The scale method specifies if the tree should be rendered using the tree's branch lengths or not (true by default). Branch lengths are computed taking the branch_length property of the tree object. This is normally set automatically when your input is a newick formatted tree that includes branch lengths. If scale is set to false, branch lengths are ignored and the tree will display in an isometric layout (all paths from leaves to root having the same length).
Last active
August 29, 2015 14:22
-
-
Save emepyc/fcf93328bd73d849ac9d to your computer and use it in GitHub Desktop.
branch lengths
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <!DOCTYPE html> | |
| <meta charset="utf-8"> | |
| <head> | |
| <link rel="stylesheet" href="http://emepyc.github.io/tnt/v0/tnt.css" type="text/css" /> | |
| <script src="http://d3js.org/d3.v3.min.js"></script> | |
| <script src="http://emepyc.github.io/tnt/v0/tnt.min.js"></script> | |
| <script src="theme.js"></script> | |
| </head> | |
| <body> | |
| <div id="mytree"></div> | |
| <script> | |
| deploy (document.getElementById("mytree")); | |
| </script> | |
| </body> |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| function deploy (div) { | |
| // toggle for branch lengths | |
| var sel = d3.select(div) | |
| .append("select") | |
| .on ("change", function () { | |
| tree_vis.layout().scale(this.value === "use_branch_lengths"); | |
| tree_vis.update(); | |
| }) | |
| sel | |
| .append("option") | |
| .attr("value", "use_branch_lengths") | |
| .text("Use branch lengths"); | |
| sel | |
| .append("option") | |
| .attr("value", "ignore_branch_lengths") | |
| .text("Ignore branch lengths"); | |
| var tree_vis = tnt.tree() | |
| .data (tnt.tree.parse_newick(newick)) | |
| .layout (tnt.tree.layout.vertical() | |
| .width(650) | |
| ) | |
| .label (tnt.tree.label.text() | |
| .height(20) | |
| ); | |
| tree_vis(div); | |
| } | |
| // The tree to plot | |
| var newick = "(((((((((Homo_sapiens:0.0067,Pan_troglodytes:0.006667):0.00225,Pongo_abelii:0.018318):0.00717,Nomascus_leucogenys:0.025488):0.00717,(Macaca_mulatta:0.007853,Papio_hamadryas:0.007637):0.029618):0.021965,Callithrix_jacchus:0.066131):0.05759,Tarsius_syrichta:0.137823):0.011062,(Microcebus_murinus:0.092749,Otolemur_garnettii:0.129725):0.035463):0.015494,Tupaia_belangeri:0.186203):0.004937,(((((Mus_musculus:0.084509,Rattus_norvegicus:0.091589):0.197773,Dipodomys_ordii:0.211609):0.022992,Cavia_porcellus:0.225629):0.01015,Ictidomys_tridecemlineatus:0.148468):0.025746,(Oryctolagus_cuniculus:0.114227,Ochotona_princeps:0.201069):0.101463):0.015313);"; |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment