exelixis
v0.0.4
Published
Interactive phylogenetic tree viewer for the web
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exelixis
Interactive and easy-to-use phylogenetic tree viewer for the web build on TnT.tree.
Getting Started
Install the module with: npm install exelixis
and build it with npm run prepublish
Have a look at the examples by starting the server with npm run sniper
var exe = require('exelixis');
var createTree = exe.createTree;
var updateTree = exe.updateTree;
Documentation
Default opts
Following default settings can be customized.
var opts = {
el : document.getElementById("yourDiv"),
tree : {
data : "(homo_sapiens:12,(mus_musculus:12,(danio_rerio:13,(pan_troglodytes:9,(taeniopygia_guttata:10,callithrix_jacchus:11):12):12):10);",
width : 500,
scale : false,
layoutInput : "vertical",
},
label : {
fontsize : 12,
usePics : false,
pics : {
pictureSource : pics,
pictureWidth : 30,
pictureHeight : 40,
},
},
nodes : {
toggle : false,
select: false,
size : 5,
fill : "grey",
stroke : "black",
selectedFill : "steelblue",
selectedSize : 4,
},
};
el
Change this to the div element you want to plot in your tree
tree
data
(string) takes as input your newick stringwidth
(int) is the width of your treeheight
(int) is the height of your labels (currently under work)scale
(boolean) scales the tree according to its branch lengths given in the newick stringlayoutInput
("vertical" or "radial") changes tree layout
label
fontsize
(int) sets the fontsizeusePics
(boolean) use pictures in the label
pics
pictureSource
(array) links to the png picture array you want to display. PicturesID has to be the same as the taxa names in the newick string.pictureWidth
(int) sets the width of the picturepictureHeight
(int) sets the picture height
nodes
toggle
(boolean) clicking nodes will toggle its subtreeselect
(boolean) change node to colorselectedFill
and sizeselectedSize
when clickedfill
(color) nodefill colorstroke
(color) nodestroke color
.createTree(opts)
Parameter: opts
a json containing settings
The 'createTree' method returns a phylogenetic tree.
How to use this method
var tree = createTree();
not using any opts creates a tree with default opts
.updateTree(tree,opts)
Parameter: tree
a tree object returned by createTree()
, opts
a json containing settings
The 'updateTree' method updates all opts properties which are given in opts
with animations on runtime and saves its opts.
All opts properties which are not mentioned stays the same as previously.
How to use this method
updateTree(tree, {tree:{data: "(Ape,(Bear,(Clown,Dolphin)))", width: 300, heigth: 20}});
Contributing
All contributions are welcome.
Support
If you have any problem or suggestion please open an issue here.
License
This software is licensed under the Apache 2 license, quoted below.
Copyright (c) 2015, David
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.