Warning (2)CORE/Cake/View/View.php , line 971 ]Code Context ob_start (); include $this -> __viewFile ; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/second_navigation.ctp'
$dataForView = array(
'navigation_bar_info' => array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false
),
'all_species' => array(
'acertr' => array(
'species' => 'acertr',
'common_name' => 'Acer truncatum',
'tax_id' => '47965',
'version' => 'v2.0'
),
'ach' => array(
'species' => 'ach',
'common_name' => 'Actinidia chinensis',
'tax_id' => '3625',
'version' => 'V3.0'
),
'aar' => array(
'species' => 'aar',
'common_name' => 'Aethionema arabicum',
'tax_id' => '228871',
'version' => 'v3.1'
),
'amhyb' => array(
'species' => 'amhyb',
'common_name' => 'Amaranthus hybridus',
'tax_id' => '3565',
'version' => 'v1.0'
),
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333',
'version' => 'JGI v1.0'
),
'aag' => array(
'species' => 'aag',
'common_name' => 'Anthoceros agrestis',
'tax_id' => '41834',
'version' => 'v1.1'
),
'aox' => array(
'species' => 'aox',
'common_name' => 'Aquilegia oxysepala',
'tax_id' => '432649',
'version' => 'v1.0'
),
'aly' => array(
'species' => 'aly',
'common_name' => 'Arabidopsis lyrata',
'tax_id' => '59689',
'version' => 'JGI v2.1'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702',
'version' => 'Araport11'
),
'arhy' => array(
'species' => 'arhy',
'common_name' => 'Arachis hypogaea',
'tax_id' => '3818',
'version' => 'v1.0'
),
'ama' => array(
'species' => 'ama',
'common_name' => 'Avicennia marina',
'tax_id' => '82927',
'version' => 'v1.1 20200527'
),
'bvu' => array(
'species' => 'bvu',
'common_name' => 'Beta vulgaris',
'tax_id' => '161934',
'version' => 'EL10_1.0'
),
'bca' => array(
'species' => 'bca',
'common_name' => 'Brassica carinata',
'tax_id' => '52824',
'version' => 'V1.0'
),
'bna' => array(
'species' => 'bna',
'common_name' => 'Brassica napus',
'tax_id' => '3708',
'version' => 'v2.0'
),
'bol' => array(
'species' => 'bol',
'common_name' => 'Brassica oleracea',
'tax_id' => '109376',
'version' => 'v1.0'
),
'bra' => array(
'species' => 'bra',
'common_name' => 'Brassica rapa',
'tax_id' => '3711',
'version' => 'v1.0'
),
'camsi' => array(
'species' => 'camsi',
'common_name' => 'Camellia sinensis var. sinensis',
'tax_id' => '542762',
'version' => 'CSS_ChrLev_20200506'
),
'cansat' => array(
'species' => 'cansat',
'common_name' => 'Cannabis sativa',
'tax_id' => '3483',
'version' => 'cs10'
),
'cru' => array(
'species' => 'cru',
'common_name' => 'Capsella rubella',
'tax_id' => '81985',
'version' => 'JGI v1.1'
),
'can' => array(
'species' => 'can',
'common_name' => 'Capsicum annuum',
'tax_id' => '4072',
'version' => 'Pepper Genome v2.0'
),
'chi' => array(
'species' => 'chi',
'common_name' => 'Cardamine hirsuta',
'tax_id' => '50463',
'version' => 'v1.0'
),
'cpa' => array(
'species' => 'cpa',
'common_name' => 'Carica papaya',
'tax_id' => '3649',
'version' => 'JGI ASGPB0.4'
),
'cfa' => array(
'species' => 'cfa',
'common_name' => 'Carpinus fangiana',
'tax_id' => '176857',
'version' => 'v1.0'
),
'cil' => array(
'species' => 'cil',
'common_name' => 'Carya illinoinensis',
'tax_id' => '32201',
'version' => 'v1.1'
),
'cde' => array(
'species' => 'cde',
'common_name' => 'Ceratophyllum demersum',
'tax_id' => '4428',
'version' => 'v1.0'
),
'cbr' => array(
'species' => 'cbr',
'common_name' => 'Chara braunii',
'tax_id' => '69332',
'version' => 'Cbr1.0'
),
'cqu' => array(
'species' => 'cqu',
'common_name' => 'Chenopodium quinoa',
'tax_id' => '63459',
'version' => 'KAUST v1.0'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055',
'version' => 'JGI v5.5'
),
'car' => array(
'species' => 'car',
'common_name' => 'Cicer arietinum L.',
'tax_id' => '3827',
'version' => 'v3.0'
),
'cla' => array(
'species' => 'cla',
'common_name' => 'Citrullus lanatus',
'tax_id' => '3654',
'version' => 'WCG v2.0'
),
'ccl' => array(
'species' => 'ccl',
'common_name' => 'Citrus clementina',
'tax_id' => '85681',
'version' => 'JGI v1.0'
),
'ccan' => array(
'species' => 'ccan',
'common_name' => 'Coffea canephora',
'tax_id' => '49390',
'version' => 'Coffee Genome Hub v1'
),
'col' => array(
'species' => 'col',
'common_name' => 'Corchorus olitorius',
'tax_id' => '93759',
'version' => 'GenBank v1.0'
),
'cav' => array(
'species' => 'cav',
'common_name' => 'Corylus avellana',
'tax_id' => '13451',
'version' => 'v1.0'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cucumis melo',
'tax_id' => '3656',
'version' => 'Melonomics v3.6.1'
),
'csa' => array(
'species' => 'csa',
'common_name' => 'Cucumis sativus L.',
'tax_id' => '3659',
'version' => 'v3.0'
),
'dca' => array(
'species' => 'dca',
'common_name' => 'Daucus carota',
'tax_id' => '4039',
'version' => 'JGI v2.0'
),
'din' => array(
'species' => 'din',
'common_name' => 'Davidia involucrata',
'tax_id' => '16924',
'version' => 'v1.0'
),
'dzi' => array(
'species' => 'dzi',
'common_name' => 'Durio zibethinus',
'tax_id' => '66656',
'version' => 'Duzib1.0'
),
'eca' => array(
'species' => 'eca',
'common_name' => 'Erigeron canadensis',
'tax_id' => '72917',
'version' => 'V1.0'
),
'egut' => array(
'species' => 'egut',
'common_name' => 'Erythranthe guttata',
'tax_id' => '4155',
'version' => 'v2.0'
),
'egr' => array(
'species' => 'egr',
'common_name' => 'Eucalyptus grandis',
'tax_id' => '71139',
'version' => 'v2.0'
),
'esa' => array(
'species' => 'esa',
'common_name' => 'Eutrema salsugineum',
'tax_id' => '72664',
'version' => 'v1.0'
),
'fve' => array(
'species' => 'fve',
'common_name' => 'Fragaria vesca',
'tax_id' => '57918',
'version' => 'V4.0.a2'
),
'fan' => array(
'species' => 'fan',
'common_name' => 'Fragaria x ananassa',
'tax_id' => '3747',
'version' => 'V1.0.a1'
),
'gma' => array(
'species' => 'gma',
'common_name' => 'Glycine max',
'tax_id' => '3847',
'version' => 'JGI Wm82.a4.v1'
),
'ghi' => array(
'species' => 'ghi',
'common_name' => 'Gossypium hirsutum',
'tax_id' => '3635',
'version' => 'v2.1'
),
'gra' => array(
'species' => 'gra',
'common_name' => 'Gossypium raimondii',
'tax_id' => '29730',
'version' => 'v2.1'
),
'han' => array(
'species' => 'han',
'common_name' => 'Helianthus annuus',
'tax_id' => '4232',
'version' => 'r1.2'
),
'hma' => array(
'species' => 'hma',
'common_name' => 'Hydrangea macrophylla',
'tax_id' => '23110',
'version' => 'v2.1'
),
'lsa' => array(
'species' => 'lsa',
'common_name' => 'Lactuca sativa',
'tax_id' => '4236',
'version' => 'v8.0'
),
'lonja' => array(
'species' => 'lonja',
'common_name' => 'Lonicera japonica',
'tax_id' => '105884',
'version' => 'v1.0'
),
'lja' => array(
'species' => 'lja',
'common_name' => 'Lotus japonicus',
'tax_id' => '34305',
'version' => 'Lj1.0v1'
),
'lal' => array(
'species' => 'lal',
'common_name' => 'Lupinus albus',
'tax_id' => '3870',
'version' => 'v1.0'
),
'mbi' => array(
'species' => 'mbi',
'common_name' => 'Magnolia biondii',
'tax_id' => '86725',
'version' => 'v1.0'
),
'mdo' => array(
'species' => 'mdo',
'common_name' => 'Malus domestica',
'tax_id' => '3750',
'version' => 'GDDH13 v1.1'
),
'mes' => array(
'species' => 'mes',
'common_name' => 'Manihot esculenta',
'tax_id' => '3983',
'version' => 'v8.1'
),
'mpo' => array(
'species' => 'mpo',
'common_name' => 'Marchantia polymorpha',
'tax_id' => '3197',
'version' => 'JGI v3.1'
),
'mtr' => array(
'species' => 'mtr',
'common_name' => 'Medicago truncatula',
'tax_id' => '3880',
'version' => 'JGI Mt4.0v1'
),
'mco' => array(
'species' => 'mco',
'common_name' => 'Micromonas commoda',
'tax_id' => '296587',
'version' => 'JGI v3.0'
),
'nnu' => array(
'species' => 'nnu',
'common_name' => 'Nelumbo nucifera',
'tax_id' => '4432',
'version' => 'v2.0'
),
'nta' => array(
'species' => 'nta',
'common_name' => 'Nicotiana tabacum',
'tax_id' => '4097',
'version' => 'Edwards2017'
),
'oeu' => array(
'species' => 'oeu',
'common_name' => 'Olea europaea',
'tax_id' => '4146',
'version' => 'v1.0'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa ssp. japonica',
'tax_id' => '39947',
'version' => 'IRGSP-1.0-2021-05-10'
),
'pso' => array(
'species' => 'pso',
'common_name' => 'Papaver somniferum',
'tax_id' => '3469',
'version' => 'ASM357369v1'
),
'pax' => array(
'species' => 'pax',
'common_name' => 'Petunia axillaris',
'tax_id' => '33119',
'version' => 'Sol Genomics v1.6.2'
),
'pvu' => array(
'species' => 'pvu',
'common_name' => 'Phaseolus vulgaris',
'tax_id' => '3885',
'version' => 'v2.1'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrium patens',
'tax_id' => '3218',
'version' => 'JGI v3.3'
),
'psa' => array(
'species' => 'psa',
'common_name' => 'Pisum sativum',
'tax_id' => '3888',
'version' => 'V1.0a'
),
'ptr' => array(
'species' => 'ptr',
'common_name' => 'Populus trichocarpa',
'tax_id' => '3694',
'version' => 'JGI v4.1'
),
'pco' => array(
