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Species Tree View
Raw
index.html
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8">
<title>Gene tree</title>
<script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.3/jquery.min.js"></script>
<link href="../libs/css/tipsy.css" rel="stylesheet" type="text/css" />
<!-- <link href="../libs/css/control_panel.css" rel="stylesheet" type="text/css" /> -->
<link href="../libs/css/treefam.css" rel="stylesheet" type="text/css" />
<link href="../libs/css/treefam_genomeview.css" rel="stylesheet" type="text/css" />
<script type="text/javascript" src="../libs/js/extern/colorbrewer.js"></script>
<script type="text/javascript" src="http://underscorejs.org/underscore-min.js"></script>
<script type="text/javascript" src="../libs/js/jquery/jquery.tipsy.js"></script>
<script type="text/javascript" src="species_tree.js"></script> -->
<!-- <script type="text/javascript" src="../libs/js/phylowidget/genome_plot.js"></script> -->
<script type="text/javascript" src="tree_functions_species_tree.js"></script>
<!-- <script type="text/javascript" src="../libs/js/extern/newick.js"></script> -->
<!-- <link href="http://www.ebi.ac.uk/web_guidelines/css/compliance/develop/ebi-visual.css" rel="stylesheet" type="text/css" /> -->
</head>
<body>
<div class="contentcontainer">
<div class="breadcrumbs">
<h4>Interactive tree display</h4>
Select Pathway: <select>
<option>Complement cascade</option>
<option>Adaptive Immune System</option>
<option>Translocation of GLUT4 to the Plasma Membrane</option>
</select>
Show identifier in tree (autocomplete): <form id="cse-search-box" action="http://google.com/cse" style="display: inline;">
<input type="hidden" name="cx" value="Search for identifier" />
<input type="text" name="q" size="31" />
<input type="submit" name="sa" value="Search" />
</form><br>
<!-- <a href="#" onclick="updateAllGenes();return false">Update</a> -->
<a href="#" onclick="showDomains();return false">Show domains</a>/
<a href="#" onclick="showBoxes();return false">Show presence/absence</a>
<a href="#" onclick="showMutationSite();return false">Show mutation site</a>
</div>
<div id="body">
<div id="header"></div>
<div id="main">
<div class="breadcrumbs">
Legend: <img src="../data/icons/Yes_check.svg.png" width="15" height="15" alt="Inner nodes" name="Inner nodes"> 1-1 ortholog,
<img src="../data/icons/question-mark.gif" width="15" height="15" alt="Inner nodes" name="Inner nodes"> 1-n ortholog,
<img src="../data/icons/No_sign.svg.png" width="15" height="15" alt="Inner nodes" name="Inner nodes"> no homolog
</div>
<div id="tree" class="tree_panel" >TreeFam Species Tree (109 species, source NCBI)</div>
<!--<div id="content-2">
<div class="gene_panel"></div>
<div id="annotation_panel" class="annotation_panel"></div>
</div>-->
</div>
<div id="footer"></div>
</div>
</div>
<div id="topHeader">
</div>
<div id="my_custom_menu" style="border=1; display:none; background-color:#white; color:#2D006B; text-decoration:none;border:1px solid #12127D;">
collapse nodes<br>
highlight stuff
</div>
<div id="my_domain_menu" style="border=1; display:none; background-color:white; color:#2D006B; text-decoration:none;border:1px solid #12127D;">
</div>
<div class="middle-display" style="width:100%">
</div>
<script type="text/javascript">
var speciesTree;
var gene_data;
jQuery(document).ready(function() {
// set the control panel
//jQuery('#menu').tabify();
//var json_tree = "../data/trees/TF300032.json";
//var no_genes = 648 * 2;
//var json_tree = "../data/trees/TF101003.json";
//var no_genes = 108 * 2;
//var json_tree = "../data/trees/species_tree_json_cleared_names.json";
//var no_genes = 109 * 2;
var json_tree = "polymerase.json";
var no_genes = 11 * 2;
//var json_tree = "../test/toy_species.json";
//var no_genes = 4 * 2;
var gene_tree = "../data/trees/TF105041.json";
gene_data = "poly.json";
//var json_tree = "../data/trees/TF105041.json";
//var no_genes = 48 * 2;
//var json_tree = "";
var alignment_length = 54 * 2;
var image_path = "../data/images/species_files";
//var highlight_gene = "ENSBTAP00000001311";
var highlight_gene = "";
//var newick_tree = "../data/trees/newick_tree.nh";
var newick_tree = "";
var load_from_variable;
var json_tree_string;
console.log("we are here");
speciesTree = speciesTree();
speciesTree({no_genes : no_genes,
alignment_length: alignment_length,
json_tree: json_tree,
image_path: image_path,
newick_tree : newick_tree,
highlight_gene : highlight_gene,
json_tree_string : json_tree_string,
load_from_variable : load_from_variable,
gene_tree : gene_tree,
gene_data : gene_data,
w : 9000,
//h : 2400,
leaf_space : 8800
});
//speciesTree.update_genes_now();
//setInterval(function() {
// gene_data = "../test/toy_genes2.json";
// console.log("updaaaate");
//gT.updateGenes({gene_data : gene_data});
//}, 3000);
// draw annotation
//var family_patterns = "../data/genome_files/treefam_family_patterns.json";
//var gA = genomeAnnotation();
//gA({no_genes : no_genes,
// alignment_length: alignment_length,
// family_patterns: family_patterns,
// image_path: image_path,
// newick_tree : newick_tree,
// highlight_gene : highlight_gene,
// json_tree_string : json_tree_string,
// load_from_variable : load_from_variable,
// gene_tree : gene_tree,
// w : 800,
// leaf_space : 0
// });
//gT.drawSequences();
// draw sequences ....
//,highlight_gene : highlight_gene});
//gB(document.getElementById("genomeBrowser"));
//draw_d3_tree({no_genes : no_genes,
// alignment_length: alignment_length,
// json_tree: json_tree,
// image_path: image_path});
//,highlight_gene : highlight_gene});
jQuery("#show_svg_code").click(function() { show_svg_code(); });
jQuery("#save_as_svg").click(function() { submit_download_form("svg"); });
jQuery("#save_as_pdf").click(function() { submit_download_form("pdf"); });
jQuery("#save_as_png").click(function() { submit_download_form("png"); });
});
function updateAllGenes(){
//setInterval(function() {
gene_data = "../test/toy_genes2.json";
console.log("updaaaate genes with ");
speciesTree.updateGenes({gene_data : gene_data});
return 1;
// }, 3000);
}
function showDomains(){
speciesTree.updateGenes({gene_data : gene_data, presentation_mode : "gene_boxes"});
return 1;
}
function showBoxes(){
speciesTree.updateGenes({gene_data : gene_data, presentation_mode : "prabsence_boxes"});
return 1;
}
</script>
</body>
</html>
Raw
poly.json
{
"POLA1" : [
{
"species_name" : "Drosophila_melanogaster",
"domains" : [
{
"evalue" : "0.00000000016",
"name" : "DNA_pol_alpha_N",
"domain_start" : "24",
"id" : "PF12254.3",
"domain_stop" : "85"
},
{
"evalue" : "6.6e-37",
"name" : "zf-DNA_Pol",
"domain_start" : "1281",
"id" : "PF08996.5",
"domain_stop" : "1459"
},
{
"evalue" : "1.9e-26",
"name" : "DNA_pol_B_exo1",
"domain_start" : "386",
"id" : "PF03104.14",
"domain_stop" : "729"
},
{
"evalue" : "6e-117",
"name" : "DNA_pol_B",
"domain_start" : "805",
"id" : "PF00136.16",
"domain_stop" : "1256"
}
],
"seq_length" : 1488,
"homology_type" : "ortholog_one2one",
"id" : "FBpp0083514"
},
{
"species_name" : "Loxodonta_africana",
"domains" : [
{
"evalue" : "2.3e-16",
"name" : "DNA_pol_alpha_N",
"domain_start" : "41",
"id" : "PF12254.3",
"domain_stop" : "103"
},
{
"evalue" : "6.2e-55",
"name" : "zf-DNA_Pol",
"domain_start" : "1270",
"id" : "PF08996.5",
"domain_stop" : "1460"
},
{
"evalue" : "1.7e-56",
"name" : "DNA_pol_B_exo1",
"domain_start" : "378",
"id" : "PF03104.14",
"domain_stop" : "716"
},
{
"evalue" : "1.2e-125",
"name" : "DNA_pol_B",
"domain_start" : "789",
"id" : "PF00136.16",
"domain_stop" : "1246"
}
],
"seq_length" : 1467,
"homology_type" : "ortholog_one2one",
"id" : "ENSLAFP00000001484"
},
{
"species_name" : "Pristionchus_pacificus",
"domains" : [
{
"evalue" : "1.3e-16",
"name" : "DNA_pol_B_exo1",
"domain_start" : "180",
"id" : "PF03104.14",
"domain_stop" : "528"
},
{
"evalue" : "1.1e-79",
"name" : "DNA_pol_B",
"domain_start" : "602",
"id" : "PF00136.16",
"domain_stop" : "951"
}
],
"seq_length" : null,
"homology_type" : "ortholog_one2one",
"id" : "PPA04993"
},
{
"species_name" : "Drosophila_ananassae",
"domains" : [
{
"evalue" : "0.00000000000037",
"name" : "DNA_pol_alpha_N",
"domain_start" : "24",
"id" : "PF12254.3",
"domain_stop" : "85"
},
{
"evalue" : "2e-38",
"name" : "zf-DNA_Pol",
"domain_start" : "1275",
"id" : "PF08996.5",
"domain_stop" : "1453"
},
{
"evalue" : "4.7e-29",
"name" : "DNA_pol_B_exo1",
"domain_start" : "382",
"id" : "PF03104.14",
"domain_stop" : "725"
},
{
"evalue" : "3.2e-117",
"name" : "DNA_pol_B",
"domain_start" : "801",
"id" : "PF00136.16",
"domain_stop" : "1249"
}
],
"seq_length" : 1481,
"homology_type" : "ortholog_one2one",
"id" : "FBpp0121000"
},
{
"species_name" : "Choloepus_hoffmanni",
"domains" : [
{
"evalue" : "2.3e-36",
"name" : "DNA_pol_B",
"domain_start" : "974",
"id" : "PF00136.16",
"domain_stop" : "1129"
}
],
"seq_length" : 1453,
"homology_type" : "ortholog_one2one",
"id" : "ENSCHOP00000005408"
},
{
"species_name" : "Drosophila_willistoni",
"domains" : [
{
"evalue" : "0.0000000000025",
"name" : "DNA_pol_alpha_N",
"domain_start" : "25",
"id" : "PF12254.3",
"domain_stop" : "87"
},
{
"evalue" : "3.6e-36",
"name" : "zf-DNA_Pol",
"domain_start" : "1260",
"id" : "PF08996.5",
"domain_stop" : "1438"
},
{
"evalue" : "3.7e-29",
"name" : "DNA_pol_B_exo1",
"domain_start" : "366",
"id" : "PF03104.14",
"domain_stop" : "706"
},
{
"evalue" : "8.7e-114",
"name" : "DNA_pol_B",
"domain_start" : "783",
"id" : "PF00136.16",
"domain_stop" : "1236"
}
],
"seq_length" : 1468,
"homology_type" : "ortholog_one2one",
"id" : "FBpp0241217"
},
{
"species_name" : "Strongyloides_ratti",
"domains" : [
{
"evalue" : "4.1e-24",
"name" : "zf-DNA_Pol",
"domain_start" : "1028",
"id" : "PF08996.5",
"domain_stop" : "1216"
},
{
"evalue" : "1.1e-24",
"name" : "DNA_pol_B_exo1",
"domain_start" : "186",
"id" : "PF03104.14",
"domain_stop" : "488"
},
{
"evalue" : "3.6e-106",
"name" : "DNA_pol_B",
"domain_start" : "563",
"id" : "PF00136.16",
"domain_stop" : "1002"
}
],
"seq_length" : null,
"homology_type" : "ortholog_one2one",
"id" : "g7538"
},
{
"species_name" : "Oryzias_latipes",
"domains" : [
{
"evalue" : "1.3e-17",
"name" : "DNA_pol_alpha_N",
"domain_start" : "44",
"id" : "PF12254.3",
"domain_stop" : "106"
},
{
"evalue" : "8.1e-53",
"name" : "zf-DNA_Pol",
"domain_start" : "1273",
"id" : "PF08996.5",
"domain_stop" : "1465"
},
{
"evalue" : "1.1e-46",
"name" : "DNA_pol_B_exo1",
"domain_start" : "382",
"id" : "PF03104.14",
"domain_stop" : "720"
},
{
"evalue" : "6.7e-124",
"name" : "DNA_pol_B",
"domain_start" : "793",
"id" : "PF00136.16",
"domain_stop" : "1238"
}
],
"seq_length" : 1472,
"homology_type" : "ortholog_one2one",
"id" : "ENSORLP00000009391"
},
{
"species_name" : "Atta_cephalotes",
"domains" : [
{
"evalue" : "9.8e-18",
"name" : "DNA_pol_alpha_N",
"domain_start" : "26",
"id" : "PF12254.3",
"domain_stop" : "88"
},
{
"evalue" : "2e-28",
"name" : "zf-DNA_Pol",
"domain_start" : "1243",
"id" : "PF08996.5",
"domain_stop" : "1421"
},
{
"evalue" : "4.6e-24",
"name" : "DNA_pol_B_exo1",
"domain_start" : "382",
"id" : "PF03104.14",
"domain_stop" : "710"
},
{
"evalue" : "1.9e-113",
