D3 Examples - phylogram options for networkD3

phylogram options for networkD3

Very early and crude implementation of a couple different phylogram options for networkD3.

Code to reproduce is in this repo code.R, but I'll also paste here for visibility.

devtools::install_github("timelyportfolio/networkD3@feature/phylogram") library(networkD3) library(htmltools) html_print(tagList( tags$h1("phylogram") ,phyloNetwork("((A7RLM8:0.6571,(B3SBJ1:0.60468,B3SB47:1.39873):0.32942):0.0564,(C3YZV6:0.63868,(B7PB18:1.48452,((Q9I9H8:0.00775,A5WVJ8:0.00101):0.44669,(Q6GNU6:0.41674,((E1BR73:0.00015,E1BS49:0.00017):0.26544,((D2HE46:0.04922,(O14727:0.00017,A7E2A2:0.00089):0.05297):0.02176,((O88879:0.0026,(A2RRK8:0.00015,Q5DU30:0.00088):0.00017):0.02035,(Q8VI66:0.00344,(D3ZA56:0.09057,Q9EPV5:0.00017):0.00098):0.02368):0.0708):0.15795):0.09069):0.11555):0.43916):0.18436):0.11567):0") ,tags$h1("phylogram radial") ,phyloNetwork("((A7RLM8:0.6571,(B3SBJ1:0.60468,B3SB47:1.39873):0.32942):0.0564,(C3YZV6:0.63868,(B7PB18:1.48452,((Q9I9H8:0.00775,A5WVJ8:0.00101):0.44669,(Q6GNU6:0.41674,((E1BR73:0.00015,E1BS49:0.00017):0.26544,((D2HE46:0.04922,(O14727:0.00017,A7E2A2:0.00089):0.05297):0.02176,((O88879:0.0026,(A2RRK8:0.00015,Q5DU30:0.00088):0.00017):0.02035,(Q8VI66:0.00344,(D3ZA56:0.09057,Q9EPV5:0.00017):0.00098):0.02368):0.0708):0.15795):0.09069):0.11555):0.43916):0.18436):0.11567):0",type ="phylogram.radial") ,tags$h1("phylonator") ,phyloNetwork("((A7RLM8:0.6571,(B3SBJ1:0.60468,B3SB47:1.39873):0.32942):0.0564,(C3YZV6:0.63868,(B7PB18:1.48452,((Q9I9H8:0.00775,A5WVJ8:0.00101):0.44669,(Q6GNU6:0.41674,((E1BR73:0.00015,E1BS49:0.00017):0.26544,((D2HE46:0.04922,(O14727:0.00017,A7E2A2:0.00089):0.05297):0.02176,((O88879:0.0026,(A2RRK8:0.00015,Q5DU30:0.00088):0.00017):0.02035,(Q8VI66:0.00344,(D3ZA56:0.09057,Q9EPV5:0.00017):0.00098):0.02368):0.0708):0.15795):0.09069):0.11555):0.43916):0.18436):0.11567):0",type ="phylonator") ,tags$h1("phylonator no scaling") ,phyloNetwork("((A7RLM8:0.6571,(B3SBJ1:0.60468,B3SB47:1.39873):0.32942):0.0564,(C3YZV6:0.63868,(B7PB18:1.48452,((Q9I9H8:0.00775,A5WVJ8:0.00101):0.44669,(Q6GNU6:0.41674,((E1BR73:0.00015,E1BS49:0.00017):0.26544,((D2HE46:0.04922,(O14727:0.00017,A7E2A2:0.00089):0.05297):0.02176,((O88879:0.0026,(A2RRK8:0.00015,Q5DU30:0.00088):0.00017):0.02035,(Q8VI66:0.00344,(D3ZA56:0.09057,Q9EPV5:0.00017):0.00098):0.02368):0.0708):0.15795):0.09069):0.11555):0.43916):0.18436):0.11567):0",type ="phylonator", skipBranchLengthScaling = T) ))