'species' => 'pco',
'common_name' => 'Prasinoderma coloniale',
'tax_id' => '156133',
'version' => 'v1.0'
),
'ppe' => array(
'species' => 'ppe',
'common_name' => 'Prunus persica',
'tax_id' => '3760',
'version' => 'v2.1'
),
'pgr' => array(
'species' => 'pgr',
'common_name' => 'Punica granatum',
'tax_id' => '22663',
'version' => 'ASM765513v2'
),
'qlo' => array(
'species' => 'qlo',
'common_name' => 'Quercus lobata',
'tax_id' => '97700',
'version' => 'v3.0'
),
'rsi' => array(
'species' => 'rsi',
'common_name' => 'Rhododendron simsii',
'tax_id' => '118357',
'version' => 'v1.0'
),
'rch' => array(
'species' => 'rch',
'common_name' => 'Rosa chinensis',
'tax_id' => '74649',
'version' => 'v2.0'
),
'sbr' => array(
'species' => 'sbr',
'common_name' => 'Salix brachista',
'tax_id' => '2182728',
'version' => 'v1.0'
),
'sbo' => array(
'species' => 'sbo',
'common_name' => 'Salvia bowleyana',
'tax_id' => '424416',
'version' => 'v1.0'
),
'shi' => array(
'species' => 'shi',
'common_name' => 'Sapria himalayana',
'tax_id' => '289637',
'version' => 'v1.0'
),
'spa' => array(
'species' => 'spa',
'common_name' => 'Schrenkiella parvula',
'tax_id' => '98039',
'version' => 'v2.2'
),
'sed' => array(
'species' => 'sed',
'common_name' => 'Sechium edule',
'tax_id' => '184140',
'version' => 'v1.0'
),
'smo' => array(
'species' => 'smo',
'common_name' => 'Selaginella moellendorffii',
'tax_id' => '88036',
'version' => 'v1.0'
),
'sun' => array(
'species' => 'sun',
'common_name' => 'Selenicereus undatus',
'tax_id' => '176265',
'version' => 'v1.0'
),
'sgi' => array(
'species' => 'sgi',
'common_name' => 'Sequoiadendron giganteum',
'tax_id' => '99814',
'version' => 'V2.0'
),
'sci' => array(
'species' => 'sci',
'common_name' => 'Simmondsia chinensis',
'tax_id' => '3999',
'version' => 'sc1'
),
'sly' => array(
'species' => 'sly',
'common_name' => 'Solanum lycopersicum',
'tax_id' => '4081',
'version' => 'ITAG4.0'
),
'spe' => array(
'species' => 'spe',
'common_name' => 'Solanum pennellii',
'tax_id' => '28526',
'version' => 'V2.0'
),
'stu' => array(
'species' => 'stu',
'common_name' => 'Solanum tuberosum',
'tax_id' => '4113',
'version' => 'JGI v4.03'
),
'sas' => array(
'species' => 'sas',
'common_name' => 'Striga asiatica',
'tax_id' => '4170',
'version' => 'v2.02'
),
'tha' => array(
'species' => 'tha',
'common_name' => 'Tarenaya hassleriana',
'tax_id' => '28532',
'version' => 'RefSeq v1'
),
'tca' => array(
'species' => 'tca',
'common_name' => 'Theobroma cacao',
'tax_id' => '3641',
'version' => 'V2.1'
),
'tpr' => array(
'species' => 'tpr',
'common_name' => 'Trifolium pratense',
'tax_id' => '57577',
'version' => 'V2.0'
),
'twi' => array(
'species' => 'twi',
'common_name' => 'Tripterygium wilfordii',
'tax_id' => '458696',
'version' => 'ASM1340144v1'
),
'tar' => array(
'species' => 'tar',
'common_name' => 'Trochodendron aralioides',
'tax_id' => '4407',
'version' => 'v1.0'
),
'ugi' => array(
'species' => 'ugi',
'common_name' => 'Utricularia gibba',
'tax_id' => '13748',
'version' => 'v1.1F'
),
'vma' => array(
'species' => 'vma',
'common_name' => 'Vaccinium macrocarpon',
'tax_id' => '13750',
'version' => 'V1.0'
),
'vpl' => array(
'species' => 'vpl',
'common_name' => 'Vanilla planifolia',
'tax_id' => '51239',
'version' => 'Elo Vpla-A Principal v1.0'
),
'vmu' => array(
'species' => 'vmu',
'common_name' => 'Vigna mungo',
'tax_id' => '3915',
'version' => 'ASM1342719v1'
),
'vvi' => array(
'species' => 'vvi',
'common_name' => 'Vitis vinifera',
'tax_id' => '29760',
'version' => 'Genoscope.12x'
),
'zma' => array(
'species' => 'zma',
'common_name' => 'Zea mays',
'tax_id' => '4577',
'version' => 'NAM v5.0'
)
),
'multiplicon_data' => array(
(int) 1933599 => array(
'species' => 'sly',
'chromosome' => 'SL4.0ch02',
'data' => array(
[maximum depth reached]
)
),
(int) 1933600 => array(
'species' => 'camsi',
'chromosome' => 'Chr2',
'data' => array(
[maximum depth reached]
)
)
),
'children_multiplicon_information' => array(),
'parental_multiplicon_information' => array(),
'multiplicon_information' => array(
'multiplicon_id' => '966800',
'exp_id' => '1',
'info' => array(
'parent' => '0',
'level' => '2',
'num_anchorpoints' => '16',
'profile_length' => '96',
'is_redundant' => '-1'
),
'profile' => array(
'num_segments' => '2',
'num_species' => '2',
'species' => array(
[maximum depth reached]
)
)
),
'multiplicon_id' => '966800',
'iadhore_exp_id' => '1',
'title_for_layout' => 'Dicots PLAZA 5.0 : Colinearity Data',
'content_for_layout' => '<!-- Load the CSS files for this view -->
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/bootstrap-multiselect.min.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/multiplicon_svg.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/multiplicon_graph.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/tipsy.css"/>
<!-- Load the JS files for this view -->
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/snap.svg-min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/bootstrap-multiselect.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/gf_colors.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/multiplicon_svg.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/d3/d3.v5.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/dagre/dagre-d3.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/dagre/tipsy.js"></script>
<h1>
Multiplicon view:
<strong>966800</strong>
(Experiment Id: 1)
<a href='https://bioinformatics.psb.ugent.be/plaza/documentation/tools#multiplicon_view' target='_blank' onclick='window.open("https://bioinformatics.psb.ugent.be/plaza/documentation/tools#multiplicon_view","HELP","width=1000,height=600,scrollbars=yes,toolbar=no,location=no");return false;'>
<span class="glyphicon glyphicon-question-sign documentation_link"></span>
</a></h1>
<div class="mb-4">
<p>
The Multiplicon view displays the aligned gene strings of a set of homologous segments.
</p>
</div>
<h2>Multiplicon Information</h2>
<div class="mb-4">
<table class='table'>
<thead>
<tr>
<th>Multiplicon Id</th>
<th>#Species</th>
<th>#Segments</th>
<th>#Anchorpoints</th>
<th>Profile Length</th>
</tr>
</thead>
<tbody>
<tr>
<td>966800</td>
<td>2</td>
<td>2</td>
<td>16</td>
<td>96</td>
</tr>
</tbody>
</table>
</div>
<div class="mb-4">
<h2>
Multiplicon Plot
</h2>
<!-- left panel: contains the multiplicon SVG -->
<div class="d-flex flex-row flex-wrap mt-3">
<div class="d-flex flex-column col-lg-9">
<!-- multiplicon itself -->
<div>
<div id="multiplicon_loading" class='loader'></div>
<div id="multiplicon_view_div">
<svg id="multiplicon_svg"></svg>
</div>
</div>
<!-- GF graph -->
<!-- <div>
<div id='multiplicon_gf_graph_div'>
<svg id="multiplicon_gf_graph_svg" height="200">
<g />
</svg>
</div>
</div> -->
</div>
<!-- right panels: contain the options etc -->
<div class="col-lg-3 ps-4">
<div style="display:none" id="gene_gf_info">
<div class="parameter_option_box mb-3">
<h5>Gene Information</h5>
<div id="gene_information"></div>
<hr>
<h5>Gene Family Information</h5>
<div id="gf_information"></div>
</div>
</div>
<div class="parameter_option_box mb-3">
<h3>Options</h3>
<span>Draw mode</span>
<select class="form form-select" name="draw_mode_form_select" id="draw_mode_form_select">
<option value='all' selected='selected'>Display all genes</option>
<option value='anchor'>Display only anchorpoints</option>
</select>
<span>Segment ordering</span>
<select class="form form-select" name="ordering_form_select" id="ordering_form_select">
<option value='standard' selected='selected'>Use standard order</option>
<option value='cluster'>Group species together</option>
</select>
<span>Species</span>
<select class="form form-select" name="species_form_select" id="species_form_select" multiple="multiple">
<option value='camsi' selected='selected'>Camellia sinensis var. sinensis</option>
<option value='sly' selected='selected'>Solanum lycopersicum</option>
</select>
</div>
</div>
</div>
<!-- JS code to load species & create multiplicon SVG -->
<script type="text/javascript">
//<![CDATA[
jQuery(document).ready(function() {
//Enable the multiselect
jQuery("#species_form_select").multiselect({
disableIfEmpty: true,
enableFiltering: false,
maxHeight: 300,
includeSelectAllOption: true,
numberDisplayed: 2,
templates: {
button: '<button type="button" class="multiselect dropdown-toggle btn btn-light border" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-list-check me-2"></i><span class="multiselect-selected-text"></span></button>'
}
});
//setup the SVG for the graph to have a fixed width based on parental size
jQuery("#multiplicon_gf_graph_svg").attr("width", jQuery('#multiplicon_gf_graph_div').width());
//Hide the gene and gf info panel
jQuery("#gene_gf_info").hide();
//Create the multiplicon SVG