"name" : "DNA_pol_B",
"domain_start" : "786",
"id" : "PF00136.16",
"domain_stop" : "1209"
}
],
"seq_length" : 1455,
"homology_type" : "ortholog_one2one",
"id" : "ACEP_00004003-PA"
},
{
"species_name" : "Vicugna_pacos",
"domains" : [
{
"evalue" : "7.2e-17",
"name" : "DNA_pol_alpha_N",
"domain_start" : "40",
"id" : "PF12254.3",
"domain_stop" : "102"
},
{
"evalue" : "1.6e-55",
"name" : "zf-DNA_Pol",
"domain_start" : "1269",
"id" : "PF08996.5",
"domain_stop" : "1459"
},
{
"evalue" : "2.4e-55",
"name" : "DNA_pol_B_exo1",
"domain_start" : "376",
"id" : "PF03104.14",
"domain_stop" : "715"
},
{
"evalue" : "9.8e-125",
"name" : "DNA_pol_B",
"domain_start" : "788",
"id" : "PF00136.16",
"domain_stop" : "1245"
}
],
"seq_length" : 1466,
"homology_type" : "ortholog_one2one",
"id" : "ENSVPAP00000007749"
},
{
"species_name" : "Lottia_gigantea",
"domains" : [
{
"evalue" : "3.7e-17",
"name" : "DNA_pol_alpha_N",
"domain_start" : "21",
"id" : "PF12254.3",
"domain_stop" : "83"
},
{
"evalue" : "1.8e-45",
"name" : "zf-DNA_Pol",
"domain_start" : "1229",
"id" : "PF08996.5",
"domain_stop" : "1415"
},
{
"evalue" : "4.2e-41",
"name" : "DNA_pol_B_exo1",
"domain_start" : "333",
"id" : "PF03104.14",
"domain_stop" : "679"
},
{
"evalue" : "6.8e-124",
"name" : "DNA_pol_B",
"domain_start" : "752",
"id" : "PF00136.16",
"domain_stop" : "1207"
}
],
"seq_length" : null,
"homology_type" : "ortholog_one2one",
"id" : "109334"
},
{
"species_name" : "Felis_catus",
"domains" : [
{
"evalue" : "7.1e-17",
"name" : "DNA_pol_alpha_N",
"domain_start" : "26",
"id" : "PF12254.3",
"domain_stop" : "88"
},
{
"evalue" : "1.3e-54",
"name" : "zf-DNA_Pol",
"domain_start" : "1255",
"id" : "PF08996.5",
"domain_stop" : "1446"
},
{
"evalue" : "1.2e-40",
"name" : "DNA_pol_B_exo1",
"domain_start" : "451",
"id" : "PF03104.14",
"domain_stop" : "701"
},
{
"evalue" : "1.1e-41",
"name" : "DNA_pol_B",
"domain_start" : "974",
"id" : "PF00136.16",
"domain_stop" : "1233"
}
],
"seq_length" : 1453,
"homology_type" : "ortholog_one2one",
"id" : "ENSFCAP00000001978"
},
{
"species_name" : "Drosophila_yakuba",
"domains" : [
{
"evalue" : "0.0000000000087",
"name" : "DNA_pol_alpha_N",
"domain_start" : "24",
"id" : "PF12254.3",
"domain_stop" : "85"
},
{
"evalue" : "1.1e-36",
"name" : "zf-DNA_Pol",
"domain_start" : "1285",
"id" : "PF08996.5",
"domain_stop" : "1463"
},
{
"evalue" : "6.5e-27",
"name" : "DNA_pol_B_exo1",
"domain_start" : "389",
"id" : "PF03104.14",
"domain_stop" : "732"
},
{
"evalue" : "1.7e-115",
"name" : "DNA_pol_B",
"domain_start" : "808",
"id" : "PF00136.16",
"domain_stop" : "1260"
}
],
"seq_length" : 1492,
"homology_type" : "ortholog_one2one",
"id" : "FBpp0269977"
},
{
"species_name" : "Equus_caballus",
"domains" : [
{
"evalue" : "4.7e-18",
"name" : "zf-DNA_Pol",
"domain_start" : "1156",
"id" : "PF08996.5",
"domain_stop" : "1235"
},
{
"evalue" : "4.3e-44",
"name" : "DNA_pol_B_exo1",
"domain_start" : "263",
"id" : "PF03104.14",
"domain_stop" : "602"
},
{
"evalue" : "8.6e-127",
"name" : "DNA_pol_B",
"domain_start" : "675",
"id" : "PF00136.16",
"domain_stop" : "1132"
}
],
"seq_length" : 1235,
"homology_type" : "ortholog_one2one",
"id" : "ENSECAP00000011308"
},
{
"species_name" : "Sarcophilus_harrisii",
"domains" : [
{
"evalue" : "4.1e-16",
"name" : "DNA_pol_alpha_N",
"domain_start" : "36",
"id" : "PF12254.3",
"domain_stop" : "97"
},
{
"evalue" : "7e-54",
"name" : "zf-DNA_Pol",
"domain_start" : "1292",
"id" : "PF08996.5",
"domain_stop" : "1484"
},
{
"evalue" : "3.6e-54",
"name" : "DNA_pol_B_exo1",
"domain_start" : "398",
"id" : "PF03104.14",
"domain_stop" : "737"
},
{
"evalue" : "6.6e-126",
"name" : "DNA_pol_B",
"domain_start" : "810",
"id" : "PF00136.16",
"domain_stop" : "1267"
}
],
"seq_length" : 1497,
"homology_type" : "ortholog_one2one",
"id" : "ENSSHAP00000015511"
},
{
"species_name" : "Sus_scrofa",
"domains" : [
{
"evalue" : "8e-115",
"name" : "DNA_pol_B",
"domain_start" : "95",
"id" : "PF00136.16",
"domain_stop" : "493"
}
],
"seq_length" : 497,
"homology_type" : "ortholog_one2one",
"id" : "ENSSSCP00000023879"
},
{
"species_name" : "Caenorhabditis_briggsae",
"domains" : [],
"seq_length" : "N/A",
"homology_type" : "no"
},
{
"species_name" : "Trichoplax_adhaerens",
"domains" : [
{
"evalue" : "3e-42",
"name" : "zf-DNA_Pol",
"domain_start" : "1023",
"id" : "PF08996.5",
"domain_stop" : "1193"
},
{
"evalue" : "3.9e-40",
"name" : "DNA_pol_B_exo1",
"domain_start" : "166",
"id" : "PF03104.14",
"domain_stop" : "484"
},
{
"evalue" : "6.3e-114",
"name" : "DNA_pol_B",
"domain_start" : "545",
"id" : "PF00136.16",
"domain_stop" : "1001"
}
],
"seq_length" : 1203,
"homology_type" : "ortholog_one2one",
"id" : "TriadP49541"
},
{
"species_name" : "Pteropus_vampyrus",
"domains" : [
{
"evalue" : "5.9e-17",
"name" : "DNA_pol_alpha_N",
"domain_start" : "38",
"id" : "PF12254.3",
"domain_stop" : "100"
},
{
"evalue" : "1.4e-54",
"name" : "zf-DNA_Pol",
"domain_start" : "1263",
"id" : "PF08996.5",
"domain_stop" : "1454"
},
{
"evalue" : "3.9e-54",
"name" : "DNA_pol_B_exo1",
"domain_start" : "372",
"id" : "PF03104.14",
"domain_stop" : "710"
},
{
"evalue" : "7.6e-110",
"name" : "DNA_pol_B",
"domain_start" : "783",
"id" : "PF00136.16",
"domain_stop" : "1235"
}
],
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"domains" : [
{
"evalue" : "1.2e-18",
"name" : "DEAD",
"domain_start" : "303",
"id" : "PF00270.24",
"domain_stop" : "475"
},
{
"evalue" : "2.8e-63",
"name" : "DNA_pol_A",
"domain_start" : "2307",
"id" : "PF00476.15",
"domain_stop" : "2570"
},
{
"evalue" : "0.0000000091",
"name" : "Helicase_C",
"domain_start" : "616",
"id" : "PF00271.26",
"domain_stop" : "688"
}
],
"seq_length" : 2576,
"homology_type" : "ortholog_one2one",
"id" : "ENSDARP00000065555"
},
{
"species_name" : "Arabidopsis_thaliana",
"domains" : [
{
"evalue" : "0.0000000000000033",
"name" : "DEAD",
"domain_start" : "526",
"id" : "PF00270.24",
"domain_stop" : "701"
},
{
"evalue" : "1.4e-72",
"name" : "DNA_pol_A",
"domain_start" : "1739",
"id" : "PF00476.15",
"domain_stop" : "2147"
},
{
"evalue" : "0.0000000037",
"name" : "Helicase_C",
"domain_start" : "836",
"id" : "PF00271.26",
"domain_stop" : "908"
}
],
"seq_length" : 2154,
"homology_type" : "ortholog_one2many",
"id" : "AT4G32700.2"
},
{
"species_name" : "Ornithorhynchus_anatinus",
"domains" : [
{
"evalue" : "5.9e-19",
"name" : "DEAD",
"domain_start" : "69",
"id" : "PF00270.24",
"domain_stop" : "234"
},
{
"evalue" : "0.000000000038",
"name" : "Helicase_C",
"domain_start" : "376",
"id" : "PF00271.26",
"domain_stop" : "448"
}
],
"seq_length" : 1886,
"homology_type" : "ortholog_one2one",
"id" : "ENSOANP00000007028"
},
{
"species_name" : "Ciona_intestinalis",
"domains" : [
{
"evalue" : "1.1e-81",
"name" : "DNA_pol_B_exo1",
"domain_start" : "92",
"id" : "PF03104.14",
"domain_stop" : "437"
},
{
"evalue" : "1.5e-142",
"name" : "DNA_pol_B",
"domain_start" : "510",
"id" : "PF00136.16",
"domain_stop" : "940"
},
{
"evalue" : "3.7e-24",
"name" : "zf-C4pol",
"domain_start" : "972",
"id" : "PF14260.1",
"domain_stop" : "1043"
}
],
"seq_length" : 1064,
"homology_type" : "ortholog_one2one",
"id" : "ENSCINP00000005791"
},
{
"species_name" : "Otolemur_garnettii",
"domains" : [
{
"evalue" : "8.1e-19",
"name" : "DEAD",
"domain_start" : "107",
"id" : "PF00270.24",
"domain_stop" : "273"
},
{
"evalue" : "0.000001",
"name" : "HHH_5",
"domain_start" : "791",
"id" : "PF14520.1",
"domain_stop" : "887"
},
{
"evalue" : "4.1e-61",
"name" : "DNA_pol_A",
"domain_start" : "2286",
"id" : "PF00476.15",
"domain_stop" : "2557"
},
{
"evalue" : "0.00000000001",
"name" : "Helicase_C",
"domain_start" : "416",
"id" : "PF00271.26",
"domain_stop" : "488"
}
],
"seq_length" : 2563,
"homology_type" : "ortholog_one2one",
"id" : "ENSOGAP00000014151"
},
{
"species_name" : "Gallus_gallus",
"domains" : [
{
"evalue" : "2.3e-19",
"name" : "DEAD",
"domain_start" : "61",
"id" : "PF00270.24",
"domain_stop" : "234"
},
{
"evalue" : "0.00000016",
"name" : "HHH_5",
"domain_start" : "755",
"id" : "PF14520.1",
"domain_stop" : "850"
},
{
"evalue" : "0.000000000032",
"name" : "Helicase_C",
"domain_start" : "378",
"id" : "PF00271.26",
"domain_stop" : "450"
}
],
"seq_length" : 904,
"homology_type" : "ortholog_one2one",
"id" : "ENSGALP00000024026"
},
{
"species_name" : "Meleagris_gallopavo",
"domains" : [
{
"evalue" : "6.8e-19",
"name" : "DEAD",
"domain_start" : "36",
"id" : "PF00270.24",
"domain_stop" : "209"
},
{
"evalue" : "0.00000043",
"name" : "HHH_5",
"domain_start" : "728",
"id" : "PF14520.1",
"domain_stop" : "823"
},
{
"evalue" : "0.00000000011",
"name" : "Helicase_C",
"domain_start" : "352",
"id" : "PF00271.26",
"domain_stop" : "424"
}
],
"seq_length" : 2012,
"homology_type" : "ortholog_one2one",
"id" : "ENSMGAP00000015086"
},
{
"species_name" : "Proterospongia_sp",
"domains" : [],
"seq_length" : "N/A",
"homology_type" : "no"
},
{
"species_name" : "Macaca_mulatta",
"domains" : [
{
"evalue" : "1.2e-87",
"name" : "DNA_pol_B_exo1",
"domain_start" : "131",
"id" : "PF03104.14",
"domain_stop" : "477"
},
{
"evalue" : "1.5e-130",
"name" : "DNA_pol_B",
"domain_start" : "617",
"id" : "PF00136.16",
"domain_stop" : "1003"
},
{
"evalue" : "0.0000000000000049",
"name" : "zf-C4pol",
"domain_start" : "1037",
"id" : "PF14260.1",
"domain_stop" : "1097"
}
],
"seq_length" : 1097,
"homology_type" : "ortholog_one2one",
"id" : "ENSMMUP00000028348"
},
{
"species_name" : "Oryctolagus_cuniculus",
"domains" : [
{
"evalue" : "3.1e-63",
"name" : "DNA_pol_A",
"domain_start" : "1773",
"id" : "PF00476.15",
"domain_stop" : "2046"
}
],
"seq_length" : 2052,
"homology_type" : "ortholog_one2one",
"id" : "ENSOCUP00000006990"
},
{
"species_name" : "Anolis_carolinensis",
"domains" : [
{
"evalue" : "2.7e-20",
"name" : "DEAD",
"domain_start" : "42",
"id" : "PF00270.24",
"domain_stop" : "210"
},
{
"evalue" : "1.4e-59",
"name" : "DNA_pol_A",
"domain_start" : "1994",
"id" : "PF00476.15",
"domain_stop" : "2266"
},
{
"evalue" : "0.0000000000049",
"name" : "Helicase_C",
"domain_start" : "351",
"id" : "PF00271.26",
"domain_stop" : "425"
}
],
"seq_length" : 2272,
"homology_type" : "ortholog_one2one",
"id" : "ENSACAP00000011328"
},
{
"species_name" : "Petromyzon_marinus",
"domains" : [
{
"evalue" : "1.3e-88",
"name" : "DNA_pol_B_exo1",
"domain_start" : "136",
"id" : "PF03104.14",
"domain_stop" : "489"
},
{
"evalue" : "6.2e-143",
"name" : "DNA_pol_B",
"domain_start" : "562",
"id" : "PF00136.16",
"domain_stop" : "997"
},
{
"evalue" : "0.000000000000043",
"name" : "zf-C4pol",
"domain_start" : "1027",
"id" : "PF14260.1",
"domain_stop" : "1089"
}
],
"seq_length" : 1089,
"homology_type" : "ortholog_one2one",
"id" : "ENSPMAP00000002259"
},
{
"species_name" : "Echinops_telfairi",
"domains" : [
{
"evalue" : "2.1e-17",
"name" : "DEAD",
"domain_start" : "105",
"id" : "PF00270.24",
"domain_stop" : "270"
},
{
"evalue" : "3.4e-44",
"name" : "DNA_pol_A",
"domain_start" : "2284",
"id" : "PF00476.15",
"domain_stop" : "2521"
},
{
"evalue" : "0.000000056",
"name" : "Helicase_C",
"domain_start" : "413",
"id" : "PF00271.26",
"domain_stop" : "484"
}
],
"seq_length" : 2523,
"homology_type" : "ortholog_one2one",
"id" : "ENSETEP00000002431"
}
]
}
Raw
polymerase.json
{