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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8"/>
<script src="htmlwidgets.js"></script>
<script src="https://d3js.org/d3.v3.min.js"></script>
<script src="d3.phylonator.js"></script>
<script src="d3.phylogram.js"></script>
<script src="newick.js"></script>
<script src="phyloNetwork.js"></script>
​
</head>
<body>
<h1>phylogram</h1>
<div id="htmlwidget-8250" style="width:960px;height:500px;" class="phyloNetwork"></div>
<script type="application/json" data-for="htmlwidget-8250">{ "x": {
 "newick": "((A7RLM8:0.6571,(B3SBJ1:0.60468,B3SB47:1.39873):0.32942):0.0564,(C3YZV6:0.63868,(B7PB18:1.48452,((Q9I9H8:0.00775,A5WVJ8:0.00101):0.44669,(Q6GNU6:0.41674,((E1BR73:0.00015,E1BS49:0.00017):0.26544,((D2HE46:0.04922,(O14727:0.00017,A7E2A2:0.00089):0.05297):0.02176,((O88879:0.0026,(A2RRK8:0.00015,Q5DU30:0.00088):0.00017):0.02035,(Q8VI66:0.00344,(D3ZA56:0.09057,Q9EPV5:0.00017):0.00098):0.02368):0.0708):0.15795):0.09069):0.11555):0.43916):0.18436):0.11567):0",
"type": "phylogram",
"options": {
 "height": null,
"width": null 
} 
},"evals": [  ] }</script>
<h1>phylogram radial</h1>
<div id="htmlwidget-5231" style="width:960px;height:500px;" class="phyloNetwork"></div>
<script type="application/json" data-for="htmlwidget-5231">{ "x": {
 "newick": "((A7RLM8:0.6571,(B3SBJ1:0.60468,B3SB47:1.39873):0.32942):0.0564,(C3YZV6:0.63868,(B7PB18:1.48452,((Q9I9H8:0.00775,A5WVJ8:0.00101):0.44669,(Q6GNU6:0.41674,((E1BR73:0.00015,E1BS49:0.00017):0.26544,((D2HE46:0.04922,(O14727:0.00017,A7E2A2:0.00089):0.05297):0.02176,((O88879:0.0026,(A2RRK8:0.00015,Q5DU30:0.00088):0.00017):0.02035,(Q8VI66:0.00344,(D3ZA56:0.09057,Q9EPV5:0.00017):0.00098):0.02368):0.0708):0.15795):0.09069):0.11555):0.43916):0.18436):0.11567):0",
"type": "phylogram.radial",
"options": {
 "height": null,
"width": null 
} 
},"evals": [  ] }</script>
<h1>phylonator</h1>
<div id="htmlwidget-2860" style="width:960px;height:500px;" class="phyloNetwork"></div>
<script type="application/json" data-for="htmlwidget-2860">{ "x": {
 "newick": "((A7RLM8:0.6571,(B3SBJ1:0.60468,B3SB47:1.39873):0.32942):0.0564,(C3YZV6:0.63868,(B7PB18:1.48452,((Q9I9H8:0.00775,A5WVJ8:0.00101):0.44669,(Q6GNU6:0.41674,((E1BR73:0.00015,E1BS49:0.00017):0.26544,((D2HE46:0.04922,(O14727:0.00017,A7E2A2:0.00089):0.05297):0.02176,((O88879:0.0026,(A2RRK8:0.00015,Q5DU30:0.00088):0.00017):0.02035,(Q8VI66:0.00344,(D3ZA56:0.09057,Q9EPV5:0.00017):0.00098):0.02368):0.0708):0.15795):0.09069):0.11555):0.43916):0.18436):0.11567):0",
"type": "phylonator",
"options": {
 "height": null,
"width": null 
} 
},"evals": [  ] }</script>
<h1>phylonator no scaling</h1>
<div id="htmlwidget-7679" style="width:960px;height:500px;" class="phyloNetwork"></div>
<script type="application/json" data-for="htmlwidget-7679">{ "x": {
 "newick": "((A7RLM8:0.6571,(B3SBJ1:0.60468,B3SB47:1.39873):0.32942):0.0564,(C3YZV6:0.63868,(B7PB18:1.48452,((Q9I9H8:0.00775,A5WVJ8:0.00101):0.44669,(Q6GNU6:0.41674,((E1BR73:0.00015,E1BS49:0.00017):0.26544,((D2HE46:0.04922,(O14727:0.00017,A7E2A2:0.00089):0.05297):0.02176,((O88879:0.0026,(A2RRK8:0.00015,Q5DU30:0.00088):0.00017):0.02035,(Q8VI66:0.00344,(D3ZA56:0.09057,Q9EPV5:0.00017):0.00098):0.02368):0.0708):0.15795):0.09069):0.11555):0.43916):0.18436):0.11567):0",
"type": "phylonator",
"options": {
 "height": null,
"width": null,
"skipBranchLengthScaling": true 
} 
},"evals": [  ] }</script>
</body>
</html>
    