try {
let multiplicon_svg = new MultipliconSVG();
multiplicon_svg.options({
apiEndpointSpecies: '/plaza.dev/_dev_instances/feedback/api/list_species',
apiEndpointMultiplicon: '/plaza.dev/_dev_instances/feedback/collinearity/multiplicon_plot_data/1/966800',
apiEndpointGfFuncAnnotBase: '/plaza.dev/_dev_instances/feedback/api/gf_functional_annotation',
urlSpeciesBase: '/plaza.dev/_dev_instances/feedback/organism/view',
urlGeneBase: '/plaza.dev/_dev_instances/feedback/genes/view',
urlGeneFamilyBase: '/plaza.dev/_dev_instances/feedback/gene_families/view',
urlGoBase: '/plaza.dev/_dev_instances/feedback/go/view',
urlInterproBase: '/plaza.dev/_dev_instances/feedback/interpro/view',
urlMapmanBase: '/plaza.dev/_dev_instances/feedback/mapman/view',
idMain: 'multiplicon_svg',
idLoading: 'multiplicon_loading',
idPanelGene: 'gene_information',
idPanelGeneFamily: 'gf_information',
idPanelGeneGF: 'gene_gf_info',
idSelectDrawMode: 'draw_mode_form_select',
idSelectOrder: 'ordering_form_select',
idSelectSpecies: 'species_form_select',
idGraph: 'multiplicon_gf_graph_svg'
});
multiplicon_svg.render();
//Allow for the resizing of the view
jQuery(window).resize(multiplicon_svg.debouncer(function(e) {
multiplicon_svg.render();
}));
} catch (error) {
jQuery("#multiplicon_loading").hide();
jQuery("#multiplicon_view_div").show();
jQuery("#multiplicon_view_div").html("Error while loading multiplicon");
}
});
//]]>
</script>
</div>
<h2>Data Table</h2>
<div id="data_table_div">
<table class='table'>
<thead>
<tr>
<th>Species</th>
<th>Chromosome</th>
<th>First Gene</th>
<th>Last Gene</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/organism/view/Camellia%2Bsinensis%2Bvar.%2Bsinensis">Camellia sinensis var. sinensis</a></td>
<td>Chr2</td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/CSS0005295">CSS0005295</a></td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/CSS0012962">CSS0012962</a></td>
</tr>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/organism/view/Solanum%2Blycopersicum">Solanum lycopersicum</a></td>
<td>SL4.0ch02</td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/Solyc02g088090.1">Solyc02g088090.1</a></td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/Solyc02g089200.4">Solyc02g089200.4</a></td>
</tr>
</tbody>
</table>
</div>
',
'scripts_for_layout' => ''
)
$navigation_bar_info = array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false
)
$all_species = array(
'acertr' => array(
'species' => 'acertr',
'common_name' => 'Acer truncatum',
'tax_id' => '47965',
'version' => 'v2.0'
),
'ach' => array(
'species' => 'ach',
'common_name' => 'Actinidia chinensis',
'tax_id' => '3625',
'version' => 'V3.0'
),
'aar' => array(
'species' => 'aar',
'common_name' => 'Aethionema arabicum',
'tax_id' => '228871',
'version' => 'v3.1'
),
'amhyb' => array(
'species' => 'amhyb',
'common_name' => 'Amaranthus hybridus',
'tax_id' => '3565',
'version' => 'v1.0'
),
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333',
'version' => 'JGI v1.0'
),
'aag' => array(
'species' => 'aag',
'common_name' => 'Anthoceros agrestis',
'tax_id' => '41834',
'version' => 'v1.1'
),
'aox' => array(
'species' => 'aox',
'common_name' => 'Aquilegia oxysepala',
'tax_id' => '432649',
'version' => 'v1.0'
),
'aly' => array(
'species' => 'aly',
'common_name' => 'Arabidopsis lyrata',
'tax_id' => '59689',
'version' => 'JGI v2.1'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702',
'version' => 'Araport11'
),
'arhy' => array(
'species' => 'arhy',
'common_name' => 'Arachis hypogaea',
'tax_id' => '3818',
'version' => 'v1.0'
),
'ama' => array(
'species' => 'ama',
'common_name' => 'Avicennia marina',
'tax_id' => '82927',
'version' => 'v1.1 20200527'
),
'bvu' => array(
'species' => 'bvu',
'common_name' => 'Beta vulgaris',
'tax_id' => '161934',
'version' => 'EL10_1.0'
),
'bca' => array(
'species' => 'bca',
'common_name' => 'Brassica carinata',
'tax_id' => '52824',
'version' => 'V1.0'
),
'bna' => array(
'species' => 'bna',
'common_name' => 'Brassica napus',
'tax_id' => '3708',
'version' => 'v2.0'
),
'bol' => array(
'species' => 'bol',
'common_name' => 'Brassica oleracea',
'tax_id' => '109376',
'version' => 'v1.0'
),
'bra' => array(
'species' => 'bra',
'common_name' => 'Brassica rapa',
'tax_id' => '3711',
'version' => 'v1.0'
),
'camsi' => array(
'species' => 'camsi',
'common_name' => 'Camellia sinensis var. sinensis',
'tax_id' => '542762',
'version' => 'CSS_ChrLev_20200506'
),
'cansat' => array(
'species' => 'cansat',
'common_name' => 'Cannabis sativa',
'tax_id' => '3483',
'version' => 'cs10'
),
'cru' => array(
'species' => 'cru',
'common_name' => 'Capsella rubella',
'tax_id' => '81985',
'version' => 'JGI v1.1'
),
'can' => array(
'species' => 'can',
'common_name' => 'Capsicum annuum',
'tax_id' => '4072',
'version' => 'Pepper Genome v2.0'
),
'chi' => array(
'species' => 'chi',
'common_name' => 'Cardamine hirsuta',
'tax_id' => '50463',
'version' => 'v1.0'
),
'cpa' => array(
'species' => 'cpa',
'common_name' => 'Carica papaya',
'tax_id' => '3649',
'version' => 'JGI ASGPB0.4'
),
'cfa' => array(
'species' => 'cfa',
'common_name' => 'Carpinus fangiana',
'tax_id' => '176857',
'version' => 'v1.0'
),
'cil' => array(
'species' => 'cil',
'common_name' => 'Carya illinoinensis',
'tax_id' => '32201',
'version' => 'v1.1'
),
'cde' => array(
'species' => 'cde',
'common_name' => 'Ceratophyllum demersum',
'tax_id' => '4428',
'version' => 'v1.0'
),
'cbr' => array(
'species' => 'cbr',
'common_name' => 'Chara braunii',
'tax_id' => '69332',
'version' => 'Cbr1.0'
),
'cqu' => array(
'species' => 'cqu',
'common_name' => 'Chenopodium quinoa',
'tax_id' => '63459',
'version' => 'KAUST v1.0'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055',
'version' => 'JGI v5.5'
),
'car' => array(
'species' => 'car',
'common_name' => 'Cicer arietinum L.',
'tax_id' => '3827',
'version' => 'v3.0'
),
'cla' => array(
'species' => 'cla',
'common_name' => 'Citrullus lanatus',
'tax_id' => '3654',
'version' => 'WCG v2.0'
),
'ccl' => array(
'species' => 'ccl',
'common_name' => 'Citrus clementina',
'tax_id' => '85681',
'version' => 'JGI v1.0'
),
'ccan' => array(
'species' => 'ccan',
'common_name' => 'Coffea canephora',
'tax_id' => '49390',
'version' => 'Coffee Genome Hub v1'
),
'col' => array(
'species' => 'col',
'common_name' => 'Corchorus olitorius',
'tax_id' => '93759',
'version' => 'GenBank v1.0'
),
'cav' => array(
'species' => 'cav',
'common_name' => 'Corylus avellana',
'tax_id' => '13451',
'version' => 'v1.0'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cucumis melo',
'tax_id' => '3656',
'version' => 'Melonomics v3.6.1'
),
'csa' => array(
'species' => 'csa',
'common_name' => 'Cucumis sativus L.',
'tax_id' => '3659',
'version' => 'v3.0'
),
'dca' => array(
'species' => 'dca',
'common_name' => 'Daucus carota',
'tax_id' => '4039',
'version' => 'JGI v2.0'
),
'din' => array(
'species' => 'din',
'common_name' => 'Davidia involucrata',
'tax_id' => '16924',
'version' => 'v1.0'
),
'dzi' => array(
'species' => 'dzi',
'common_name' => 'Durio zibethinus',
'tax_id' => '66656',
'version' => 'Duzib1.0'
),
'eca' => array(
'species' => 'eca',
'common_name' => 'Erigeron canadensis',
'tax_id' => '72917',
'version' => 'V1.0'
),
'egut' => array(
'species' => 'egut',
'common_name' => 'Erythranthe guttata',
'tax_id' => '4155',
'version' => 'v2.0'
),
'egr' => array(
'species' => 'egr',
'common_name' => 'Eucalyptus grandis',
'tax_id' => '71139',
'version' => 'v2.0'
),
'esa' => array(
'species' => 'esa',
'common_name' => 'Eutrema salsugineum',
'tax_id' => '72664',
'version' => 'v1.0'
),
'fve' => array(
'species' => 'fve',
'common_name' => 'Fragaria vesca',
'tax_id' => '57918',
'version' => 'V4.0.a2'
),
'fan' => array(
'species' => 'fan',
'common_name' => 'Fragaria x ananassa',
'tax_id' => '3747',
'version' => 'V1.0.a1'
),
'gma' => array(
'species' => 'gma',
'common_name' => 'Glycine max',
'tax_id' => '3847',
'version' => 'JGI Wm82.a4.v1'
),
'ghi' => array(
'species' => 'ghi',
'common_name' => 'Gossypium hirsutum',
'tax_id' => '3635',
'version' => 'v2.1'
),
'gra' => array(
'species' => 'gra',
'common_name' => 'Gossypium raimondii',
'tax_id' => '29730',
'version' => 'v2.1'
),
'han' => array(
'species' => 'han',
'common_name' => 'Helianthus annuus',
'tax_id' => '4232',
'version' => 'r1.2'
),
'hma' => array(
'species' => 'hma',
'common_name' => 'Hydrangea macrophylla',
'tax_id' => '23110',
'version' => 'v2.1'
),
'lsa' => array(
'species' => 'lsa',
'common_name' => 'Lactuca sativa',
'tax_id' => '4236',
'version' => 'v8.0'
),
'lonja' => array(
'species' => 'lonja',
'common_name' => 'Lonicera japonica',
'tax_id' => '105884',
'version' => 'v1.0'
),
'lja' => array(
'species' => 'lja',
'common_name' => 'Lotus japonicus',