"name" : "",
"children" : [
{
"name" : "Opisthokonta",
"children" : [
{
"name" : "Bilateria",
"children" : [
{
"name" : "Chordata",
"children" : [
{
"name" : "Euteleostomi",
"children" : [
{
"name" : "Tetrapoda",
"children" : [
{
"name" : "Amniota",
"children" : [
{
"name" : "Euarchontoglires",
"children" : [
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Homo_sapiens",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Homo_sapiens"
},
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Mus_musculus",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Mus_musculus"
}
],
"bootstrap" : "NaN",
"taxon" : "Euarchontoglires",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
},
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Gallus_gallus",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Gallus_gallus"
}
],
"bootstrap" : "NaN",
"taxon" : "Amniota",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
},
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Xenopus_tropicalis",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Xenopus_tropicalis"
}
],
"bootstrap" : "NaN",
"taxon" : "Tetrapoda",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
},
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Danio_rerio",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Danio_rerio"
}
],
"bootstrap" : "NaN",
"taxon" : "Euteleostomi",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
},
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Ciona_intestinalis",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Ciona_intestinalis"
}
],
"bootstrap" : "NaN",
"taxon" : "Chordata",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
},
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Drosophila_melanogaster",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Drosophila_melanogaster"
}
],
"bootstrap" : "NaN",
"taxon" : "Bilateria",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
},
{
"name" : "Ascomycota",
"children" : [
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Saccharomyces_cerevisiae",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Saccharomyces_cerevisiae"
},
{
"length" : "5",
"common_name" : "NaN",
"duplication" : "N",
"name" : "Schizosaccharomyces_pombe",
"type" : "node",
"bootstrap" : "NaN",
"taxon" : "Schizosaccharomyces_pombe"
}
],
"bootstrap" : "NaN",
"taxon" : "Ascomycota",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
}
],
"bootstrap" : "NaN",
"taxon" : "Opisthokonta",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
}
],
"bootstrap" : "NaN",
"taxon" : "",
"common_name" : "NaN",
"length" : "5",
"duplication" : "N",
"type" : "node"
}
Raw
species_tree.js
var speciesTree = function () {
var image_path;
var root;
var vis;
var gene_data;
var vis_annotation;
var animGroup;
var domain_txt;
var circle_size = 3;
var offset = 50;
var duplication_circle_size = 15;
var sequence_rect_width = 12;
var presentation_mode = "";
var leaf_group_x = 198;
var highlight_gene;
var sequence_start_y = 200;
var domain_div;
var link_type = "elbow";
var load_from_variable;
var json_tree_string;
// Defined showable taxa
var show_taxa = new Object();
show_taxa['Metazoa'] = 1;
show_taxa['Bilateria'] = 1;
show_taxa['Mammalia'] = 1;
show_taxa['Dipteria'] = 1;
show_taxa['Primates'] = 1;
show_taxa['Arabidopsis_thaliana'] = 1;
var domain_colors = new Object();
domain_colors[0] = "domain_gradient";
domain_colors[1] = "domain_gradient2";
domain_colors[2] = "domain_gradient3";
domain_colors[3] = "domain_gradient4";
domain_colors[3] = "domain_gradient5";
var model_organisms = new Object(); // or just {}
model_organisms['Homo_sapiens'] = "red";
model_organisms['Mus_musculus'] = "blue";
model_organisms['Xenopus_tropicalis'] = "blue";
model_organisms['Gallus_gallus'] = "blue";
model_organisms['Drosophila_melanogaster'] = "blue";
model_organisms['Arabidopsis_thaliana'] = "blue";
model_organisms['Caenorhabditis_elegans'] = "blue";
//var no_internal_nodes;
var w, h, i, duration, root, leaf_space;
var margin, width, height;
var tree;
var domainScale = d3.scale.linear().domain([20,4000]).range([1, 250]);
// Returned closure
var SpeciesTree = function (args) {
//function draw_d3_tree(args){
json_tree = args.json_tree;
newick_tree = args.newick_tree;
no_genes = args.no_genes;
highlight_gene = args.highlight_gene;
load_from_variable = args.load_from_variable;
json_tree_string = args.json_tree_string;
presentation_mode = args.presentation_mode || presentation_mode;
gene_tree = args.gene_tree;
gene_data = args.gene_data;
h = args.h || no_genes * 10;
w = args.w || 1800;
var leaf_space = args.leaf_space || "600";
image_path = args.image_path;
var id_label;
console.log("value of w is "+w);
h = h, i = 0, duration = 100, root;
//var leaf_space = "600";
margin = {top: 0, right: 0, bottom: 0, left: 0},
width = 960 - margin.left - margin.right,
height = 500 - margin.top - margin.bottom;
var diagonal = d3.svg.diagonal() .projection(function(d) { return [d.y, d.x]; });
tree = d3.layout.cluster()
.separation(function(a, b) { return a.parent === b.parent ? 4 : 4; })
.size([h, w -leaf_space]);
vis = d3.select("#tree")
.append("svg:svg")
.attr("width", w)
.attr("height", h + 100);
//vis_annotation = d3.select("#annotation_panel")
// .append("svg:svg")
// .attr("width", w)
// .attr("height", h);
//vis.attr("transform", "translate(40,40)")
//.attr("pointer-events", "all")
// .append('svg:g')
//.attr("transform", "translate(40,0)")
//.attr("pointer-events", "all")
//.call(d3.behavior.zoom().on("zoom", redraw))
//.append('svg:g')
// ;
// Add the clipping path
vis.append("svg:clipPath").attr("id", "clipper")
.append("svg:rect")
.attr('id', 'clip-rect');
var gradient = vis.append("svg:defs").append("svg:linearGradient")
.attr("id", "line_gradient")
.attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("x1", "0").attr("y1", "0").attr("x2", "2").attr("y2", "0").attr("gradientTransform", "matrix(1,0,0,1,0,0)");
gradient.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "0%").attr("stop-color", "#999999");
gradient.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "40%").attr("stop-color", "#eeeeee");
gradient.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "60%").attr("stop-color", "#cccccc");
gradient.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "100%").attr("stop-color", "#999999");
var gradient2 = vis.append("svg:defs").append("svg:linearGradient")
.attr("id", "domain_gradient")
.attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("x1", "0").attr("y1", "1").attr("x2", "6.12").attr("y2", "0").attr("gradientTransform", "matrix(1,0,0,1,0,0)");
gradient2.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "0%").attr("stop-color", "#FF8585");
gradient2.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "50%").attr("stop-color", "#7a1e74");
gradient2.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "60%").attr("stop-color", "#7a1e74");
gradient2.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "100%").attr("stop-color", "#ffffff");
var gradient3 = vis.append("svg:defs").append("svg:linearGradient")
.attr("id", "domain_gradient2")
.attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("x1", "0").attr("y1", "1").attr("x2", "6.12").attr("y2", "0").attr("gradientTransform", "matrix(1,0,0,1,0,0)");
gradient3.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "0%").attr("stop-color", "#0099CC");
gradient3.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "50%").attr("stop-color", "#7a1e74");
gradient3.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "60%").attr("stop-color", "#7a1e74");
gradient3.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "100%").attr("stop-color", "#ffffff");
var gradient4 = vis.append("svg:defs").append("svg:linearGradient")
.attr("id", "domain_gradient3")
.attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("x1", "0").attr("y1", "1").attr("x2", "6.12").attr("y2", "0").attr("gradientTransform", "matrix(1,0,0,1,0,0)");
gradient4.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "0%").attr("stop-color", "#CCF2CC");
gradient4.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "50%").attr("stop-color", "#7a1e74");
gradient4.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "60%").attr("stop-color", "#7a1e74");
gradient4.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "100%").attr("stop-color", "#ffffff");
var gradient5 = vis.append("svg:defs").append("svg:linearGradient")
.attr("id", "domain_gradient4")
.attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("x1", "0").attr("y1", "1").attr("x2", "6.12").attr("y2", "0").attr("gradientTransform", "matrix(1,0,0,1,0,0)");
gradient5.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "0%").attr("stop-color", "#14101f");
gradient5.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "50%").attr("stop-color", "#7a1e74");
gradient5.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "60%").attr("stop-color", "#7a1e74");
gradient5.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "100%").attr("stop-color", "#ffffff");
var gradient6 = vis.append("svg:defs").append("svg:linearGradient")
.attr("id", "domain_gradient5")
.attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("x1", "0").attr("y1", "1").attr("x2", "6.12").attr("y2", "0").attr("gradientTransform", "matrix(1,0,0,1,0,0)");
gradient6.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "0%").attr("stop-color", "#623e32");
gradient6.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "50%").attr("stop-color", "#7a1e74");
gradient6.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "60%").attr("stop-color", "#7a1e74");
gradient6.append("svg:stop").attr("webkit-tap-highlight-color", "rgba(0, 0, 0, 0)").attr("offset", "100%").attr("stop-color", "#ffffff");
if(load_from_variable){
console.log("load from variable selected");
json = JSON.parse( json_tree_string );
SpeciesTree.update(root = json);
}
else if(json_tree ){
console.log("json selected");
var final_json;
var species2genes = new Object();
d3.json(json_tree, function(json) {
console.log("combine information now");
//console.log(species2genes);
//add2species_tree({jsonObj : json,species2genes : species2genes});
SpeciesTree.update(root = json);
SpeciesTree.updateGenes({gene_data : gene_data, presentation_mode : presentation_mode});
});
//setInterval(function() {
// gene_data = "../test/toy_genes2.json";
// console.log("updaaaate genes");
// updateGenes({gene_data : gene_data});
// return 1;
//}, 3000);
//updateGenes({gene_data : gene_data});
}
else{
console.log("newick selected");
d3.text(newick_tree, function(text) {
var x = newick.parse(text);
var cluster = d3.layout.cluster()
.size([360, 1])
.sort(null)
.value(function(d) { return d.length; })
.children(function(d) { return d.branchset; })
.separation(function(a, b) { return 1; });
var nodes = cluster(x);
console.log(x);
SpeciesTree.updateGenes({gene_data : gene_data, presentation_mode : presentation_mode});
//SpeciesTree.update(root = nodes, presentation_mode);
});
}
return SpeciesTree;
}
SpeciesTree.update = function (source){
//function update(source) {
// Compute the new tree layout.
