Annotations and Pre-Order Traversal

Here is an example that demonstrating how developers might work with node annotations and employ a pre-order traversal of a tree. We choose to demonstrate these together, since it makes sense to use them together. - If you want do do something to once node, it's likely you might want to apply it to other nodes given some logical condition.

In this example, we develop a function to calculate the internal to external branch length ratio (IE ratio) of a tree - a measure of 'tippiness' with larger values corresponding to shorter external branch lengths. We then calculate the IE ratio of the subtree descending from each internal node of a starting tree, and annotate each node with this value.

For those coming to PhyloJS without a computer sciance background (like the writer of this tutorial), a pre-order traversal refers to the process of applying an operation to each node in a tree starting at the root and interating through each descending node. There are many other way of trversing a tree here.

We also present this example in TypeScript, since it's a good example of something that might be part of a larger application where type-safety is valuable. If you want to run the example in JavaScript, just delete the type annotations (eg. delete : number, : string, and so on after variable declarations). You can then use the JavaScript compiler if you go to the Codepen link.

One final thing to note is that the pre-order traversal in PhyloJS is a method on the Node class rather than the Tree class. Hence, when we do a pre-order traversal in the example code, we apply it as tree.root.applyPreOrder() to start at the root node. Why is it a method on Nodes rather than Trees? This is for flexibilty. - You might want to begin a pre-order traversal at an internal node, rather than for the tree as a whole.

See the Pen preorder-annotations by Leo Featherstone (@LeoFeatherstone) on CodePen.