'tax_id' => '34305',
'version' => 'Lj1.0v1'
),
'lal' => array(
'species' => 'lal',
'common_name' => 'Lupinus albus',
'tax_id' => '3870',
'version' => 'v1.0'
),
'mbi' => array(
'species' => 'mbi',
'common_name' => 'Magnolia biondii',
'tax_id' => '86725',
'version' => 'v1.0'
),
'mdo' => array(
'species' => 'mdo',
'common_name' => 'Malus domestica',
'tax_id' => '3750',
'version' => 'GDDH13 v1.1'
),
'mes' => array(
'species' => 'mes',
'common_name' => 'Manihot esculenta',
'tax_id' => '3983',
'version' => 'v8.1'
),
'mpo' => array(
'species' => 'mpo',
'common_name' => 'Marchantia polymorpha',
'tax_id' => '3197',
'version' => 'JGI v3.1'
),
'mtr' => array(
'species' => 'mtr',
'common_name' => 'Medicago truncatula',
'tax_id' => '3880',
'version' => 'JGI Mt4.0v1'
),
'mco' => array(
'species' => 'mco',
'common_name' => 'Micromonas commoda',
'tax_id' => '296587',
'version' => 'JGI v3.0'
),
'nnu' => array(
'species' => 'nnu',
'common_name' => 'Nelumbo nucifera',
'tax_id' => '4432',
'version' => 'v2.0'
),
'nta' => array(
'species' => 'nta',
'common_name' => 'Nicotiana tabacum',
'tax_id' => '4097',
'version' => 'Edwards2017'
),
'oeu' => array(
'species' => 'oeu',
'common_name' => 'Olea europaea',
'tax_id' => '4146',
'version' => 'v1.0'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa ssp. japonica',
'tax_id' => '39947',
'version' => 'IRGSP-1.0-2021-05-10'
),
'pso' => array(
'species' => 'pso',
'common_name' => 'Papaver somniferum',
'tax_id' => '3469',
'version' => 'ASM357369v1'
),
'pax' => array(
'species' => 'pax',
'common_name' => 'Petunia axillaris',
'tax_id' => '33119',
'version' => 'Sol Genomics v1.6.2'
),
'pvu' => array(
'species' => 'pvu',
'common_name' => 'Phaseolus vulgaris',
'tax_id' => '3885',
'version' => 'v2.1'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrium patens',
'tax_id' => '3218',
'version' => 'JGI v3.3'
),
'psa' => array(
'species' => 'psa',
'common_name' => 'Pisum sativum',
'tax_id' => '3888',
'version' => 'V1.0a'
),
'ptr' => array(
'species' => 'ptr',
'common_name' => 'Populus trichocarpa',
'tax_id' => '3694',
'version' => 'JGI v4.1'
),
'pco' => array(
'species' => 'pco',
'common_name' => 'Prasinoderma coloniale',
'tax_id' => '156133',
'version' => 'v1.0'
),
'ppe' => array(
'species' => 'ppe',
'common_name' => 'Prunus persica',
'tax_id' => '3760',
'version' => 'v2.1'
),
'pgr' => array(
'species' => 'pgr',
'common_name' => 'Punica granatum',
'tax_id' => '22663',
'version' => 'ASM765513v2'
),
'qlo' => array(
'species' => 'qlo',
'common_name' => 'Quercus lobata',
'tax_id' => '97700',
'version' => 'v3.0'
),
'rsi' => array(
'species' => 'rsi',
'common_name' => 'Rhododendron simsii',
'tax_id' => '118357',
'version' => 'v1.0'
),
'rch' => array(
'species' => 'rch',
'common_name' => 'Rosa chinensis',
'tax_id' => '74649',
'version' => 'v2.0'
),
'sbr' => array(
'species' => 'sbr',
'common_name' => 'Salix brachista',
'tax_id' => '2182728',
'version' => 'v1.0'
),
'sbo' => array(
'species' => 'sbo',
'common_name' => 'Salvia bowleyana',
'tax_id' => '424416',
'version' => 'v1.0'
),
'shi' => array(
'species' => 'shi',
'common_name' => 'Sapria himalayana',
'tax_id' => '289637',
'version' => 'v1.0'
),
'spa' => array(
'species' => 'spa',
'common_name' => 'Schrenkiella parvula',
'tax_id' => '98039',
'version' => 'v2.2'
),
'sed' => array(
'species' => 'sed',
'common_name' => 'Sechium edule',
'tax_id' => '184140',
'version' => 'v1.0'
),
'smo' => array(
'species' => 'smo',
'common_name' => 'Selaginella moellendorffii',
'tax_id' => '88036',
'version' => 'v1.0'
),
'sun' => array(
'species' => 'sun',
'common_name' => 'Selenicereus undatus',
'tax_id' => '176265',
'version' => 'v1.0'
),
'sgi' => array(
'species' => 'sgi',
'common_name' => 'Sequoiadendron giganteum',
'tax_id' => '99814',
'version' => 'V2.0'
),
'sci' => array(
'species' => 'sci',
'common_name' => 'Simmondsia chinensis',
'tax_id' => '3999',
'version' => 'sc1'
),
'sly' => array(
'species' => 'sly',
'common_name' => 'Solanum lycopersicum',
'tax_id' => '4081',
'version' => 'ITAG4.0'
),
'spe' => array(
'species' => 'spe',
'common_name' => 'Solanum pennellii',
'tax_id' => '28526',
'version' => 'V2.0'
),
'stu' => array(
'species' => 'stu',
'common_name' => 'Solanum tuberosum',
'tax_id' => '4113',
'version' => 'JGI v4.03'
),
'sas' => array(
'species' => 'sas',
'common_name' => 'Striga asiatica',
'tax_id' => '4170',
'version' => 'v2.02'
),
'tha' => array(
'species' => 'tha',
'common_name' => 'Tarenaya hassleriana',
'tax_id' => '28532',
'version' => 'RefSeq v1'
),
'tca' => array(
'species' => 'tca',
'common_name' => 'Theobroma cacao',
'tax_id' => '3641',
'version' => 'V2.1'
),
'tpr' => array(
'species' => 'tpr',
'common_name' => 'Trifolium pratense',
'tax_id' => '57577',
'version' => 'V2.0'
),
'twi' => array(
'species' => 'twi',
'common_name' => 'Tripterygium wilfordii',
'tax_id' => '458696',
'version' => 'ASM1340144v1'
),
'tar' => array(
'species' => 'tar',
'common_name' => 'Trochodendron aralioides',
'tax_id' => '4407',
'version' => 'v1.0'
),
'ugi' => array(
'species' => 'ugi',
'common_name' => 'Utricularia gibba',
'tax_id' => '13748',
'version' => 'v1.1F'
),
'vma' => array(
'species' => 'vma',
'common_name' => 'Vaccinium macrocarpon',
'tax_id' => '13750',
'version' => 'V1.0'
),
'vpl' => array(
'species' => 'vpl',
'common_name' => 'Vanilla planifolia',
'tax_id' => '51239',
'version' => 'Elo Vpla-A Principal v1.0'
),
'vmu' => array(
'species' => 'vmu',
'common_name' => 'Vigna mungo',
'tax_id' => '3915',
'version' => 'ASM1342719v1'
),
'vvi' => array(
'species' => 'vvi',
'common_name' => 'Vitis vinifera',
'tax_id' => '29760',
'version' => 'Genoscope.12x'
),
'zma' => array(
'species' => 'zma',
'common_name' => 'Zea mays',
'tax_id' => '4577',
'version' => 'NAM v5.0'
)
)
$multiplicon_data = array(
(int) 1933599 => array(
'species' => 'sly',
'chromosome' => 'SL4.0ch02',
'data' => array(
(int) 0 => array(
[maximum depth reached]
),
(int) 1 => array(
[maximum depth reached]
),
(int) 2 => array(
[maximum depth reached]
),
(int) 3 => array(
[maximum depth reached]
),
(int) 4 => array(
[maximum depth reached]
),
(int) 5 => array(
[maximum depth reached]
),
(int) 6 => array(
[maximum depth reached]
),
(int) 7 => array(
[maximum depth reached]
),
(int) 8 => array(
[maximum depth reached]
),
(int) 9 => array(
[maximum depth reached]
),
(int) 10 => array(
[maximum depth reached]
),
(int) 11 => array(
[maximum depth reached]
),
(int) 12 => array(
[maximum depth reached]
),
(int) 13 => array(
[maximum depth reached]
),
(int) 14 => array(
[maximum depth reached]
),
(int) 15 => array(
[maximum depth reached]
),
(int) 16 => array(
[maximum depth reached]
),
(int) 17 => array(
[maximum depth reached]
),
(int) 18 => array(
[maximum depth reached]
),
(int) 19 => array(
[maximum depth reached]
),
(int) 20 => array(
[maximum depth reached]
),
(int) 21 => array(
[maximum depth reached]
),
(int) 22 => array(
[maximum depth reached]
),
(int) 23 => array(
[maximum depth reached]
),
(int) 24 => array(
[maximum depth reached]
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(int) 25 => array(
[maximum depth reached]
),
(int) 26 => array(
[maximum depth reached]
),
(int) 27 => array(
[maximum depth reached]
),
(int) 28 => array(
[maximum depth reached]
),
(int) 29 => array(
[maximum depth reached]
),
(int) 30 => array(
[maximum depth reached]
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(int) 31 => array(
[maximum depth reached]
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(int) 32 => array(
[maximum depth reached]
),
(int) 33 => array(
[maximum depth reached]
),
(int) 34 => array(
[maximum depth reached]
),
(int) 35 => array(
[maximum depth reached]
),
(int) 36 => array(
[maximum depth reached]
),
(int) 37 => array(
[maximum depth reached]
),
(int) 38 => array(
[maximum depth reached]
),
(int) 39 => array(
[maximum depth reached]
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(int) 40 => array(
[maximum depth reached]
),
(int) 41 => array(
[maximum depth reached]
),
(int) 42 => array(
[maximum depth reached]
),
(int) 43 => array(
[maximum depth reached]
),
(int) 44 => array(
[maximum depth reached]
),
(int) 45 => array(
[maximum depth reached]
),
(int) 46 => array(
[maximum depth reached]
),
(int) 47 => array(
[maximum depth reached]
),
(int) 48 => array(
[maximum depth reached]
),
(int) 49 => array(
[maximum depth reached]
),
(int) 50 => array(
[maximum depth reached]
),
(int) 51 => array(
[maximum depth reached]
),
(int) 52 => array(
[maximum depth reached]
),
(int) 53 => array(
[maximum depth reached]
),
(int) 54 => array(
[maximum depth reached]
),
(int) 55 => array(
[maximum depth reached]
),
(int) 56 => array(
[maximum depth reached]
),
(int) 57 => array(
[maximum depth reached]
),
(int) 58 => array(
[maximum depth reached]
),
(int) 59 => array(
[maximum depth reached]
),
(int) 60 => array(
[maximum depth reached]
),
(int) 61 => array(
[maximum depth reached]
),
(int) 62 => array(
[maximum depth reached]
),
(int) 63 => array(
[maximum depth reached]
),
(int) 64 => array(
[maximum depth reached]
),
(int) 65 => array(
[maximum depth reached]
),
(int) 66 => array(
[maximum depth reached]
),
(int) 67 => array(
[maximum depth reached]
),
(int) 68 => array(
[maximum depth reached]
),
(int) 69 => array(
[maximum depth reached]
),
(int) 70 => array(
[maximum depth reached]
),
(int) 71 => array(
[maximum depth reached]
),
(int) 72 => array(
[maximum depth reached]
),
(int) 73 => array(
[maximum depth reached]
),
(int) 74 => array(
[maximum depth reached]
),
(int) 75 => array(
[maximum depth reached]
),
(int) 76 => array(
[maximum depth reached]
),
(int) 77 => array(
[maximum depth reached]
),
(int) 78 => array(
[maximum depth reached]
),
(int) 79 => array(
[maximum depth reached]
),
(int) 80 => array(
[maximum depth reached]
),
(int) 81 => array(
[maximum depth reached]
),
(int) 82 => array(
[maximum depth reached]
),
(int) 83 => array(
[maximum depth reached]
),
(int) 84 => array(
[maximum depth reached]
),
(int) 85 => array(
[maximum depth reached]
),
(int) 86 => array(
[maximum depth reached]
),
(int) 87 => array(
[maximum depth reached]
),
(int) 88 => array(
[maximum depth reached]
),
(int) 89 => array(
[maximum depth reached]
),
(int) 90 => array(
[maximum depth reached]
),
(int) 91 => array(
[maximum depth reached]
),
(int) 92 => array(
[maximum depth reached]
),
(int) 93 => array(
[maximum depth reached]
),
(int) 94 => array(
[maximum depth reached]
),
(int) 95 => array(
[maximum depth reached]
)
)
),
(int) 1933600 => array(
'species' => 'camsi',
'chromosome' => 'Chr2',
'data' => array(
(int) 0 => array(
[maximum depth reached]
),
(int) 1 => array(
[maximum depth reached]
),
(int) 2 => array(
[maximum depth reached]
),
(int) 3 => array(
[maximum depth reached]
),
(int) 4 => array(
[maximum depth reached]
),
(int) 5 => array(
[maximum depth reached]
),
(int) 6 => array(
[maximum depth reached]
),
(int) 7 => array(
[maximum depth reached]
),
(int) 8 => array(
[maximum depth reached]
),
(int) 9 => array(
[maximum depth reached]
),
(int) 10 => array(
[maximum depth reached]
),
(int) 11 => array(
[maximum depth reached]
),
(int) 12 => array(
[maximum depth reached]
),
(int) 13 => array(
[maximum depth reached]
),
(int) 14 => array(
[maximum depth reached]
),
(int) 15 => array(
[maximum depth reached]
),
(int) 16 => array(
[maximum depth reached]
),
(int) 17 => array(
[maximum depth reached]
),
(int) 18 => array(
[maximum depth reached]
),
(int) 19 => array(
[maximum depth reached]
),
(int) 20 => array(
[maximum depth reached]
),
(int) 21 => array(
[maximum depth reached]
),
(int) 22 => array(
[maximum depth reached]
),
(int) 23 => array(
[maximum depth reached]
),
(int) 24 => array(
[maximum depth reached]
),
(int) 25 => array(
[maximum depth reached]
),
(int) 26 => array(
[maximum depth reached]
),
(int) 27 => array(
[maximum depth reached]
),
(int) 28 => array(
[maximum depth reached]
),
(int) 29 => array(
[maximum depth reached]
),
(int) 30 => array(
[maximum depth reached]
),
(int) 31 => array(
[maximum depth reached]
),
(int) 32 => array(
[maximum depth reached]
),
(int) 33 => array(
[maximum depth reached]
),
(int) 34 => array(
[maximum depth reached]
),
(int) 35 => array(
[maximum depth reached]
),
(int) 36 => array(
[maximum depth reached]
),
(int) 37 => array(
[maximum depth reached]
),
(int) 38 => array(
[maximum depth reached]
),
(int) 39 => array(
[maximum depth reached]
),
(int) 40 => array(
[maximum depth reached]
),
(int) 41 => array(
[maximum depth reached]
),
(int) 42 => array(
[maximum depth reached]
),
(int) 43 => array(
[maximum depth reached]
),
(int) 44 => array(
[maximum depth reached]
),
(int) 45 => array(
[maximum depth reached]
),
(int) 46 => array(
[maximum depth reached]
),
(int) 47 => array(
[maximum depth reached]
),
(int) 48 => array(
[maximum depth reached]
),
(int) 49 => array(
[maximum depth reached]
),
(int) 50 => array(
[maximum depth reached]
),
(int) 51 => array(
[maximum depth reached]
),
(int) 52 => array(
[maximum depth reached]
),
(int) 53 => array(
[maximum depth reached]
),
(int) 54 => array(
[maximum depth reached]
),
(int) 55 => array(
[maximum depth reached]
),
(int) 56 => array(
[maximum depth reached]
),
(int) 57 => array(
[maximum depth reached]
),
(int) 58 => array(
[maximum depth reached]
),
(int) 59 => array(
[maximum depth reached]
),
(int) 60 => array(
[maximum depth reached]
),
(int) 61 => array(
[maximum depth reached]
),
(int) 62 => array(
[maximum depth reached]
),
(int) 63 => array(
[maximum depth reached]
),
(int) 64 => array(
[maximum depth reached]
),
(int) 65 => array(
[maximum depth reached]
),
(int) 66 => array(
[maximum depth reached]
),
(int) 67 => array(
[maximum depth reached]
),
(int) 68 => array(
[maximum depth reached]
),
(int) 69 => array(
[maximum depth reached]
),
(int) 70 => array(
[maximum depth reached]
),
(int) 71 => array(
[maximum depth reached]
),
(int) 72 => array(
[maximum depth reached]
),
(int) 73 => array(
[maximum depth reached]
),
(int) 74 => array(
[maximum depth reached]
),
(int) 75 => array(
[maximum depth reached]
)
)
)
)
$children_multiplicon_information = array()
$parental_multiplicon_information = array()
$multiplicon_information = array(
'multiplicon_id' => '966800',
'exp_id' => '1',
'info' => array(
'parent' => '0',
'level' => '2',
'num_anchorpoints' => '16',
'profile_length' => '96',
'is_redundant' => '-1'
),
'profile' => array(
'num_segments' => '2',
'num_species' => '2',
'species' => array(
'aag' => '0',
'aar' => '0',
'acertr' => '0',
'ach' => '0',
'aly' => '0',
'ama' => '0',
'amhyb' => '0',
'aox' => '0',
'arhy' => '0',
'ath' => '0',
'atr' => '0',
'bca' => '0',
'bna' => '0',
'bol' => '0',
'bra' => '0',
'bvu' => '0',
'camsi' => '1',
'can' => '0',
'cansat' => '0',
'car' => '0',
'cav' => '0',
'cbr' => '0',
'ccan' => '0',
'ccl' => '0',
'cde' => '0',
'cfa' => '0',
'chi' => '0',
'cil' => '0',
'cla' => '0',
'cme' => '0',
'col' => '0',
'cpa' => '0',
'cqu' => '0',
'cre' => '0',
'cru' => '0',
'csa' => '0',
'dca' => '0',
'din' => '0',
'dzi' => '0',
'eca' => '0',
'egr' => '0',
'egut' => '0',
'esa' => '0',
'fan' => '0',
'fve' => '0',
'ghi' => '0',
'gma' => '0',
'gra' => '0',
'han' => '0',
'hma' => '0',
'lal' => '0',
'lja' => '0',
'lonja' => '0',
'lsa' => '0',
'mbi' => '0',
'mco' => '0',
'mdo' => '0',
'mes' => '0',
'mpo' => '0',
'mtr' => '0',
'nnu' => '0',
'nta' => '0',
'oeu' => '0',
'osa' => '0',
'pax' => '0',
'pco' => '0',
'pgr' => '0',
'ppa' => '0',
'ppe' => '0',
'psa' => '0',
'pso' => '0',
'ptr' => '0',
'pvu' => '0',
'qlo' => '0',
'rch' => '0',
'rsi' => '0',
'sas' => '0',
'sbo' => '0',
'sbr' => '0',
'sci' => '0',
'sed' => '0',
'sgi' => '0',
'shi' => '0',
'sly' => '1',
'smo' => '0',
'spa' => '0',
'spe' => '0',
'stu' => '0',
'sun' => '0',
'tar' => '0',
'tca' => '0',
'tha' => '0',
'tpr' => '0',
'twi' => '0',
'ugi' => '0',
'vma' => '0',
'vmu' => '0',
'vpl' => '0',
'vvi' => '0',
'zma' => '0'
)
)
)
$multiplicon_id = '966800'
$iadhore_exp_id = '1'
$title_for_layout = 'Dicots PLAZA 5.0 : Colinearity Data'
$content_for_layout = '<!-- Load the CSS files for this view -->
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/bootstrap-multiselect.min.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/multiplicon_svg.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/multiplicon_graph.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/tipsy.css"/>
<!-- Load the JS files for this view -->
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/snap.svg-min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/bootstrap-multiselect.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/gf_colors.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/multiplicon_svg.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/d3/d3.v5.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/dagre/dagre-d3.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/dagre/tipsy.js"></script>
<h1>
Multiplicon view:
<strong>966800</strong>
(Experiment Id: 1)
<a href='https://bioinformatics.psb.ugent.be/plaza/documentation/tools#multiplicon_view' target='_blank' onclick='window.open("https://bioinformatics.psb.ugent.be/plaza/documentation/tools#multiplicon_view","HELP","width=1000,height=600,scrollbars=yes,toolbar=no,location=no");return false;'>
<span class="glyphicon glyphicon-question-sign documentation_link"></span>
</a></h1>
<div class="mb-4">
<p>
The Multiplicon view displays the aligned gene strings of a set of homologous segments.
