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.
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.
In addition to linear/cladogram layouts, phylotree.js also implements a radial or cicrular layout. Invoking it is a matter of overriding the default setting.
It is important to set the radial option prior to binding Newick data to the tree, because at that time nodes are mapped to screen coordinates using current settings.
The layout mode can be changed after the tree has been rendered, but then it is
| /* 1. include a file to define the genetic code | |
| Note the use of base directory and path forming variables to make this analysis | |
| independent of directory placement | |
| */ | |
| /*incFileName = HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"chooseGeneticCode.def"; */ | |
| /* ExecuteCommands ("#include \""+incFileName+"\";"); */ | |
| /* #include "functions.txt";*/ /*functions.txt has the genetic code*/ |
| RequireVersion ("2.22"); | |
| VERBOSITY_LEVEL = 1; | |
| // namespace 'io' for interactive/datamonkey i/o functions | |
| LoadFunctionLibrary("lib2014/IOFunctions.bf"); | |
| // namespace 'utility' for convenience functions | |
| LoadFunctionLibrary("lib2014/UtilityFunctions.bf"); | |
| io.displayAnalysisBanner ({"info" : "EDEPS is a modification of DEPS to look for directional evolution along all or |
| /* | |
| THIS HyPhy BATCH LANGUAGE FILE IS PROVIDED AS AN EXAMPLE/TOOL FOR | |
| THE 2nd EDITION OF 'The Phylogenetic Handbook' | |
| Written by | |
| Sergei L Kosakovsky Pond (spond@ucsd.edu) | |
| Art FY Poon (apoon@ucsd.edu) | |
| Simon DW Frost (sdfrost@ucsd.edu) |
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.
Take the output (main .CSV) of FUBAR, and create a D3 plot over sites. Optionally, partition the plot into chunks of different color (e.g. gene/genome regions), and annotate them with horizontal bars.