euphrasiologist / lwphylo

A lightweight, low level javascript library to plot phylogenies from a Newick file.

lwPhylo

A lightweight, low level javascript library to plot phylogenies from a Newick file. It uses no dependencies on any other package, but is designed to be given to the D3 library for visualisation.

Functionality

Newick trees can be parsed using the readTree() function. This object can then be wrapped in three main functions; rectangleLayout() to produce a "regular" phylogenetic tree, radialLayout() to produce a circular phylogeny, and unrooted() to produce an unrooted tree via the equal angle layout algorithm.

Examples

A quick tutorial is now available to see on Observable: https://observablehq.com/@euphrasiologist/lwphylo-tutorial
It goes over the three tree layout functions, and hopefully is all quite straightforward.

Stay tuned for examples in the browser.

Acknowledgements

Original implementation of tree layout schemes are found here: https://github.com/ArtPoon/ggfree.

Citation

Brown, M (2020). lwPhylo: A lightweight, low level javascript library to plot phylogenies from a Newick file, version 1.1.2

lwphylo's Issues

Align labels in radial and unrooted trees

Hello

Is there a way to align the labels for radial (and unrooted) trees so they look similar to the second example?
See the first example to see what they currently look like.
p.s. I'm using the data.radii object and x0 and y0 keys to align inside the svg

Mean$1 is not a function

Hello

First of all, thank you for building this library - it's such a great tool!

I'm having some issues though when I'm trying to use the rectangular layout. I'm getting the following error in the console:

ERROR TypeError: mean$1 is not a function
    at getHorizontal (lwphylo.js:613)

this is what I'm using to load it:

treeString = "(((t13:0.7790112703,(t1:0.5220431073,t20:0.202340699):0.4815443838):0.3861331961,((t2:0.6067991166,t14:0.8800587754):0.9964700027,((((((t3:0.4080314219,t18:0.3741820636):0.009094102541,(t17:0.4135466665,t7:0.5426334133):0.3566526775):0.2189731502,(t19:0.1208170669,t5:0.1075042752):0.09370149556):0.5956722216,t6:0.8589682591):0.805277324,t15:0.8797334728):0.4385470266,t8:0.2457124488):0.426782382):0.365341407):0.2617313648,((t11:0.5743931823,t16:0.5058572968):0.2053716865,((t10:0.3861640515,t12:0.6367075392):0.739508104,(t4:0.6088686911,t9:0.02072311775):0.856660692):0.5528816739):0.4895316709);";
const parsedTree = lwphylo.readTree(treeString);
const rectPhylo = lwphylo.rectangleLayout(parsedTree);

This only happens when I'm trying to use the rectangleLayout. It works fine with unrooted and radialLayout and it draws the content as expected.

Also, I'm using npm to install it, version 1.1.3. And in my application, I'm loading the lwphylo.js file. However, if I'm loading the lwphylo.min.js I get a different error
ERROR TypeError: o is not a function - but I assume it's referring to the same issue
Any ideas where the problem is?