</p>
</div>
<h2>Multiplicon Information</h2>
<div class="mb-4">
<table class='table'>
<thead>
<tr>
<th>Multiplicon Id</th>
<th>#Species</th>
<th>#Segments</th>
<th>#Anchorpoints</th>
<th>Profile Length</th>
</tr>
</thead>
<tbody>
<tr>
<td>966800</td>
<td>2</td>
<td>2</td>
<td>16</td>
<td>96</td>
</tr>
</tbody>
</table>
</div>
<div class="mb-4">
<h2>
Multiplicon Plot
</h2>
<!-- left panel: contains the multiplicon SVG -->
<div class="d-flex flex-row flex-wrap mt-3">
<div class="d-flex flex-column col-lg-9">
<!-- multiplicon itself -->
<div>
<div id="multiplicon_loading" class='loader'></div>
<div id="multiplicon_view_div">
<svg id="multiplicon_svg"></svg>
</div>
</div>
<!-- GF graph -->
<!-- <div>
<div id='multiplicon_gf_graph_div'>
<svg id="multiplicon_gf_graph_svg" height="200">
<g />
</svg>
</div>
</div> -->
</div>
<!-- right panels: contain the options etc -->
<div class="col-lg-3 ps-4">
<div style="display:none" id="gene_gf_info">
<div class="parameter_option_box mb-3">
<h5>Gene Information</h5>
<div id="gene_information"></div>
<hr>
<h5>Gene Family Information</h5>
<div id="gf_information"></div>
</div>
</div>
<div class="parameter_option_box mb-3">
<h3>Options</h3>
<span>Draw mode</span>
<select class="form form-select" name="draw_mode_form_select" id="draw_mode_form_select">
<option value='all' selected='selected'>Display all genes</option>
<option value='anchor'>Display only anchorpoints</option>
</select>
<span>Segment ordering</span>
<select class="form form-select" name="ordering_form_select" id="ordering_form_select">
<option value='standard' selected='selected'>Use standard order</option>
<option value='cluster'>Group species together</option>
</select>
<span>Species</span>
<select class="form form-select" name="species_form_select" id="species_form_select" multiple="multiple">
<option value='camsi' selected='selected'>Camellia sinensis var. sinensis</option>
<option value='sly' selected='selected'>Solanum lycopersicum</option>
</select>
</div>
</div>
</div>
<!-- JS code to load species & create multiplicon SVG -->
<script type="text/javascript">
//<![CDATA[
jQuery(document).ready(function() {
//Enable the multiselect
jQuery("#species_form_select").multiselect({
disableIfEmpty: true,
enableFiltering: false,
maxHeight: 300,
includeSelectAllOption: true,
numberDisplayed: 2,
templates: {
button: '<button type="button" class="multiselect dropdown-toggle btn btn-light border" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-list-check me-2"></i><span class="multiselect-selected-text"></span></button>'
}
});
//setup the SVG for the graph to have a fixed width based on parental size
jQuery("#multiplicon_gf_graph_svg").attr("width", jQuery('#multiplicon_gf_graph_div').width());
//Hide the gene and gf info panel
jQuery("#gene_gf_info").hide();
//Create the multiplicon SVG
try {
let multiplicon_svg = new MultipliconSVG();
multiplicon_svg.options({
apiEndpointSpecies: '/plaza.dev/_dev_instances/feedback/api/list_species',
apiEndpointMultiplicon: '/plaza.dev/_dev_instances/feedback/collinearity/multiplicon_plot_data/1/966800',
apiEndpointGfFuncAnnotBase: '/plaza.dev/_dev_instances/feedback/api/gf_functional_annotation',
urlSpeciesBase: '/plaza.dev/_dev_instances/feedback/organism/view',
urlGeneBase: '/plaza.dev/_dev_instances/feedback/genes/view',
urlGeneFamilyBase: '/plaza.dev/_dev_instances/feedback/gene_families/view',
urlGoBase: '/plaza.dev/_dev_instances/feedback/go/view',
urlInterproBase: '/plaza.dev/_dev_instances/feedback/interpro/view',
urlMapmanBase: '/plaza.dev/_dev_instances/feedback/mapman/view',
idMain: 'multiplicon_svg',
idLoading: 'multiplicon_loading',
idPanelGene: 'gene_information',
idPanelGeneFamily: 'gf_information',
idPanelGeneGF: 'gene_gf_info',
idSelectDrawMode: 'draw_mode_form_select',
idSelectOrder: 'ordering_form_select',
idSelectSpecies: 'species_form_select',
idGraph: 'multiplicon_gf_graph_svg'
});
multiplicon_svg.render();
//Allow for the resizing of the view
jQuery(window).resize(multiplicon_svg.debouncer(function(e) {
multiplicon_svg.render();
}));
} catch (error) {
jQuery("#multiplicon_loading").hide();
jQuery("#multiplicon_view_div").show();
jQuery("#multiplicon_view_div").html("Error while loading multiplicon");
}
});
//]]>
</script>
</div>
<h2>Data Table</h2>
<div id="data_table_div">
<table class='table'>
<thead>
<tr>
<th>Species</th>
<th>Chromosome</th>
<th>First Gene</th>
<th>Last Gene</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/organism/view/Camellia%2Bsinensis%2Bvar.%2Bsinensis">Camellia sinensis var. sinensis</a></td>
<td>Chr2</td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/CSS0005295">CSS0005295</a></td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/CSS0012962">CSS0012962</a></td>
</tr>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/organism/view/Solanum%2Blycopersicum">Solanum lycopersicum</a></td>
<td>SL4.0ch02</td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/Solyc02g088090.1">Solyc02g088090.1</a></td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/Solyc02g089200.4">Solyc02g089200.4</a></td>
</tr>
</tbody>
</table>
</div>
'
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[main] - APP/webroot/index.php, line 151 Warning (2)CORE/Cake/View/View.php , line 971 ]Code Context ob_start (); include $this -> __viewFile ; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/second_navigation.ctp'
$dataForView = array(
'navigation_bar_info' => array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false
),
'all_species' => array(
'acertr' => array(
'species' => 'acertr',
'common_name' => 'Acer truncatum',
'tax_id' => '47965',
'version' => 'v2.0'
),
'ach' => array(
'species' => 'ach',
'common_name' => 'Actinidia chinensis',
'tax_id' => '3625',
'version' => 'V3.0'
),
'aar' => array(
'species' => 'aar',
'common_name' => 'Aethionema arabicum',
'tax_id' => '228871',
'version' => 'v3.1'
),
'amhyb' => array(
'species' => 'amhyb',
'common_name' => 'Amaranthus hybridus',
'tax_id' => '3565',
'version' => 'v1.0'
),
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333',
'version' => 'JGI v1.0'
),
'aag' => array(
'species' => 'aag',
'common_name' => 'Anthoceros agrestis',
'tax_id' => '41834',
'version' => 'v1.1'
),
'aox' => array(
'species' => 'aox',
'common_name' => 'Aquilegia oxysepala',
'tax_id' => '432649',
'version' => 'v1.0'
),
'aly' => array(
'species' => 'aly',
'common_name' => 'Arabidopsis lyrata',
'tax_id' => '59689',
'version' => 'JGI v2.1'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702',
'version' => 'Araport11'
),
'arhy' => array(
'species' => 'arhy',
'common_name' => 'Arachis hypogaea',
'tax_id' => '3818',
'version' => 'v1.0'
),
'ama' => array(
'species' => 'ama',
'common_name' => 'Avicennia marina',
'tax_id' => '82927',
'version' => 'v1.1 20200527'
),
'bvu' => array(
'species' => 'bvu',
'common_name' => 'Beta vulgaris',
'tax_id' => '161934',
'version' => 'EL10_1.0'
),
'bca' => array(
'species' => 'bca',
'common_name' => 'Brassica carinata',
'tax_id' => '52824',
'version' => 'V1.0'
),
'bna' => array(
'species' => 'bna',
'common_name' => 'Brassica napus',
'tax_id' => '3708',
'version' => 'v2.0'
),
'bol' => array(
'species' => 'bol',
'common_name' => 'Brassica oleracea',
'tax_id' => '109376',
'version' => 'v1.0'
),
'bra' => array(
'species' => 'bra',
'common_name' => 'Brassica rapa',
'tax_id' => '3711',
'version' => 'v1.0'
),
'camsi' => array(
'species' => 'camsi',
'common_name' => 'Camellia sinensis var. sinensis',
'tax_id' => '542762',
'version' => 'CSS_ChrLev_20200506'
),
'cansat' => array(
'species' => 'cansat',
'common_name' => 'Cannabis sativa',
'tax_id' => '3483',
'version' => 'cs10'
),
'cru' => array(
'species' => 'cru',
'common_name' => 'Capsella rubella',
'tax_id' => '81985',
'version' => 'JGI v1.1'
),
'can' => array(
'species' => 'can',
'common_name' => 'Capsicum annuum',
'tax_id' => '4072',
'version' => 'Pepper Genome v2.0'
),
'chi' => array(
'species' => 'chi',
'common_name' => 'Cardamine hirsuta',
'tax_id' => '50463',
'version' => 'v1.0'
),
'cpa' => array(
'species' => 'cpa',
'common_name' => 'Carica papaya',
'tax_id' => '3649',
'version' => 'JGI ASGPB0.4'
),
'cfa' => array(
'species' => 'cfa',
'common_name' => 'Carpinus fangiana',
'tax_id' => '176857',
'version' => 'v1.0'
),
'cil' => array(
'species' => 'cil',
'common_name' => 'Carya illinoinensis',
'tax_id' => '32201',
'version' => 'v1.1'
),
'cde' => array(
'species' => 'cde',
'common_name' => 'Ceratophyllum demersum',
'tax_id' => '4428',
'version' => 'v1.0'
),
'cbr' => array(
'species' => 'cbr',
'common_name' => 'Chara braunii',
'tax_id' => '69332',
'version' => 'Cbr1.0'
),
'cqu' => array(
'species' => 'cqu',
'common_name' => 'Chenopodium quinoa',
'tax_id' => '63459',
'version' => 'KAUST v1.0'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055',
'version' => 'JGI v5.5'
),
'car' => array(
'species' => 'car',
'common_name' => 'Cicer arietinum L.',
'tax_id' => '3827',
'version' => 'v3.0'
),
'cla' => array(
'species' => 'cla',
'common_name' => 'Citrullus lanatus',
'tax_id' => '3654',
'version' => 'WCG v2.0'
),
'ccl' => array(
'species' => 'ccl',
'common_name' => 'Citrus clementina',
'tax_id' => '85681',
'version' => 'JGI v1.0'
),
'ccan' => array(
'species' => 'ccan',
'common_name' => 'Coffea canephora',
'tax_id' => '49390',
'version' => 'Coffee Genome Hub v1'
),
'col' => array(
'species' => 'col',
'common_name' => 'Corchorus olitorius',
'tax_id' => '93759',
'version' => 'GenBank v1.0'
),
'cav' => array(
'species' => 'cav',
'common_name' => 'Corylus avellana',
'tax_id' => '13451',
'version' => 'v1.0'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cucumis melo',
'tax_id' => '3656',
'version' => 'Melonomics v3.6.1'
),
'csa' => array(
'species' => 'csa',
'common_name' => 'Cucumis sativus L.',
'tax_id' => '3659',
'version' => 'v3.0'
),
'dca' => array(
'species' => 'dca',
'common_name' => 'Daucus carota',
'tax_id' => '4039',
'version' => 'JGI v2.0'
),
'din' => array(
'species' => 'din',
'common_name' => 'Davidia involucrata',
'tax_id' => '16924',
'version' => 'v1.0'
),
'dzi' => array(
'species' => 'dzi',
'common_name' => 'Durio zibethinus',
'tax_id' => '66656',
'version' => 'Duzib1.0'
),
'eca' => array(
'species' => 'eca',
'common_name' => 'Erigeron canadensis',
'tax_id' => '72917',
'version' => 'V1.0'
),
'egut' => array(
'species' => 'egut',
'common_name' => 'Erythranthe guttata',
'tax_id' => '4155',
'version' => 'v2.0'
),
'egr' => array(
'species' => 'egr',
'common_name' => 'Eucalyptus grandis',
'tax_id' => '71139',
'version' => 'v2.0'
),
'esa' => array(
'species' => 'esa',
'common_name' => 'Eutrema salsugineum',
'tax_id' => '72664',
'version' => 'v1.0'
),
'fve' => array(
'species' => 'fve',
'common_name' => 'Fragaria vesca',
'tax_id' => '57918',
'version' => 'V4.0.a2'
),
'fan' => array(
'species' => 'fan',
'common_name' => 'Fragaria x ananassa',
'tax_id' => '3747',
'version' => 'V1.0.a1'
),
'gma' => array(
'species' => 'gma',
'common_name' => 'Glycine max',
'tax_id' => '3847',
'version' => 'JGI Wm82.a4.v1'
),
'ghi' => array(
'species' => 'ghi',
'common_name' => 'Gossypium hirsutum',
'tax_id' => '3635',
'version' => 'v2.1'
),
'gra' => array(
'species' => 'gra',
'common_name' => 'Gossypium raimondii',
'tax_id' => '29730',
'version' => 'v2.1'
),
'han' => array(
'species' => 'han',
'common_name' => 'Helianthus annuus',
'tax_id' => '4232',
'version' => 'r1.2'
),
'hma' => array(
'species' => 'hma',
'common_name' => 'Hydrangea macrophylla',
'tax_id' => '23110',
'version' => 'v2.1'
),
'lsa' => array(
'species' => 'lsa',
'common_name' => 'Lactuca sativa',
'tax_id' => '4236',
'version' => 'v8.0'
),
'lonja' => array(
'species' => 'lonja',
'common_name' => 'Lonicera japonica',
'tax_id' => '105884',
'version' => 'v1.0'
),
'lja' => array(
'species' => 'lja',
'common_name' => 'Lotus japonicus',
'tax_id' => '34305',
'version' => 'Lj1.0v1'
),
'lal' => array(
'species' => 'lal',
'common_name' => 'Lupinus albus',
'tax_id' => '3870',
'version' => 'v1.0'
),
'mbi' => array(
'species' => 'mbi',
'common_name' => 'Magnolia biondii',
'tax_id' => '86725',
'version' => 'v1.0'
),
'mdo' => array(
'species' => 'mdo',
'common_name' => 'Malus domestica',
'tax_id' => '3750',
'version' => 'GDDH13 v1.1'
),
'mes' => array(
'species' => 'mes',
'common_name' => 'Manihot esculenta',
'tax_id' => '3983',
'version' => 'v8.1'
),
'mpo' => array(
'species' => 'mpo',
'common_name' => 'Marchantia polymorpha',
'tax_id' => '3197',
'version' => 'JGI v3.1'
),
'mtr' => array(
'species' => 'mtr',
'common_name' => 'Medicago truncatula',
'tax_id' => '3880',
'version' => 'JGI Mt4.0v1'
),
'mco' => array(
'species' => 'mco',
'common_name' => 'Micromonas commoda',
'tax_id' => '296587',
'version' => 'JGI v3.0'
),
'nnu' => array(
'species' => 'nnu',
'common_name' => 'Nelumbo nucifera',
'tax_id' => '4432',
'version' => 'v2.0'
),
'nta' => array(
'species' => 'nta',
'common_name' => 'Nicotiana tabacum',
'tax_id' => '4097',
'version' => 'Edwards2017'
),
'oeu' => array(
'species' => 'oeu',
'common_name' => 'Olea europaea',
'tax_id' => '4146',
'version' => 'v1.0'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa ssp. japonica',
'tax_id' => '39947',
'version' => 'IRGSP-1.0-2021-05-10'
),
'pso' => array(
'species' => 'pso',
'common_name' => 'Papaver somniferum',
'tax_id' => '3469',
'version' => 'ASM357369v1'
),
'pax' => array(
'species' => 'pax',
'common_name' => 'Petunia axillaris',
'tax_id' => '33119',
'version' => 'Sol Genomics v1.6.2'
),
'pvu' => array(
'species' => 'pvu',
'common_name' => 'Phaseolus vulgaris',
'tax_id' => '3885',
'version' => 'v2.1'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrium patens',
'tax_id' => '3218',
'version' => 'JGI v3.3'
),
'psa' => array(
'species' => 'psa',
'common_name' => 'Pisum sativum',
'tax_id' => '3888',
'version' => 'V1.0a'
),
'ptr' => array(
'species' => 'ptr',
'common_name' => 'Populus trichocarpa',
'tax_id' => '3694',
'version' => 'JGI v4.1'
),
'pco' => array(
'species' => 'pco',
'common_name' => 'Prasinoderma coloniale',
'tax_id' => '156133',
'version' => 'v1.0'
),
'ppe' => array(
'species' => 'ppe',
'common_name' => 'Prunus persica',
'tax_id' => '3760',
'version' => 'v2.1'
),
'pgr' => array(
'species' => 'pgr',
'common_name' => 'Punica granatum',
'tax_id' => '22663',
'version' => 'ASM765513v2'
),
'qlo' => array(
'species' => 'qlo',
'common_name' => 'Quercus lobata',
'tax_id' => '97700',
'version' => 'v3.0'
),
'rsi' => array(
'species' => 'rsi',
'common_name' => 'Rhododendron simsii',
'tax_id' => '118357',
'version' => 'v1.0'
),
'rch' => array(
'species' => 'rch',
'common_name' => 'Rosa chinensis',
'tax_id' => '74649',
'version' => 'v2.0'
),
'sbr' => array(
'species' => 'sbr',
'common_name' => 'Salix brachista',
'tax_id' => '2182728',
'version' => 'v1.0'
),
'sbo' => array(
'species' => 'sbo',
'common_name' => 'Salvia bowleyana',
'tax_id' => '424416',
'version' => 'v1.0'
),
'shi' => array(
'species' => 'shi',
'common_name' => 'Sapria himalayana',
'tax_id' => '289637',
'version' => 'v1.0'
),
'spa' => array(
'species' => 'spa',
'common_name' => 'Schrenkiella parvula',
'tax_id' => '98039',
'version' => 'v2.2'
),
'sed' => array(
'species' => 'sed',
'common_name' => 'Sechium edule',
'tax_id' => '184140',
'version' => 'v1.0'
),
'smo' => array(
'species' => 'smo',
'common_name' => 'Selaginella moellendorffii',
'tax_id' => '88036',
'version' => 'v1.0'
),
'sun' => array(
'species' => 'sun',
'common_name' => 'Selenicereus undatus',
'tax_id' => '176265',
'version' => 'v1.0'
),
'sgi' => array(
'species' => 'sgi',
'common_name' => 'Sequoiadendron giganteum',
'tax_id' => '99814',
'version' => 'V2.0'
),
'sci' => array(
'species' => 'sci',
'common_name' => 'Simmondsia chinensis',
'tax_id' => '3999',
'version' => 'sc1'
),
'sly' => array(
'species' => 'sly',
'common_name' => 'Solanum lycopersicum',
'tax_id' => '4081',
'version' => 'ITAG4.0'
),
'spe' => array(
'species' => 'spe',
'common_name' => 'Solanum pennellii',
'tax_id' => '28526',
'version' => 'V2.0'
),
'stu' => array(
'species' => 'stu',
'common_name' => 'Solanum tuberosum',
'tax_id' => '4113',
'version' => 'JGI v4.03'
),
'sas' => array(
'species' => 'sas',
'common_name' => 'Striga asiatica',
'tax_id' => '4170',
'version' => 'v2.02'
),
'tha' => array(
'species' => 'tha',
'common_name' => 'Tarenaya hassleriana',
'tax_id' => '28532',
'version' => 'RefSeq v1'
),
'tca' => array(
'species' => 'tca',
'common_name' => 'Theobroma cacao',
'tax_id' => '3641',
'version' => 'V2.1'
),
'tpr' => array(
'species' => 'tpr',
'common_name' => 'Trifolium pratense',
'tax_id' => '57577',
'version' => 'V2.0'
),
'twi' => array(
'species' => 'twi',
'common_name' => 'Tripterygium wilfordii',
'tax_id' => '458696',
'version' => 'ASM1340144v1'
),
'tar' => array(
'species' => 'tar',
'common_name' => 'Trochodendron aralioides',
'tax_id' => '4407',
'version' => 'v1.0'
),
'ugi' => array(
'species' => 'ugi',
'common_name' => 'Utricularia gibba',
'tax_id' => '13748',
'version' => 'v1.1F'
),
'vma' => array(
'species' => 'vma',
'common_name' => 'Vaccinium macrocarpon',
'tax_id' => '13750',
'version' => 'V1.0'
),
'vpl' => array(
'species' => 'vpl',
'common_name' => 'Vanilla planifolia',
'tax_id' => '51239',
'version' => 'Elo Vpla-A Principal v1.0'
),
'vmu' => array(
'species' => 'vmu',
'common_name' => 'Vigna mungo',
'tax_id' => '3915',
'version' => 'ASM1342719v1'
),
'vvi' => array(
'species' => 'vvi',
'common_name' => 'Vitis vinifera',
'tax_id' => '29760',
'version' => 'Genoscope.12x'
),
'zma' => array(
'species' => 'zma',
'common_name' => 'Zea mays',
'tax_id' => '4577',
'version' => 'NAM v5.0'
)
),
'multiplicon_data' => array(
(int) 1933599 => array(
'species' => 'sly',
'chromosome' => 'SL4.0ch02',
'data' => array(
[maximum depth reached]
)
),
(int) 1933600 => array(
'species' => 'camsi',
'chromosome' => 'Chr2',
'data' => array(
[maximum depth reached]
)
)
),
'children_multiplicon_information' => array(),
'parental_multiplicon_information' => array(),
'multiplicon_information' => array(
'multiplicon_id' => '966800',
'exp_id' => '1',
'info' => array(
'parent' => '0',
'level' => '2',
'num_anchorpoints' => '16',
'profile_length' => '96',
'is_redundant' => '-1'
),
'profile' => array(
'num_segments' => '2',
'num_species' => '2',
'species' => array(
[maximum depth reached]
)
)
),
'multiplicon_id' => '966800',
'iadhore_exp_id' => '1',
'title_for_layout' => 'Dicots PLAZA 5.0 : Colinearity Data',
'content_for_layout' => '<!-- Load the CSS files for this view -->
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/bootstrap-multiselect.min.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/multiplicon_svg.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/multiplicon_graph.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/tipsy.css"/>
<!-- Load the JS files for this view -->
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/snap.svg-min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/bootstrap-multiselect.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/gf_colors.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/multiplicon_svg.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/d3/d3.v5.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/dagre/dagre-d3.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/dagre/tipsy.js"></script>
<h1>
Multiplicon view:
<strong>966800</strong>
(Experiment Id: 1)
<a href='https://bioinformatics.psb.ugent.be/plaza/documentation/tools#multiplicon_view' target='_blank' onclick='window.open("https://bioinformatics.psb.ugent.be/plaza/documentation/tools#multiplicon_view","HELP","width=1000,height=600,scrollbars=yes,toolbar=no,location=no");return false;'>
<span class="glyphicon glyphicon-question-sign documentation_link"></span>
</a></h1>
<div class="mb-4">
<p>
The Multiplicon view displays the aligned gene strings of a set of homologous segments.