var nodes = tree.nodes(root);
console.log("tree has "+nodes.length+" nodes");
// Update the nodes…
var node = d3.select("#tree svg").selectAll("g.node").data(nodes, function(d) { return d.id || (d.id = ++i); });
var nodeEnter = node.enter().append("svg:g")
.attr("class", function(d){
return d.children ? "node":"node leaf";
});
draw_nodes({nodeEnter : nodeEnter,node : node ,source : source , offset : offset })
// Update the links…
var link = d3.select("#tree svg")
.selectAll("path.link")
.data(tree.links(nodes), function(d) { return d.target.id; });
set_links({link: link, link_type : link_type, duration : duration, offset : offset});
// CIRCLE
var circles = draw_circles({nodeEnter : nodeEnter, circle_size : circle_size, offset : offset});
// Text
var texts = draw_taxon_names({nodeEnter : nodeEnter, show_taxa : show_taxa, highlight_gene : highlight_gene, model_organisms : model_organisms, offset : offset});
// Bootstrap
var texts = draw_bootstraps({nodeEnter : nodeEnter, visibility : "hidden", offset : offset});
// IMAGE
draw_images({nodeEnter : nodeEnter , image_path : image_path, offset : offset});
animGroup = vis.append("svg:g").attr("clip-path", "url(#clipper)");
// Cache the UI elements
ui = {
svgRoot: vis,
nodeGroup: node,
linkGroup: link,
animGroup: animGroup
};
// Stash the old positions for transition.
nodes.forEach(function(d) {
d.x0 = d.x;
d.y0 = d.y;
});
}
//d3.select(self.frameElement).style("height", "2000px");
SpeciesTree.duration = function (d) {
if (!arguments.length) {
return duration;
}
duration = d;
return SpeciesTree;
};
SpeciesTree.sequences = function (d) {
// Sequences
var rects = draw_sequences({nodeEnter: nodeEnter,
domainScale : domainScale ,
leaf_group_x : leaf_group_x,
sequence_start_y : sequence_start_y,
visibility : ""});
// Domains
var domains = rects.selectAll(".domain").data(function(d) { return d.domains; })
var all_domains = draw_domains({domains : domains,
sequence_start_y : sequence_start_y,
domainScale:domainScale,
sequence_rect_width : sequence_rect_width,
leaf_group_x : leaf_group_x,
domain_colors : domain_colors,
visibility: "" });
return SpeciesTree;
};
SpeciesTree.updateGenes = function (args){
//function updateGenes(args){
var gene_data = args.gene_data;
var presentation_mode = args.presentation_mode;
console.log("reading gene data from file "+gene_data+" with presentation mode: "+presentation_mode);
// get all leaves
var leaves = vis.selectAll(".leaf");
//console.log(leaves);
var column_width = (presentation_mode == "gene_boxes") ? 300 : 100;
var printable_column_width = (presentation_mode == "gene_boxes") ? 250 : 100;;
var visibility = "hidden";
var all_domains;
var gene2column = [];
var genename_duplicates = new Object();
var column_count = 0;
var gene2column_index = new Object();
// Load gene data
d3.json(gene_data, function(json) {
console.log("reading gene data here");
var genes = json;
var id = "BRCA1";
//console.log(genes['BRCA1'][0]);
//end
for(gene in genes){
//jQuery.each(genes,function(i,gene){
//console.log("looking at gene "+gene);
if( genename_duplicates[gene] === undefined ){
gene2column.push(gene);
// console.log("looking at gene "+gene);
genename_duplicates[gene] = 1;
}
};
console.log("Finished reading data");
//console.log(gene2column);
var sorted_genes = gene2column.sort();
console.log(sorted_genes);
jQuery.each(sorted_genes, function(i,d){ gene2column_index[d] = i ; })
// get all gene names
console.log("gene2column_index");
console.log(gene2column_index);
//endhere
//console.log("printed gene names");
// sort gene names
// assign gene names to slot
d3.selectAll(".prabsence_box").remove();
d3.selectAll(".gene_label_dividers").remove();
d3.selectAll(".domain").remove();
d3.selectAll(".gene_box").remove();
// class: gene_box || prabsence_box
draw_leaves({leaves : leaves,
genes : genes,
gene2column_index : gene2column_index,
column_width : column_width,
sorted_genes : sorted_genes,
presentation_mode : presentation_mode})
// Axis + gene labels
// clear all old things
d3.selectAll(".gene_label_text").remove();
d3.selectAll(".gene_label_box").remove();
d3.selectAll(".x_axis").remove();
draw_gene_labels({
leaves : leaves,
sorted_genes : sorted_genes,
sequence_start_y : 400,
gene2column_index : gene2column_index,
column_width : column_width,
presentation_mode : presentation_mode});
});
}
SpeciesTree.update_genes_now = function (source){
console.log("updating nowwwwww!");
//updateGenes();
}
// Domains
function draw_blocks(args){
var leaf_group_x = args.leaf_group_x;
var sequence_start_y = args.sequence_start_y;
var nodeEnter = args.nodeEnter;
var domainScale = args.domainScale;
var visibility = args.visibility;
var nodes = args.nodes;
var y_value_for_genes = 40;
var column_width = 100;
var leafs = d3.select("#tree svg").selectAll(".leaf_label");
//var leafs = d3.select("#annotation_panel").selectAll("g.node").data(nodes, function(d) { return d.id || (d.id = ++i); });
//var leafsEnter = node.enter().append("svg:g")
// .attr("class", "node")
var data_array = [[10,20,30,40],[10,20,30,40],[10,20,30,40],[10,20,30,40] ];
var species2gene_mapping_json;
//d3.json(gene_data, function(gene_data_json) {
// //console.log(error);
// species2gene_mapping_json = gene_data_json;
//});
var species_row = d3.select("#annotation_panel svg").selectAll("g.node").data(data_array);
var speciesEnter = species_row.enter().append("svg:g").attr("class", "node")
d3.select("#annotation_panel svg")
.append("a") .attr(" xlink:href", "www.treefam.org/family/TF101001")
.append("text") // text label for the x axis
.attr("x", 230 ).attr("y", 10 )
.style("text-anchor", "middle")
.text("TF101001 = Cyclin B");
d3.select("#annotation_panel svg").append("text") // text label for the x axis
.attr("x", 30 ).attr("y", 30 )
.style("text-anchor", "middle").text("FBX1");
d3.select("#annotation_panel svg").append("text") // text label for the x axis
.attr("x", 140 ).attr("y", 30 )
.style("text-anchor", "middle").text("FBX1");
d3.select("#annotation_panel svg").append("text") // text label for the x axis
.attr("x", 240 ).attr("y", 30 )
.style("text-anchor", "middle").text("FBX2");
d3.select("#annotation_panel svg").append("text") // text label for the x axis
.attr("x", 340 ).attr("y", 30 )
.style("text-anchor", "middle").text("FBX4");
//console.log(leafs);
//var leafs = nodeEnter.filter(function(d){ return d.type == "leaf"});
//console.log(leafs);
leafs.each(function(d,i){
var species_counter = i;
console.log("plotting species "+d.name+" at "+d.x);
var x_value = d.x;
//console.log(d);
//console.log(i);
//var species = d3.select("#annotation_panel").selectAll("rect").data(data_array);
var speciesEnter_somethingelse = speciesEnter.append("rect")
.attr("class", "node")
.attr("x", function(d){ //console.log("loop values: i "+species_counter+" xvalue:"+x_value);
return -(x_value + y_value_for_genes-5);})
.attr("y", function(d,i){ return (i *column_width); })
//.attr("class", "seq_string")
//.attr("visibility",visibility)
.attr("width", "8")
.attr("height", "90")
.attr("fill", "url(#line_gradient)")
.attr("transform", function(d){return d.children ? "":"rotate(-90 )";})
;
})
// add to other svg
// then we should be done
// function(d){return d.children ? "":"grey";});
//return rects;
}
function draw_domains_species_tree(args){
var domains = args.domains;
var sequence_start_y = args.sequence_start_y;
var domainScale = args.domainScale;
var leaf_group_x = args.leaf_group_x;
var domain_colors = args.domain_colors;
var sequence_rect_width = args.sequence_rect_width;
var visibility = args.visibility;
var column_width = args.column_width;
var gene2column_index = args.gene2column_index;
var domain2color = {};
var all_domains = domains.enter()
.append("a")
.attr("xlink:href", function(d) {return "http://pfam.sanger.ac.uk//family/"+d.name})
.append("rect")
.attr("x", leaf_group_x + 4)
.attr("y", function(d){
console.log("draw domain for "+d.name+" to "+domainScale(d.domain_start)+" ("+d.domain_start+")");
//console.log("draw domain for "+d.name+" from "+sequence_start_y+" index ("+d.column+" * "+column_width+" + "+domainScale(d.domain_start)+" )");
return sequence_start_y +(d.column * column_width) + domainScale(d.domain_start) + 50;
})
.attr("class", "domain")
.attr("visibility",visibility)
.attr("rx", 5)
.attr("ry", 5)
.attr("transform", "matrix(1,0,0,1,100,0)")
.attr("stroke", "none")
.attr("width", function(d){return sequence_rect_width;})
.attr("height", function(d){
var length = domainScale(d.domain_stop - d.domain_start);
//console.log("sequence_rect: appending source is "+d.x);
//console.log("transform domain length "+(d.domain_stop - d.domain_start)+" to "+length);
return length;
})
.attr("transform", "rotate(-90 100 100)")
.attr("fill",
// "url(#domain_gradient)")
// ;
function(d,i){
//console.log("checking for "+d.name+" in domain2color");
// if( d.name in domain2color ) {
if( domain2color[d.name] === undefined ) {
//console.log("not found");
domain2color[d.name] = domain_colors[i % 5];
//console.log(d.name+" is "+i+" and will use: "+domain_colors[i]+ " length is "+domain_colors);
return "url(#"+domain_colors[i % 5]+")";
}
else{
//console.log("found! using "+domain2color[d.name]);
return "url(#"+domain2color[d.name]+")";
}
// return "url(#"+domain_colors[i]+")";
})
.on('mouseover', show_domain_information);
return all_domains;
}
function draw_gene_labels(args){
var sorted_genes = args.sorted_genes;
var leaves = args.leaves;
var sequence_start_y = args.sequence_start_y;
var gene2column_index = args.gene2column_index;
var column_width = args.column_width;
var presentation_mode = args.presentation_mode;
// draw each gene/column separately
jQuery.each(sorted_genes, function(i,current_label){
console.log("looking at gene: "+current_label);
var label_svg = d3.select("#tree svg").append("svg:svg")
.attr("width", 9000)
.attr("height", 2500);
var label_text = d3.select("#tree svg").append("svg:text")
.attr("x", function(d,i){
return sequence_start_y + 33 + ((gene2column_index[current_label]) * column_width)
})
.attr("y", 12)
.attr("dy", ".35em")
.attr("class", "gene_label_text")
.attr("text-anchor", "middle")
.style("font", "300 20px Helvetica Neue")
.text(current_label);
var bbox = label_text.node().getBBox();
var label_rect = d3.select("#tree svg").append("svg:rect")
.attr("x", bbox.x)
.attr("y", bbox.y)
.attr("width", bbox.width)
.attr("height", bbox.height)
.attr("class", "gene_label_box")
//.attr("transform", function(d) { return "rotate(" + (d.x + d.dx / 2 - Math.PI / 2) / Math.PI * 180 + ")"; })
.style("fill", "#ccc")
.style("fill-opacity", ".3")
.style("stroke", "#666")
.style("stroke-width", "1.5px");
var columnLine = label_svg.append("svg:line")
.attr("x1", function(d){
//console.log("line has "+(sequence_start_y - 20 + ((gene2column_index[current_label] + 1) * column_width)));
//console.log("line has "+sequence_start_y+" + 80 + "+gene2column_index[current_label]+" * "+column_width);
return sequence_start_y -20 + ((gene2column_index[current_label] + 1) * column_width);
})
.attr("y1", 25)
.attr("x2", sequence_start_y -20 +((gene2column_index[current_label] + 1) * column_width))
.attr("y2", h + 50)
.style("stroke", "rgb(6,120,155)")
.attr("class", "gene_label_dividers");
if( presentation_mode == "gene_boxes"){
var annotation_scale = d3.scale.linear().domain([0, 4000]).range([0, 250]);
var xAnnotation_axis = d3.svg.axis()
.scale(annotation_scale)
//.tickValues([0, 4, 7, 1000, 2000, 3000, 4000])
.orient("top");
d3.select("#tree svg").append("g")
.attr("class", "x_axis")
.attr("transform", "translate("+( sequence_start_y + ((gene2column_index[current_label]) * column_width) )+",50)")
.call(xAnnotation_axis);
}
})
// plot species dividers
leaves.each(function(d,i){
var current_leaf = d3.select(this);
var speciesLine = current_leaf.append("svg:line")
.attr("x1", function(d){
console.log("plotting for "+d.name+" (x: "+d.x+", y: "+d.y+") leaf_group: "+leaf_group_x+" seq_start "+sequence_start_y+" i "+i+"x2: ");
return d.y - 175;
})
.attr("y1", 8)
.attr("x2", (leaf_group_x + (sorted_genes.length + 1) * column_width))
.attr("y2", 8)
.style("stroke", "rgb(120,120,155)")
.attr("class", "species_label_dividers");
})
add_tipsy({ where : ".gene_label_box"});
}
function draw_leaves(args){
var leaves = args.leaves;
var genes = args.genes;
var sorted_genes = args.sorted_genes;
var gene2column_index = args.gene2column_index;
var column_width = args.column_width;
var presentation_mode = args.presentation_mode;
console.log("presentation mode is "+presentation_mode);
// clear display
leaves.each(function(d,i){
// get single-element selection
var current_leaf = d3.select(this);
var x_value = current_leaf.attr("x");
var y_value = current_leaf.attr("y");
var current_leaf_text = current_leaf.select("text").text();
var current_leaf_x = current_leaf.select("text").attr("x");
var x_value = current_leaf.select("text").attr("x");
var y_value = current_leaf.select("text").attr("y");
//console.log("x: "+x_value+" y: "+y_value+"");
//console.log(current_leaf_text);
var all_genes4leaf = [];
var genes4leaf;
for(gene in genes){
var species_with_gene = genes[gene];
jQuery.each(species_with_gene, function(i,species){
if(species.species_name == current_leaf_text){
species.name = gene;
all_genes4leaf.push(species);
}
});
};
//test
if(all_genes4leaf){
var leaf_bound = current_leaf.selectAll("g.node").data(all_genes4leaf, function(d) { return d.name; });
// node enter
var leaf_boundEnter = leaf_bound.enter().append("svg:g");
console.log(leaf_boundEnter);
console.log("presentation mode is now: "+presentation_mode);
if(presentation_mode == "gene_boxes"){
console.log("in drawing gene_boxes");
// draw sequences
var rects = leaf_boundEnter;
rects.append("rect")
.attr("x", function(d){
console.log("looking at the x value");
return leaf_group_x;
})
.attr("y", function(d,i){
var column4domains = gene2column_index[d.name];
if(d.domains){
//console.log(d.name+" has domains");
jQuery.each(d.domains,function(i,d){
//console.log(" is "+d.name+" goes into bin "+column4domains);
d.column = column4domains;
})
}
return sequence_start_y + (gene2column_index[d.name] * column_width);
})
.attr("class", function(d){
return ( presentation_mode == "gene_boxes") ? "gene_box" : "prabsence_box";
})
//.attr("visibility",visibility)
.attr("width", function(d){
return ( presentation_mode == "gene_boxes") ? "5": 15;
})
.attr("height", function(d){
// remember the order of domains here
if(d.seq_length == "N/A"){
return 0;
}
else{
return domainScale(d.seq_length);
}
})
.attr("transform", function(d){return d.children ? "":"rotate(-90 100 100)";})
.attr("fill", function(d){
if( presentation_mode == "gene_boxes"){
return "url(#line_gradient)";
}
else{ return "url(#line_gradient)"; }
})
.transition().duration(1750);
// remove
leaf_bound.exit()
.transition()
.duration(1750)
.attr("y", 160)
.attr("height", 30)
.style("color", "red")
.style("fill-opacity", 1e-6)
.remove();
// bind domains
var test_domains;
var domains = rects.selectAll(".domain").data(function(d) {
return d.domains;
})
var all_domains = draw_domains_species_tree({domains : domains,
sequence_start_y : sequence_start_y - 40,
domainScale:domainScale,
sequence_rect_width : sequence_rect_width,
leaf_group_x : leaf_group_x-8,
domain_colors : domain_colors,
visibility: "" ,
column_width : column_width,
gene2column_index : gene2column_index});
// domains remove
var all_domains_exit = domains.exit().transition()
.duration(1750)
.attr("y", 460)
.style("fill-opacity", 1e-6)
.remove();
}
else{
console.log("drawing the boxes here");
var present_file = "../data/icons/Yes_check.svg.png";
var maybe_file = "../data/icons/question-mark.gif";
var absent_file = "../data/icons/No_sign.svg.png";
var images = leaf_boundEnter.append("svg:image")
.attr("x", function(d,i){
var column4domains = gene2column_index[d.name];
if(d.domains){
//console.log(d.name+" has domains");
jQuery.each(d.domains,function(i,d){
//console.log(" is "+d.name+" goes into bin "+column4domains);
d.column = column4domains;
})
}
var image_coord = sequence_start_y + (gene2column_index[d.name] * column_width);
//console.log("plotting image at "+image_coord+" leaf group is "+leaf_group_x+" element has:"+d.x+" and "+d.y)
return image_coord + 20;
})
.attr("y", function(d){
return -10;
})
.attr("class", "prabsence_box")
//.attr("x", 12.5)
.attr("text-anchor", function(d){ return "end";})
.attr("width", 15).attr("height", 15)
//.attr("xlink:href", function(d) { return d.children == null? image_path+"/thumb_"+d.taxon+".png" : ""; });
.attr("xlink:href", function(d){
//console.log("for species :"+d.species_name);
if(d.homology_type == "ortholog_one2one"){ //console.log(d.homology_type+"linking to image present");
return present_file;}
else if(d.homology_type == "ortholog_one2many"){
//console.log(d.homology_type+"linking to image maybe");
return maybe_file;}
else {
//console.log(d.homology_type+"linking to image absent");
return absent_file;}
});
}
}
});
}
function parse_gene_data(args){
var gene2column = args.gene2column;
return gene2column;
}
return SpeciesTree;
};
Raw
tree_functions_species_tree.js
// Basic components
function draw_circles(args){
var nodeEnter = args.nodeEnter;
var circle_size = args.circle_size;
var offset = args.offset;
//console.log("drawing with size "+circle_size);
var circles = nodeEnter.append("svg:circle")
.attr("r", function(d){ return d.children ? circle_size : 0; })
.attr("fill", function(d){return d.duplication == "Y"? "red":"green"})
.on("click", click)
//.on("click", focus)
//.on("click", get_all_children)
//.on("click", color_subtree)
.on("contextmenu", function(data, index) {
//console.log("right-clicked on node");
d3.select('#my_custom_menu')
.style('position', 'absolute')
.style('left', d3.event.x + "px")
.style('top', d3.event.y + "px")
.style('display', 'block');
d3.event.preventDefault();
});
return circles;
}
function draw_nodes(args){
var nodeEnter = args.nodeEnter;
var node = args.node;
var source = args.source;
var offset = args.offset;
var duration = args.duration;
// Transition nodes to their new position.
nodeEnter.transition()
.duration(duration)
.attr("transform", function(d) {
return "translate(" + d.y + "," + (d.x + offset) + ")"; })
.style("opacity", 1)
.select("circle");
node.transition()
.duration(duration)
.attr("transform", function(d) { return "translate(" + d.y + "," + (d.x + offset) + ")"; })
.style("opacity", 1);
node.exit().transition()
.duration(duration)
.attr("transform", function(d) { return "translate(" + source.y + "," + (source.x + offset )+ ")"; })
.style("opacity", 1e-6)
.remove();
}
function draw_taxon_names(args){
var nodeEnter = args.nodeEnter;
var show_taxa = args.show_taxa;
var highlight_gene = args.highlight_gene;
var model_organisms = args.model_organisms;
var offset = args.offset;
var texts = nodeEnter.append("svg:text")
.attr("x", function(d) { return d.children ? -5 : 25; })
.attr("y", function(d) { return d.children ? -5: 3; })
//.attr("class","innerNode_label")
.attr("text-anchor", function(d){ return d.children ? "end" : "start";})
//.attr("font-style", "italic")
.attr("class",function(d){
if(d.children){ return "innerNode_label"}
else{
if(model_organisms.hasOwnProperty(d.taxon)){
return "leaf_label species_name model_organism";
}
else{
return "leaf_label species_name";
}
}
})
.attr("fill", function(d){
if(d.name == highlight_gene){
return "red";
}
else{
return "";
}
})
.text(function(d) {
if(d.children){
if(show_taxa.hasOwnProperty(d.name)){
if(d.duplication == "Y"){return "";}
else{return d.name;}
}
}
else{
//if(d.sequences){
// return d.taxon+" ( "+d.sequences.length+" genes)";
//}
//else{
return d.taxon;
//}
}})
//.on('mouseover', function(d, i){
// d3.select(this).select("circle").classed("hover", true);
//})
//.on('mouseout', function(d, i){
// d3.select(this).select("circle").classed("hover", false);
//})
.on('mouseover', show_gene_information)
;
return texts;
}
function draw_bootstraps(args){
var nodeEnter = args.nodeEnter;
var show_taxa = args.show_taxa;
var visibility = args.visibility;
var texts = nodeEnter.append("svg:text")
.attr("x", function(d) { if(d.children){return -5; }})
.attr("y", function(d) { if(d.children){return -12; }})
.attr("text-anchor", function(d){ return d.children ? "end" : "start";})
.attr("class",function(d){ if(d.children){ return "bootstrap"; }})
.attr("visibility",visibility)
.text(function(d) {
if(d.children){
return d.bootstrap;
}
});
return texts;
}
function set_links(args){
var link = args.link;
var link_type = args.link_type;
var node_thickness = args.node_thickness;
var duration = args.duration;
link_type = "elbow";
// Enter any new links at the parent's previous position.
link.enter().insert("svg:path", "g")
.attr("class", "link")
.attr("stroke-width", function(d){
//console.log("drawing line with thickness "+node_thickness);
return node_thickness;
})
.attr("stroke", function(d){
return "black";
//return taxon_colors.hasOwnProperty(d.name)? taxon_colors[d.name]: "black";
})
.attr("d", elbow)
//.attr("d", diagonal)
//.attr("d", function(d) {
// var o = {x: source.x0, y: source.y0};
// return diagonal({source: o, target: o});
//})
.transition()
.duration(duration)
.attr("d", elbow)
//.attr("d", diagonal)
;
// Transition links to their new position.
link.transition()
.duration(duration)
.attr("d", elbow)
//.attr("d", diagonal)
;
// Transition exiting nodes to the parent's new position.
link.exit().transition()
.duration(duration)
.attr("d", elbow)
//.attr("d", diagonal)
//.attr("d", function(d) {
// var o = {x: source.x, y: source.y};
// return diagonal({source: o, target: o});
//})
.remove();
}
// For lines between nodes
function elbow(d, i) {
var offset = 50;
// console.log("use M" + d.source.y + "," + d.source.x
// + "H" + d.target.y + "V" + d.target.x
// + (d.target.children ? "" : "h" + margin.right));
return "M" + d.source.y + "," + (d.source.x + offset)
+ "V" + (d.target.x + offset) + "H" + d.target.y;
// return "M" + d.source.y + "," + d.source.x
// + "H" + d.target.y + "V" + d.target.x
// + (d.target.children ? "" : "h" + margin.right);
}
function redraw() {
//console.log("here", d3.event.translate, d3.event.scale);
vis.attr("transform", "translate(" + d3.event.translate + ")"+ " scale(" + d3.event.scale + ")");
}
// Toggle children on click.
function click(d) {
var circle_size = 4;
var duplication_circle_size = 15;
if (d.children) {
d._children = d.children;
d.children = null;
} else {
d.children = d._children;
d._children = null;
}
console.log("clicked on "+d.name);
//console.log(d);
//d3.select(this).text("hahaha");
console.log("this node data: "+this.parentNode.__data__ );
//var dad = this.parentNode;
//d3.select(this).select("text").text(function(d){
//console.log("trying to select: "+d.name)
// return "hahhaaa";
//});
// update node
d3.select(this) .append("svg:path")
.attr("d", function(d){
var x = 200, y = 100;
return 'M ' + x +' '+ y + ' l 4 4 l -8 0 z';
})
.attr("r",function(d){return d.duplication == "Y"? duplication_circle_size:circle_size;})
.attr("class", "collapsed")
.attr("fill",function(d){return d.children? "":"white";})
.attr("stroke",function(d){return d.children? "":"black";})
.attr("stroke-width", function(d){return d.children? "":"2.5px";});
console.log("clicked updating");
//gTree.update(d);
update(d);
}
function focus(d) {
var duplication_circle_size = 15;
var circle_size = 4;
if (d.children) {
d._children = d.children;
d.children = null;
} else {
d.children = d._children;
d._children = null;
}
console.log("clicked on "+d.name);
//console.log(d);
d3.select(this).text("hahaha");
console.log("this node data: "+this.parentNode.__data__ );
//var dad = this.parentNode;
d3.select(this).select("text").text(function(d){
//console.log("trying to select: "+d.name)
return "hahhaaa";
});
// update node
d3.select(this).append("svg:path")
.attr("d", function(d){
var x = 200, y = 100;
return 'M ' + x +' '+ y + ' l 4 4 l -8 0 z';
})
.attr("r",function(d){return d.duplication == "Y"? duplication_circle_size:circle_size;})
.attr("class", "collapsed")
.attr("fill",function(d){return d.children? "":"white";})
.attr("stroke",function(d){return d.children? "":"black";})
.attr("stroke-width", function(d){return d.children? "":"2.5px";});
update(d);
}
function collapse(d) {
if (d.children) {
d._children = d.children;
d._children.forEach(collapse);
d.children = null;
}
}
// Domains
function draw_sequences(args){
var leaf_group_x = args.leaf_group_x;
var sequence_start_y = args.sequence_start_y;
var nodeEnter = args.nodeEnter;
var domainScale = args.domainScale;
var visibility = args.visibility;
var rects = nodeEnter.filter(function(d){ return d.type == "leaf"});
rects.append("rect")
//.on('mouseover', show_gene_information)
.attr("x", leaf_group_x +8)
.attr("y", sequence_start_y)
.attr("class", "seq_string")
.attr("visibility",visibility)
.attr("width", function(d){return d.children ? "":"5";})
.attr("height", function(d){
if(!d.children){
//console.log("draw sequence from "+sequence_start_y+" to "+(sequence_start_y + sequenceScale(d.seq_length))+"("+d.seq_length+")");
//console.log("transform "+d.seq_length+" to "+sequenceScale(d.seq_length)+" (start drawing at: "+sequence_start_y+")");
}
return d.children ? "": domainScale(d.seq_length);
})
.attr("transform", function(d){return d.children ? "":"rotate(-90 100 100)";})
.attr("fill", "url(#line_gradient)");
// function(d){return d.children ? "":"grey";});
return rects;
}
function draw_domains(args){
var domains = args.domains;
var sequence_start_y = args.sequence_start_y;
var domainScale = args.domainScale;
var leaf_group_x = args.leaf_group_x;
var domain_colors = args.domain_colors;
var sequence_rect_width = args.sequence_rect_width;
var visibility = args.visibility;
var domain2color = {};
var all_domains = domains.enter()
.append("a")
.attr("xlink:href", function(d) {return "http://pfam.sanger.ac.uk//family/"+d.name})
.append("rect")
.attr("x", leaf_group_x + 4)
.attr("y", function(d){
//console.log("draw domain from "+sequence_start_y+" to ("+d.domain_start+")");
//console.log("draw domain from "+sequence_start_y+" to "+(sequence_start_y + domainOnlyScale(d.domain_start))+"("+d.domain_start+")");
return sequence_start_y + domainScale(d.domain_start);
})
.attr("class", "domain")
.attr("visibility",visibility)
.attr("rx", 5)
.attr("ry", 5)
.attr("transform", "matrix(1,0,0,1,100,0)")
.attr("stroke", "none")
.attr("width", function(d){return sequence_rect_width;})
.attr("height", function(d){
var length = domainScale(d.domain_stop - d.domain_start);
//console.log("sequence_rect: appending source is "+d.x);
//console.log("transform domain length "+(d.domain_stop - d.domain_start)+" to "+length);
return length;
})
.attr("transform", "rotate(-90 100 100)")
.attr("fill",
// "url(#domain_gradient)")
// ;
function(d,i){
//console.log("checking for "+d.name+" in domain2color");
// if( d.name in domain2color ) {
if( domain2color[d.name] === undefined ) {
//console.log("not found");
domain2color[d.name] = domain_colors[i % 5];
//console.log(d.name+" is "+i+" and will use: "+domain_colors[i]+ " length is "+domain_colors);
return "url(#"+domain_colors[i % 5]+")";
}
else{
//console.log("found! using "+domain2color[d.name]);
return "url(#"+domain2color[d.name]+")";
}
// return "url(#"+domain_colors[i]+")";
})
.on('mouseover', show_domain_information);
return all_domains;
}
// Conservation
function draw_aligned_sequences(args){
var leaf_group_x = args.leaf_group_x;
var sequence_start_y = args.sequence_start_y;
var nodeEnter = args.nodeEnter;
var domainScale = args.domainScale;
var visibility = args.visibility;
var rects = nodeEnter.filter(function(d){ return d.type == "leaf"});
rects.append("rect")
.attr("x", leaf_group_x +8)
.attr("y", sequence_start_y)
.attr("class", "aligned_seq_string")
.attr("visibility",visibility)
.attr("width", function(d){return d.children ? "":"10";})
.attr("height", function(d){
if(!d.children){
//console.log("draw sequence from "+sequence_start_y+" to "+(sequence_start_y + sequenceScale(d.seq_length))+"("+d.seq_length+")");
//console.log("transform "+d.seq_length+" to "+sequenceScale(d.seq_length)+" (start drawing at: "+sequence_start_y+")");
}
return d.children ? "": domainScale(4000);
return d.children ? "": domainScale(d.seq_length);
})
.attr("transform", function(d){return d.children ? "":"rotate(-90 100 100)";})
.attr("fill",
"green");
// function(d){return d.children ? "":"grey";});
return rects;
}
function draw_gaps(args){
var gaps = args.gaps;
var sequence_start_y = args.sequence_start_y;
var domainScale = args.domainScale;
var leaf_group_x = args.leaf_group_x;
var sequence_rect_width = args.sequence_rect_width;
var visibility = args.visibility;
var all_gaps = gaps.enter().append("rect")
.attr("x", leaf_group_x + 9)
.attr("y", function(d){
//console.log("draw domain from "+sequence_start_y+" to "+(sequence_start_y + domainOnlyScale(d.domain_start))+"("+d.domain_start+")");
return sequence_start_y + domainScale(d.domain_start);
})
.attr("class", "gap")
.attr("visibility",visibility)
//.attr("rx", 5)
//.attr("ry", 5)
//.attr("transform", "matrix(1,0,0,1,100,0)")
//.attr("stroke", "none")
.attr("width", function(d){return sequence_rect_width - 4;})
.attr("height", function(d){
var length = domainScale(d.domain_stop - d.domain_start);
//console.log("sequence_rect: appending source is "+d.x);
//console.log("transform domain length "+(d.domain_stop - d.domain_start)+" to "+length);
return length;
})
.attr("transform", "rotate(-90 100 100)")
.attr("fill", "white");
return all_gaps;
}
// Synteny
function draw_synteny_seqs(args){
var leaf_group_x = args.leaf_group_x;
var sequence_start_y = args.sequence_start_y;
var nodeEnter = args.nodeEnter;
var domainScale = args.domainScale;
var visibility = args.visibility;
var synteny_rects = nodeEnter.filter(function(d){ return d.type == "leaf"});
synteny_rects.append("rect")
.attr("x", leaf_group_x +11)
.attr("y", sequence_start_y)
.attr("class", "synteny_seq_string")
.attr("visibility",visibility)
.attr("width", function(d){return d.children ? "":"2";})
.attr("height", function(d){
if(!d.children){
//console.log("draw sequence from "+sequence_start_y+" to "+(sequence_start_y + sequenceScale(d.seq_length))+"("+d.seq_length+")");
//console.log("transform "+d.seq_length+" to "+sequenceScale(d.seq_length)+" (start drawing at: "+sequence_start_y+")");
}
return d.children ? "": domainScale(4000);
return d.children ? "": domainScale(d.seq_length);
})
.attr("transform", function(d){return d.children ? "":"rotate(-90 100 100)";})
.attr("fill", "grey");
// function(d){return d.children ? "":"grey";});
return synteny_rects;
}
function draw_synteny(args){
var syntenties = args.syntenties;
var sequence_start_y = args.sequence_start_y;
var domainScale = args.domainScale;
var leaf_group_x = args.leaf_group_x;
var sequence_rect_width = args.sequence_rect_width;
var visibility = args.visibility;
var all_syntenies = syntenties.enter().append("rect")
.attr("x", leaf_group_x + 6)
.attr("y", function(d){
//console.log("draw domain from "+sequence_start_y+" to "+(sequence_start_y + domainOnlyScale(d.domain_start))+"("+d.domain_start+")");
return sequence_start_y + domainScale(d.length);
})
.attr("class", "synteny")
.attr("visibility",visibility)
//.attr("rx", 5)
//.attr("ry", 5)
//.attr("transform", "matrix(1,0,0,1,100,0)")
//.attr("stroke", "none")
.attr("width", function(d){return sequence_rect_width;})
.attr("height", function(d){
var length = domainScale(d.length);
//console.log("sequence_rect: appending source is "+d.x);
//console.log("transform domain length "+(d.domain_stop - d.domain_start)+" to "+length);
return length;
})
.attr("transform", "rotate(-90 100 100)")
.attr("fill", "green");
return all_syntenies;
}
// Images
function draw_images(args){
var nodeEnter = args.nodeEnter;
var image_path = args.image_path;
var images = nodeEnter.append("svg:image")
.attr("y", -10)
//.attr("x", 12.5)
.attr("text-anchor", function(d){ return "end";})
.attr("width", 20).attr("height", 20)
//.attr("xlink:href", function(d) { return d.children == null? image_path+"/thumb_"+d.taxon+".png" : ""; });
.attr("xlink:href", function(d) { return d.children == null? image_path+"/thumb_"+d.taxon+".png" : ""; });
}
// ToolTip
function add_tipsy(args){
var where = args.where;
console.log("where is "+where);
if(where == ".leaf_label"){
console.log("in leaf label");
jQuery(where).tipsy({
gravity: 'se',
html: true,
title: function() {
var c = "red";
var e = this.__data__;
return 'ID: '+e.name+'<br>Taxon: '+e.taxon+" <br>Gene name: "+e.swissprot_gene_name+"<br>Swiss-Prot annotation: "+e.swissprot_protein_name+"";
}
});
}
else{
jQuery(where).tipsy({
gravity: 'se',
html: true,
title: function() {
var c = "red";
var e = this.__data__;
var length = e.domain_stop - e.domain_start;
return 'Domain: '+e.name+'<br>Length: '+length+" AA<br> E-value: "+e.evalue+"<br>Start: "+e.domain_start+" End: "+e.domain_stop;
}
});
}
}
function toggleAll(d) {
if (d.children) {
d.children.forEach(toggle);
click(d);
}
}
// Toggle children.
function toggle(d) {
if (d.children) {
d._children = d.children;
d.children = null;
} else {
d.children = d._children;
d._children = null;
}
}
function draw_taxon_colors(args){
var ID2Color = args.ID2Color;
var SwissProt2colorDictionary = new Object();
var p=d3.scale.category10();
var r=p.range(); // ["#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd",
// "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"]
var s=d3.scale.ordinal().range(r);
var i = 0;
var html ="";
//console.log("one color is "+p(0));
//d3.select("#tree svg").selectAll(".leaf_label")
d3.select("#tree svg").selectAll("g.node").append("rect")
.on('mouseover', show_gene_information)
.attr("x", 192)
.attr("y", 22)
.attr("class", "tax_color_rect")
//.attr("visibility",visibility)
.attr("width", function(d){return d.children ? "1":"17";})
.attr("height", function(d){
return d.children ? "1": 200;
})
.attr("transform", function(d){return d.children ? "1":"rotate(-90 100 100)";})
.attr("fill", function(d){
//console.log("looking at "+d.swissprot_gene_name);
if(d.swissprot_gene_name == 'NaN' || d.swissprot_gene_name == "undefined"){
//console.log("no color");
return "none";
}
else if( SwissProt2colorDictionary[d.swissprot_gene_name] === undefined ) {
console.log("not found");
SwissProt2colorDictionary[d.swissprot_gene_name] = p(i % p.range().length);
html = html + "<span style='opacity:0.6; background-color:"+SwissProt2colorDictionary[d.swissprot_gene_name]+"'>";
html = html + "<a href='http://www.uniprot.org/uniprot/?query="+d.swissprot_gene_name+"+AND+reviewed%3Ayes&sort=score'>";
html = html + d.swissprot_gene_name+"</a></span>: "+d.swissprot_protein_name+"</div><br>";
console.log("use color "+p(i % p.range().length)+" name : "+d.swissprot_gene_name);
//ID2Color[d.name] = p(0) SwissProt2color[i % p.domain().length];
//console.log("will use: "+p(i % p.domain().length);
//console.log(" draw "+d.swissprot_gene_name+" using "+SwissProt2colorDictionary[d.swissprot_gene_name]);
//return "red";
i++;
return SwissProt2colorDictionary[d.swissprot_gene_name];
}
else{
//console.log("found! using "+domain2color[d.name]);
//ID2Color[d.name] = SwissProt2colorDictionary[d.swissprot_gene_name];
return SwissProt2colorDictionary[d.swissprot_gene_name];
}
})
.attr("fill-opacity",0.2);
// draw legend
show_general_information({swissprot_annotation: html});
}
function draw_taxon_colors_gene(args){
var ID2Color = args.ID2Color;
var SwissProt2colorDictionary = new Object();
var p=d3.scale.category10();
var r=p.range(); // ["#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd",
// "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf"]
var s=d3.scale.ordinal().range(r);
var i = 0;
var html ="";
//console.log("one color is "+p(0));
//d3.select("#tree svg").selectAll(".leaf_label")
d3.select("#tree svg").selectAll("g.node").append("rect")
.on('mouseover', show_gene_information)
.attr("x", 192)
.attr("y", 22)
.attr("class", "tax_color_rect")
//.attr("visibility",visibility)
.attr("width", function(d){return d.children ? "1":"17";})
.attr("height", function(d){
return d.children ? "1": 200;
})
.attr("transform", function(d){return d.children ? "1":"rotate(-90 100 100)";})
.attr("fill", function(d){
//console.log("looking at "+d.swissprot_gene_name);
if(d.display_label == 'NaN' || d.display_label == "undefined"){
//console.log("no color");
return "none";
}
else if( SwissProt2colorDictionary[d.display_label] === undefined ) {
console.log("not found");
SwissProt2colorDictionary[d.display_label] = p(i % p.range().length);
html = html + "<span style='opacity:0.6; background-color:"+SwissProt2colorDictionary[d.display_label]+"'>";
html = html + "<a href='http://www.uniprot.org/uniprot/?query="+d.display_label+"+AND+reviewed%3Ayes&sort=score'>";
html = html + d.display_label+"</a></span>: "+d.swissprot_protein_name+"</div><br>";
console.log("use color "+p(i % p.range().length)+" name : "+d.display_label);
//ID2Color[d.name] = p(0) SwissProt2color[i % p.domain().length];
//console.log("will use: "+p(i % p.domain().length);
//console.log(" draw "+d.swissprot_gene_name+" using "+SwissProt2colorDictionary[d.swissprot_gene_name]);
//return "red";
i++;
return SwissProt2colorDictionary[d.display_label];
}
else{
//console.log("found! using "+domain2color[d.name]);
//ID2Color[d.name] = SwissProt2colorDictionary[d.swissprot_gene_name];
return SwissProt2colorDictionary[d.display_label];
}
})
.attr("fill-opacity",0.2);
// draw legend
show_general_information({swissprot_annotation: html});
}
function show_general_information(args){
// will populate the following fields
var swissprot_annotation = args.swissprot_annotation|| "NaN";
// room for more annotation
// draw legend
//console.log('ID: '+id+'<br>Taxon: '+taxon+" <br>Gene name: "+gene_name+"<br>Swiss-Prot annotation: "+swissprot_annotation+"");
jQuery("#swissprot_annotation_container").html(swissprot_annotation);
}
function show_gene_information(d){
//d3.select("#domain_annotation_container").style("visibility", "hidden");
//d3.select("#sequence_annotation_container").attr("visibility", "");
// will populate the following fields
var id = d.name|| "NaN";
var taxon = d.taxon|| "NaN";
var gene_name = d.swissprot_gene_name|| "NaN";
var swissprot_annotation = d.swissprot_protein_name|| "NaN";
// draw legend
var url = species2sourceDB_mapping({species : taxon, identifier: id});
//console.log('ID: '+id+'<br>Taxon: '+taxon+" <br>Gene name: "+gene_name+"<br>Swiss-Prot annotation: "+swissprot_annotation+"");
jQuery("#container_seq_id").html("<a href='"+url+"'>"+id+"</a> ");
jQuery("#container_taxon_id").html("<font font-style='italic'>"+taxon+"</font>");
jQuery("#container_gene_name").html(gene_name);
jQuery("#container_swissprot_annotation").html(swissprot_annotation);
}
function show_domain_information(d){
// hide gene_information
//d3.select("#sequence_annotation_container").style("visibility", "hidden");
//d3.select("#domain_annotation_container").style("visibility", "");
// will populate the following fields
var name = d.name|| "NaN";
var start = d.domain_start|| "NaN";
var stop = d.domain_stop|| "NaN";
var annotation = d.swissprot_protein_name|| "NaN";
var evalue = d.evalue|| "NaN";
var length = d.domain_stop - d.domain_start || "NaN";
// draw legend
// console.log('Domain: '+name+'<br>Length: '+length+" AA<br> E-value: "+evalue+"<br>Start: "+start+" End: "+stop);
jQuery("#container_domain_name").html("<a href='http://pfam.sanger.ac.uk/family/"+name+"'>"+name+"</a>");
jQuery("#container_domain_coord").html(start+"-"+stop);
jQuery("#container_evalue_stop").html(evalue);
//jQuery("#container_domain_annotation").html(annotation);
jQuery("#container_domain_length").html(length);
}
function draw_gene_copies(args){
var gene_copies = args.gene_copies;
var sequence_start_y = args.sequence_start_y;
var domainScale = args.domainScale;
var leaf_group_x = args.leaf_group_x;
var domain_colors = args.domain_colors;
var sequence_rect_width = args.sequence_rect_width;
var visibility = args.visibility;
var domain2color = {};
//var sequences = nodeEnter.selectAll(".sequences").data(function(d) { return d.domains; });
console.log(gene_copies);
//var all_genes = sequences.append("rect")
var all_gene_copies = gene_copies.enter().append("rect")
.attr("x", leaf_group_x + 4)
.attr("y", function(d, i){
//console.log("draw domain from "+sequence_start_y+" to "+(sequence_start_y + domainOnlyScale(d.domain_start))+"("+d.domain_start+")");
return sequence_start_y + 40 + (i * 50);
})
.attr("class", "domain")
.attr("visibility",visibility)
.attr("rx", 5)
.attr("ry", 5)
.attr("transform", "matrix(1,0,0,1,100,0)")
.attr("stroke", "none")
.attr("width", function(d){return sequence_rect_width;})
.attr("height", function(d){
var length = 40;
console.log("sequence_rect: appending source is "+d.x);
//console.log("transform domain length "+(d.domain_stop - d.domain_start)+" to "+length);
return length;
})
.attr("transform", "rotate(-90 100 100)")
.attr("fill",
// "url(#domain_gradient)")
// ;
function(d,i){
//console.log("checking for "+d.name+" in domain2color");
// if( d.name in domain2color ) {
if( domain2color[d.name] === undefined ) {
//console.log("not found");
domain2color[d.name] = domain_colors[i % 5];
//console.log(d.name+" is "+i+" and will use: "+domain_colors[i]+ " length is "+domain_colors);
return "url(#"+domain_colors[i % 5]+")";
}
else{
//console.log("found! using "+domain2color[d.name]);
return "url(#"+domain2color[d.name]+")";
}
// return "url(#"+domain_colors[i]+")";
})
.on('mouseover', show_gene_information);
return all_gene_copies;
}
//
// interactive functions
//
// Internal text
function hide_internal_text(d) {
d3.select("#tree svg").selectAll(".innerNode_label").text(function(d){
return d.children ? "": d.taxon;
});
}
function show_internal_text(d) {
//console.log("we are here");
d3.select("#tree svg").selectAll(".innerNode_label").text(function(d) {
if(d.duplication == "Y"){
return "";
}
else{
return d.children ? d.name:d.taxon;
}
});
}
function show_internal_text_important(d) {
d3.select("#tree svg").selectAll(".innerNode_label").text(function(d) {
if(d.children){
if(show_taxa.hasOwnProperty(d.name)){
if(d.duplication == "Y"){
return "";
}
else{
return d.name;
}
}
}
else{
return d.taxon;
}
});
}
// show/hide IDS
function show_leaf_ids(d) {
d3.select("#tree svg").selectAll(".tax_color_rect").attr("visibility", "hidden");
d3.select("#tree svg").selectAll(".leaf_label").text(function(d) {
return d.name;
})
.classed("species_name", false);
}
// show/hide IDS
function show_gene_names(d) {
var ID2Color = new Object();
d3.select("#tree svg").selectAll(".tax_color_rect").attr("visibility", "hidden");
d3.select("#tree svg").selectAll(".leaf_label").text(function(d) {
//console.log("species "+d.taxon+" has common_name: "+d.display_label);
if( d.display_label === undefined || !d.display_label) {
return "N/A,"+d.common_name;
}
else{
return d.display_label+","+d.common_name;
}
})
.classed("species_name", false);
draw_taxon_colors_gene({ID2Color: ID2Color});
}
function show_common_names(d) {
d3.select("#tree svg").selectAll(".tax_color_rect").attr("visibility", "hidden");
d3.select("#tree svg").selectAll(".leaf_label").text(function(d) {
//console.log("species "+d.taxon+" has common_name: "+d.common_name);
if( d.common_name === undefined || !d.common_name) {
return "no common name";
}
else{
return d.common_name;
}
})
.classed("species_name", false);
}
function show_leaf_taxa(d) {
d3.select("#tree svg").selectAll(".tax_color_rect").attr("visibility", "hidden");
d3.select("#tree svg").selectAll(".leaf_label").text(function(d) {
return d.children ? d.name:d.taxon;
})
.classed("species_name", true);
}
function show_leaf_uniprot(d) {
d3.select("#tree svg").selectAll(".tax_color_rect").attr("visibility", "hidden");
var UniProt2color = ["grey","lightblue","lightgreen", "blue","green"];
var UniProt2colorDictionary = new Object();
d3.select("#tree svg").selectAll(".leaf_label")
.classed("species_name", false)
.text(function(d) {
if(d.uniprot_name == "NaN"){
d.uniprot_name = "not mapped";
}
return d.children ? d.name:d.uniprot_name;
})
.style("fill", function(d,i){
//if(!d.children){
// var matches = d.uniprot_name.match(/(.*)_(.*)/); // Match uniprot KB
// if(matches){
// console.log("looking at: "+d.uniprot_name+" with "+matches.length);
// if(typeof matches[1] !== 'undefined') {
// var uniprot_id = matches[1];
// console.log("found first part: "+uniprot_id);
// if( UniProt2colorDictionary[uniprot_id] === undefined ) {
// //console.log("not found");
// UniProt2colorDictionary[uniprot_id] = UniProt2color[i % UniProt2color.length];
// console.log("will use: "+UniProt2color[i % UniProt2color.length]);
// //return "red";
// return UniProt2color[i % UniProt2color.length];
// }
// else{
// //console.log("found! using "+domain2color[d.name]);
// return UniProt2colorDictionary[uniprot_id];
// }
// }
// if(typeof matches[2] !== 'undefined') {
// console.log("found second part: "+matches[2]);
// }
//
// }
// // console.log("matches: "+firstPart+" and: "+secondPart);
//
// }
});
// color uniprotkb ids
// e.g. BRCA2_HUMAN
// e.g all BRCA2 make color x
}
function show_leaf_swissprot(d) {
var SwissProt2color = ["darkgreen","red","blue","grey"];
var SwissProt2colorDictionary = new Object();
var ID2Color = new Object();
d3.select("#tree svg").selectAll(".leaf_label")
.text(function(d) {
if(d.swissprot_gene_name == "NaN"){
d.swissprot_gene_name = "not mapped";
}
return d.children ? d.name : ""+d.swissprot_gene_name+" ("+d.taxon+")";
});
// .style("fill", function(d,i){
// if(!d.children){
// if( SwissProt2colorDictionary[d.swissprot_gene_name] === undefined ) {
// //console.log("not found");
// SwissProt2colorDictionary[d.swissprot_gene_name] = SwissProt2color[i % SwissProt2color.length];
// ID2Color[d.name] = SwissProt2color[i % SwissProt2color.length];
//
// console.log("will use: "+SwissProt2color[i % SwissProt2color.length]);
// //return "red";
// return SwissProt2color[i % SwissProt2color.length];
// }
// else{
// //console.log("found! using "+domain2color[d.name]);
// ID2Color[d.name] = SwissProt2colorDictionary[d.swissprot_gene_name];
// return SwissProt2colorDictionary[d.swissprot_gene_name];
// }
// }
// });
draw_taxon_colors({ID2Color: ID2Color});
}
// show/hide Domains
function hide_domains(d) {
d3.select("#tree svg").selectAll(".domain").attr("visibility", "hidden");
d3.select("#tree svg").selectAll(".seq_string").attr("visibility", "hidden");
d3.select("#tree svg").selectAll(".domainlabel").attr("visibility", "hidden");
}
function show_domains(d) {
hide_conservation();
hide_synteny();
d3.select("#tree svg").selectAll(".domain").attr("visibility", "");
d3.select("#tree svg").selectAll(".seq_string").attr("visibility", "");
d3.select("#tree svg").selectAll(".domainlabel").attr("visibility", "");
}
// show/hide Conservation
function hide_conservation(d) {
d3.select("#tree svg").selectAll(".gap").attr("visibility", "hidden");
d3.select("#tree svg").selectAll(".aligned_seq_string").attr("visibility", "hidden");
//d3.select("#tree svg").selectAll(".domainlabel").attr("visibility", "hidden");
}
function show_conservation(d) {
hide_domains();
hide_synteny();
d3.select("#tree svg").selectAll(".gap").attr("visibility", "");
d3.select("#tree svg").selectAll(".aligned_seq_string").attr("visibility", "");
//d3.select("#tree svg").selectAll(".domainlabel").attr("visibility", "");
}
// show/hide Gene neighborhood
function hide_synteny(d) {
d3.select("#tree svg").selectAll(".synteny").attr("visibility", "hidden");
d3.select("#tree svg").selectAll(".synteny_seq_string").attr("visibility", "hidden");
//d3.select("#tree svg").selectAll(".domainlabel").attr("visibility", "hidden");
}
function show_synteny(d) {
hide_domains();
hide_conservation();
d3.select("#tree svg").selectAll(".synteny").attr("visibility", "");
d3.select("#tree svg").selectAll(".synteny_seq_string").attr("visibility", "");
//d3.select("#tree svg").selectAll(".domainlabel").attr("visibility", "");
}
// show/hide Bootstrap
function show_bootstrap(d){
d3.select("#tree svg").selectAll(".bootstrap").attr("visibility", "");
}
function hide_bootstrap(d){
d3.select("#tree svg").selectAll(".bootstrap").attr("visibility", "hidden");
}
// Images
function hide_images(d) {
d3.select("#tree svg").selectAll("image").attr("visibility", "hidden");
}
function show_images(d) {
d3.select("#tree svg").selectAll("image").attr("visibility", "");
}
// evolutionary events
function hide_evol_nodes(d) {
d3.select("#tree svg").selectAll("circle").attr("fill", "black");
}
function show_evol_nodes(d) {
