Create a phylotree.js object from a Newick tree string, and display it in an SVG element using default settings and styles. Because the default tree view supports clickable nodes, it is necessary to include jQuery and Bootstrap. It is always necessary to include d3, and phylotree.js script and styles (unless overridden by the user).
Click on internal nodes to bring up menus that allow you to collapse/select them.
| { | |
| "analysis":{ | |
| "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", | |
| "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models", | |
| "contact":"spond@temple.edu", | |
| "info":"aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.", | |
| "requirements":"in-frame codon alignment and a phylogenetic tree", | |
| "version":"2.2" | |
| }, | |
| "branch attributes":{ |
In this example, we read in trees with branch lengths (FastTree2), based on haplotypes and counts reported in Lorenzo-Redondo et al, construct root-to-tip distances for time-stamped tips, and regress those on time to obtain crude evolutionary rate estimates.
The initial rooting of the tree is obtained by considering all time-point 0 sequences and selecting one that maximizes R2 (regardless of the slope). The user can perform arbitrary rerooting and see what the effect on the regression slope is.
Further, 1000 simulated perturbation of haplotype counts are considered for a given rooting: the estimated frequency of each haplotype (encoded in the tip name) is multiplied by a random number from [0.05-10] distributed uniformly. The proportion of perturbations with positive inferred regression slopes is shown on the chart.
This example uses tree.style_nodes to append colored rectangles to the node names
as annotations. It requires some less than pretty spacing calculations in the handler, but
both radial and rectangular layouts are supported.
This is in reference to veg/phylotree.js#64
This is an example which parses leaf names for meta information, including compartment, sample date, and copy number, and then annotates the tree accordingly. This example demonstrates how to use styling callbacks, e.g. style_nodes, and node_span.
The example also uses Bootstrap to allow interactive tree input via a model dialog.
More documentation forthcoming.
This is an example of using phylotree.js settings to create a tree which is suitable for a static display: no clickable nodes, nothing is selectable, fixed sizes in both dimensions.
The Newick string is loaded from a file using an asynchronous d3.text call.
This is accomplished via a call to d3_add_custom_menu which
adds a menu to a specific node with callback defining
node object and associated data).on handlers will be called on the menu item, not the node
object).node object and associated data)