw your first tree
Parsing Newick/Nexus data
Accessing tree data
Tree Classes
Drawing trees: basics
Drawing trees: styles
Drawing trees: nodes
Drawing: saving figures
Drawing: The Canvas, Axes, and coordinates
The Canvas and Axes
The Coordinates
ToyTree objects
Selecting parts of a tree
Selecting subtrees with tip labels
Fuzzy tip label matching
Get node idx label from tip labels
Get TreeNode object from node idx label
Get tip labels from a node idx label
Modifying ToyTrees
Rooting trees
Drop tips
Ladderize
Rotate nodes
Resolve polytomy
Chaining functions and arguments
Attributes and functions
Saving/writing ToyTrees
TreeNode objects
Traversing TreeNodes
Adding features to TreeNodes
Modifying features of TreeNodes
Accessing features from ToyTrees
MultiTree objects
Parsing data into MultiTrees
Consensus trees
Access ToyTrees in the treelist
TreeGrid plot
Fixing the tip order
CloudTree plot
Styling tip labels in cloud trees
Example: Xiphophorus fishes
Tree grid styling
Fixed tip order
Custom tip order
CloudTree Styling
Save to disk as PDF
Styling individual trees: color edges differently
Reset tree styles
Xiphophorus consensus tree
Styling toytree drawings
Tip label styling
tip_labels
tip_labels_align
tip_labels_colors
tip_labels_style
Node labels styling
node_labels
node_labels_style
Node styling
node_sizes
node_colors
node_markers
node_style
node_hover
Layout
layout
todo
Aligned Edge Styling
edge_align_style
Styles
Scalebar
Parsing and drawing networks/admixture
Quick example
Styling admixture edges
Admixture timing
Admixture edge style
Label
Parsing SNAQ newick format
Works with re-rooting
Muliple admixture arguments
Parsing networks extended
Using built-in Tree Styles
Examples
Extend styling
Tree style overrides style applied to toytree objects
Cookbook gallery
1. ToyTree + barplot
2. Spacing tree vs. tip names
3. Node size/color from features
4. Variable edge colors and widths
5. Colored rectangles to highlight clades
6. Plot histograms associated with tip trait values (ridge plot)
7. Plot tree with matrix/heatmap
Method 1:
Method 2:
toytree
Docs
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Welcome to Toytree
Edit on GitHub
Welcome to Toytree
¶
Documentation
¶
The toytree ethos
Try it now
Installation
Conda install (recommended)
Pip install
Dependencies:
Quick Guide
Load and draw your first tree
Parsing Newick/Nexus data
Accessing tree data
Tree Classes
Drawing trees: basics
Drawing trees: styles
Drawing trees: nodes
Drawing: saving figures
Drawing: The Canvas, Axes, and coordinates
ToyTree objects
Selecting parts of a tree
Modifying ToyTrees
Chaining functions and arguments
Attributes and functions
Saving/writing ToyTrees
TreeNode objects
Traversing TreeNodes
Adding features to TreeNodes
Modifying features of TreeNodes
Accessing features from ToyTrees
MultiTree objects
Parsing data into MultiTrees
Consensus trees
Access ToyTrees in the treelist
TreeGrid plot
Fixing the tip order
CloudTree plot
Styling tip labels in cloud trees
Example: Xiphophorus fishes
Reset tree styles
Styling toytree drawings
Tip label styling
Node labels styling
Node styling
Layout
Aligned Edge Styling
Styles
Scalebar
Parsing and drawing networks/admixture
Quick example
Styling admixture edges
Parsing SNAQ newick format
Works with re-rooting
Muliple admixture arguments
Parsing networks extended
Using built-in Tree Styles
Examples
Extend styling
Tree style overrides style applied to toytree objects
Cookbook gallery
1. ToyTree + barplot
2. Spacing tree vs. tip names
3. Node size/color from features
4. Variable edge colors and widths
5. Colored rectangles to highlight clades
6. Plot histograms associated with tip trait values (ridge plot)
7. Plot tree with matrix/heatmap
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Downloads
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