d3.select("#tree svg").selectAll("image").attr("visibility", "");
d3.select("#tree svg").selectAll("circle")
//.attr("r", function(d){
// if(d.children){
// return d.duplication == "Y"? 10:5;
// }
//})
.attr("fill", function(d){return d.duplication == "Y"? "red":"green"})
.on("click", click);
}
// Taxon colors
function show_taxon_colors(d){
d3.select("#tree svg").selectAll(".tax_color").attr("visibility", "");
}
function hide_taxon_colors(d){
d3.select("#tree svg").selectAll(".tax_color").attr("visibility", "hidden");
}
// Font size
function increase_font_size(d){
console.log("in ")
d3.select("svg").selectAll("text").attr("font-size", "30");
}
function decrease_font_size(d){
d3.select("svg").selectAll("text").attr("font-size", "4");
}
// Functions to be tested
function show_orthologs(d){
// Walk parent chain
var ancestors = [];
var parent = d;
while (!_.isUndefined(parent) && parent.duplication != "Y") {
ancestors.push(parent);
parent = parent.parent;
}
// console.log(parent);
// console.log("(before: Found "+ancestors.length+" ancestors");
// ancestors = ancestors.slice(0,ancestors.length -1);
// console.log("(sliced: "+ancestors.length+" ancestors");
// console.log(ancestors);
// console.log("getting children for "+parent.name+"");
//
// var additional_children = get_all_children(parent);
// if(additional_children != null){
// console.log("(from children: Found "+additional_children.length+" children");
// additional_children.forEach(function(node){
// console.log(node);
// ancestors.push(node);
// })
// }
// ok, we now have all parents, but lets now collect all children
//while (!_.isUndefined(parent.children)) {
// parent.children.forEach(function(d) {
// while (!_.isUndefined(d.children)) {
// }
// ancestors.push(parent.children)
//}
//console.log("(after: Found "+ancestors.length+" ancestors");
// Get the matched links
var matchedLinks = [];
d3.selectAll('path.link')
.filter(function(d, i)
{
return _.any(ancestors, function(p)
{
return p === d.target;
});
})
.each(function(d)
{
matchedLinks.push(d);
});
//console.log("found "+matchedLinks.length+" links");
//console.log("found "+ancestors.length+" ancestors");
animateParentChain(matchedLinks, ancestors);
//matchedLinks.attr("stroke-width", "2.5px");
}
function animateParentChain(links, nodes, color){
console.log("coloring with "+color);
d3.selectAll("circle")
.data(nodes)
.enter().append("svg:circle")
.attr("r", function(d){ return d.children ? circle_size : 0; })
.attr("fill", color);
var linkRenderer = d3.svg.diagonal()
.projection(function(d)
{
return [d.y, d.x];
});
// Links
ui.animGroup.selectAll("path.selected")
.data([])
.exit().remove();
//console.log("removed previous links");
ui.animGroup
.selectAll("path.selected")
.data(links)
.enter().append("svg:path")
.attr("class", "selected link")
.attr("d", elbow);
// .attr("stroke-width", function(d){
// return "3.5px";
// })
// .attr("stroke", function(d){
// //console.log("has property for "+d.source.name);
// return "black";
// //return taxon_colors.hasOwnProperty(d.name)? taxon_colors[d.name]: "black";
// })
// .attr("d", elbow)
//console.log("selected new links");
// Animate the clipping path
var overlayBox = ui.svgRoot.node().getBBox();
//console.log("initiated overlay box");
ui.svgRoot.select("#clip-rect")
.attr("x", overlayBox.x + overlayBox.width)
.attr("y", overlayBox.y)
.attr("width", 0)
.attr("height", overlayBox.height)
.transition().duration(500)
.attr("x", overlayBox.x)
.attr("width", overlayBox.width);
//console.log("attached animation");
}
function show_tax_group(d){
// have predefined set of inner nodes
// iterate over those nodes and find them in the tree
for(var taxon in show_taxa){
console.log("ok, collect them all for "+taxon);
var chosen_nodes = d3.select("#tree svg").selectAll("[name=Eutheria]");
console.log(chosen_nodes);
chosen_nodes.each(function(chosen_node){
var collected_nodes = get_all_children(chosen_node);
if(collected_nodes != null){
console.log("end, collected: "+collected_nodes.length+" elements");
}
})
//console.log("well, we return after the first one");
return;
}
// get all children for
}
function color_subtree(d, color){
console.log("Color subtree for "+d.name);
var collected_nodes = get_all_children(d);
if(collected_nodes != null){
console.log("end, collected: "+collected_nodes.length+" elements");
}
// Get the matched links
var matchedLinks = [];
d3.selectAll('path.link')
.filter(function(d, i)
{
return _.any(collected_nodes, function(p)
{
return p === d.target;
});
})
.each(function(d)
{
matchedLinks.push(d);
});
color = "darkgreen";
animateParentChain(matchedLinks, collected_nodes, color);
}
function get_all_children(d){
var all_children = new Array;
//return ;
all_children = get_all_childs(d);
if(all_children != null){
//console.log("end, our array has: "+all_children.length+" elements");
all_children.forEach(function(elem){
//console.log(elem);
});
}
else{
console.log("Could not find children");
}
return all_children;
}
function get_all_childs(d){
var temp_array = new Array;
//console.log("in the get_all_childs for "+d.name+" with id: "+d.id);
if(d.children){
var children = d.children;
for (var i = 0; i < children.length; i++) {
var temp_array_child = new Array;
if(temp_array_child != null){
temp_array_child = get_all_childs(children[i]);
// console.log("got from child: : "+temp_array_child.length+" children");
temp_array_child.forEach(function(elem){
//console.log(elem);
temp_array.push(elem);
})
}
//temp_array.push(temp_array_child);
}
temp_array.push(d);
}
else{
//console.log("well, this is a child, return its name: "+d);
temp_array.push(d);
return temp_array;
}
return temp_array;
}
function submit_download_form(output_format){
// Get the d3js SVG element
var tmp = document.getElementById("tree");
var svg = tmp.getElementsByTagName("svg")[0];
// Extract the data as SVG text string
var svg_xml = (new XMLSerializer).serializeToString(svg);
// Submit the <FORM> to the server.
// The result will be an attachment file to download.
var form = document.getElementById("svgform");
form['output_format'].value = output_format;
form['data'].value = svg_xml ;
form.submit();
}
function show_svg_code(){
// Get the d3js SVG element
var tmp = document.getElementById("tree");
var svg = tmp.getElementsByTagName("svg")[0];
// Extract the data as SVG text string
var svg_xml = (new XMLSerializer).serializeToString(svg);
//Optional: prettify the XML with proper indentations
svg_xml = vkbeautify.xml(svg_xml);
// Set the content of the <pre> element with the XML
jQuery("#svg_code").text(svg_xml);
//Optional: Use Google-Code-Prettifier to add colors.
prettyPrint();
}
function search_gene(d, highlight_gene){
//console.log("we are here");
d3.select("#tree svg").selectAll(".leaf_label").text(function(d) {
console.log("checking "+highlight_gene+" = "+d.name);
if(d.name == highlight_gene){
return "";
}
else{
return d.children ? d.name:d.taxon;
}
});
}
function species2sourceDB_mapping(args){
var species = args.species;
var id = args.identifier;
var ensembl_species = new Object();
var ensembl_genomes_species = new Object();
var species2db = new Object();
var url = "";
species2db["acyrthosiphon_pisum"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["aedes_aegypti"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["ailuropoda_melanoleuca"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["amphimedon_queenslandica"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["anolis_carolinensis"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["anopheles_darlingi"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["anopheles_gambiae"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["apis_mellifera"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["arabidopsis_thaliana"] = "http://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["atta_cephalotes"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["bombyx_mori"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["bos_taurus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["bursaphelenchus_xylophilus"] = "http://www.wormbase.org/search/gene/";
species2db["caenorhabditis_brenneri"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["caenorhabditis_briggsae"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["caenorhabditis_elegans"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["caenorhabditis_japonica"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["caenorhabditis_remanei"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["callithrix_jacchus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["canis_familiaris"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["capitella_teleta"] = "http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=Capca1&id=";
species2db["cavia_porcellus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["choloepus_hoffmanni"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["ciona_intestinalis"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["ciona_savignyi"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["culex_quinquefasciatus"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["danaus_plexippus"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["danio_rerio"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["daphnia_pulex"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["dasypus_novemcinctus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["dipodomys_ordii"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["drosophila_ananassae"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_erecta"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_grimshawi"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_melanogaster"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_mojavensis"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_persimilis"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_pseudoobscura"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_sechellia"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_simulans"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_virilis"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_willistoni"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["drosophila_yakuba"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["echinops_telfairi"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["equus_caballus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["erinaceus_europaeus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["felis_catus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["gadus_morhua"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["gallus_gallus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["gasterosteus_aculeatus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["gorilla_gorilla"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["heliconius_melpomene"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["helobdella_robusta"] = "http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=Helro1&id=";
species2db["heterorhabditis_bacteriophora"] = "http://www.wormbase.org/search/gene/";
species2db["homo_sapiens"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["ictidomys_tridecemlineatus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["ixodes_scapularis"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["latimeria_chalumnae"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["lottia_gigantea"] = "http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=Lotgi1&id=";
species2db["loxodonta_africana"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["macaca_mulatta"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["macropus_eugenii"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["meleagris_gallopavo"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["meloidogyne_hapla"] = "http://www.wormbase.org/search/gene/";
species2db["microcebus_murinus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["monodelphis_domestica"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["monosiga_brevicollis"] = "http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=Monbr1&id=";
species2db["mustela_putorius_furo"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["mus_musculus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["myotis_lucifugus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["nasonia_vitripennis"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["nematostella_vectensis"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["nomascus_leucogenys"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["ochotona_princeps"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["oreochromis_niloticus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["ornithorhynchus_anatinus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["oryctolagus_cuniculus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["oryzias_latipes"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["otolemur_garnettii"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["pan_troglodytes"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["pediculus_humanus"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["pelodiscus_sinensis"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["petromyzon_marinus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["pongo_abelii"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["pristionchus_pacificus"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["procavia_capensis"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["proterospongia_sp"] = "nle_MAKER_updated_Ensembl";
species2db["pteropus_vampyrus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["rattus_norvegicus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["saccharomyces_cerevisiae"] = "http://fungi.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["sarcophilus_harrisii"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["schistosoma_mansoni"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["schizosaccharomyces_pombe"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["sorex_araneus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["strongylocentrotus_purpuratus"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["strongyloides_ratti"] = "http://www.wormbase.org/search/gene/";
species2db["sus_scrofa"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["taeniopygia_guttata"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["takifugu_rubripes"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["tarsius_syrichta"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["tetraodon_nigroviridis"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["tribolium_castaneum"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["trichinella_spiralis"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["trichoplax_adhaerens"] = "http://metazoa.ensembl.org/Multi/Search/Results?species=all;q=";
species2db["tupaia_belangeri"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["tursiops_truncatus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["vicugna_pacos"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["xenopus_tropicalis"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
species2db["xiphophorus_maculatus"] = "http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q=";
if(species == "capitella_teleta"){
}
//console.log("Looking at id "+id+" from species "+species);
url = species2db[species.toLowerCase()]+id;
//console.log("url is "+url);
// return URL for given ID
return url;
}
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