</p>
</div>
<h2>Multiplicon Information</h2>
<div class="mb-4">
<table class='table'>
<thead>
<tr>
<th>Multiplicon Id</th>
<th>#Species</th>
<th>#Segments</th>
<th>#Anchorpoints</th>
<th>Profile Length</th>
</tr>
</thead>
<tbody>
<tr>
<td>966800</td>
<td>2</td>
<td>2</td>
<td>16</td>
<td>96</td>
</tr>
</tbody>
</table>
</div>
<div class="mb-4">
<h2>
Multiplicon Plot
</h2>
<!-- left panel: contains the multiplicon SVG -->
<div class="d-flex flex-row flex-wrap mt-3">
<div class="d-flex flex-column col-lg-9">
<!-- multiplicon itself -->
<div>
<div id="multiplicon_loading" class='loader'></div>
<div id="multiplicon_view_div">
<svg id="multiplicon_svg"></svg>
</div>
</div>
<!-- GF graph -->
<!-- <div>
<div id='multiplicon_gf_graph_div'>
<svg id="multiplicon_gf_graph_svg" height="200">
<g />
</svg>
</div>
</div> -->
</div>
<!-- right panels: contain the options etc -->
<div class="col-lg-3 ps-4">
<div style="display:none" id="gene_gf_info">
<div class="parameter_option_box mb-3">
<h5>Gene Information</h5>
<div id="gene_information"></div>
<hr>
<h5>Gene Family Information</h5>
<div id="gf_information"></div>
</div>
</div>
<div class="parameter_option_box mb-3">
<h3>Options</h3>
<span>Draw mode</span>
<select class="form form-select" name="draw_mode_form_select" id="draw_mode_form_select">
<option value='all' selected='selected'>Display all genes</option>
<option value='anchor'>Display only anchorpoints</option>
</select>
<span>Segment ordering</span>
<select class="form form-select" name="ordering_form_select" id="ordering_form_select">
<option value='standard' selected='selected'>Use standard order</option>
<option value='cluster'>Group species together</option>
</select>
<span>Species</span>
<select class="form form-select" name="species_form_select" id="species_form_select" multiple="multiple">
<option value='camsi' selected='selected'>Camellia sinensis var. sinensis</option>
<option value='sly' selected='selected'>Solanum lycopersicum</option>
</select>
</div>
</div>
</div>
<!-- JS code to load species & create multiplicon SVG -->
<script type="text/javascript">
//<![CDATA[
jQuery(document).ready(function() {
//Enable the multiselect
jQuery("#species_form_select").multiselect({
disableIfEmpty: true,
enableFiltering: false,
maxHeight: 300,
includeSelectAllOption: true,
numberDisplayed: 2,
templates: {
button: '<button type="button" class="multiselect dropdown-toggle btn btn-light border" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-list-check me-2"></i><span class="multiselect-selected-text"></span></button>'
}
});
//setup the SVG for the graph to have a fixed width based on parental size
jQuery("#multiplicon_gf_graph_svg").attr("width", jQuery('#multiplicon_gf_graph_div').width());
//Hide the gene and gf info panel
jQuery("#gene_gf_info").hide();
//Create the multiplicon SVG
try {
let multiplicon_svg = new MultipliconSVG();
multiplicon_svg.options({
apiEndpointSpecies: '/plaza.dev/_dev_instances/feedback/api/list_species',
apiEndpointMultiplicon: '/plaza.dev/_dev_instances/feedback/collinearity/multiplicon_plot_data/1/966800',
apiEndpointGfFuncAnnotBase: '/plaza.dev/_dev_instances/feedback/api/gf_functional_annotation',
urlSpeciesBase: '/plaza.dev/_dev_instances/feedback/organism/view',
urlGeneBase: '/plaza.dev/_dev_instances/feedback/genes/view',
urlGeneFamilyBase: '/plaza.dev/_dev_instances/feedback/gene_families/view',
urlGoBase: '/plaza.dev/_dev_instances/feedback/go/view',
urlInterproBase: '/plaza.dev/_dev_instances/feedback/interpro/view',
urlMapmanBase: '/plaza.dev/_dev_instances/feedback/mapman/view',
idMain: 'multiplicon_svg',
idLoading: 'multiplicon_loading',
idPanelGene: 'gene_information',
idPanelGeneFamily: 'gf_information',
idPanelGeneGF: 'gene_gf_info',
idSelectDrawMode: 'draw_mode_form_select',
idSelectOrder: 'ordering_form_select',
idSelectSpecies: 'species_form_select',
idGraph: 'multiplicon_gf_graph_svg'
});
multiplicon_svg.render();
//Allow for the resizing of the view
jQuery(window).resize(multiplicon_svg.debouncer(function(e) {
multiplicon_svg.render();
}));
} catch (error) {
jQuery("#multiplicon_loading").hide();
jQuery("#multiplicon_view_div").show();
jQuery("#multiplicon_view_div").html("Error while loading multiplicon");
}
});
//]]>
</script>
</div>
<h2>Data Table</h2>
<div id="data_table_div">
<table class='table'>
<thead>
<tr>
<th>Species</th>
<th>Chromosome</th>
<th>First Gene</th>
<th>Last Gene</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/organism/view/Camellia%2Bsinensis%2Bvar.%2Bsinensis">Camellia sinensis var. sinensis</a></td>
<td>Chr2</td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/CSS0005295">CSS0005295</a></td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/CSS0012962">CSS0012962</a></td>
</tr>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/organism/view/Solanum%2Blycopersicum">Solanum lycopersicum</a></td>
<td>SL4.0ch02</td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/Solyc02g088090.1">Solyc02g088090.1</a></td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/Solyc02g089200.4">Solyc02g089200.4</a></td>
</tr>
</tbody>
</table>
</div>
',
'scripts_for_layout' => ''
)
$navigation_bar_info = array(
'num_colinearity_runs' => (int) 1,
'num_colinearity_with_dating_runs' => (int) 0,
'num_functional_clusters_runs' => (int) 6,
'has_pan_genomes' => false
)
$all_species = array(
'acertr' => array(
'species' => 'acertr',
'common_name' => 'Acer truncatum',
'tax_id' => '47965',
'version' => 'v2.0'
),
'ach' => array(
'species' => 'ach',
'common_name' => 'Actinidia chinensis',
'tax_id' => '3625',
'version' => 'V3.0'
),
'aar' => array(
'species' => 'aar',
'common_name' => 'Aethionema arabicum',
'tax_id' => '228871',
'version' => 'v3.1'
),
'amhyb' => array(
'species' => 'amhyb',
'common_name' => 'Amaranthus hybridus',
'tax_id' => '3565',
'version' => 'v1.0'
),
'atr' => array(
'species' => 'atr',
'common_name' => 'Amborella trichopoda',
'tax_id' => '13333',
'version' => 'JGI v1.0'
),
'aag' => array(
'species' => 'aag',
'common_name' => 'Anthoceros agrestis',
'tax_id' => '41834',
'version' => 'v1.1'
),
'aox' => array(
'species' => 'aox',
'common_name' => 'Aquilegia oxysepala',
'tax_id' => '432649',
'version' => 'v1.0'
),
'aly' => array(
'species' => 'aly',
'common_name' => 'Arabidopsis lyrata',
'tax_id' => '59689',
'version' => 'JGI v2.1'
),
'ath' => array(
'species' => 'ath',
'common_name' => 'Arabidopsis thaliana',
'tax_id' => '3702',
'version' => 'Araport11'
),
'arhy' => array(
'species' => 'arhy',
'common_name' => 'Arachis hypogaea',
'tax_id' => '3818',
'version' => 'v1.0'
),
'ama' => array(
'species' => 'ama',
'common_name' => 'Avicennia marina',
'tax_id' => '82927',
'version' => 'v1.1 20200527'
),
'bvu' => array(
'species' => 'bvu',
'common_name' => 'Beta vulgaris',
'tax_id' => '161934',
'version' => 'EL10_1.0'
),
'bca' => array(
'species' => 'bca',
'common_name' => 'Brassica carinata',
'tax_id' => '52824',
'version' => 'V1.0'
),
'bna' => array(
'species' => 'bna',
'common_name' => 'Brassica napus',
'tax_id' => '3708',
'version' => 'v2.0'
),
'bol' => array(
'species' => 'bol',
'common_name' => 'Brassica oleracea',
'tax_id' => '109376',
'version' => 'v1.0'
),
'bra' => array(
'species' => 'bra',
'common_name' => 'Brassica rapa',
'tax_id' => '3711',
'version' => 'v1.0'
),
'camsi' => array(
'species' => 'camsi',
'common_name' => 'Camellia sinensis var. sinensis',
'tax_id' => '542762',
'version' => 'CSS_ChrLev_20200506'
),
'cansat' => array(
'species' => 'cansat',
'common_name' => 'Cannabis sativa',
'tax_id' => '3483',
'version' => 'cs10'
),
'cru' => array(
'species' => 'cru',
'common_name' => 'Capsella rubella',
'tax_id' => '81985',
'version' => 'JGI v1.1'
),
'can' => array(
'species' => 'can',
'common_name' => 'Capsicum annuum',
'tax_id' => '4072',
'version' => 'Pepper Genome v2.0'
),
'chi' => array(
'species' => 'chi',
'common_name' => 'Cardamine hirsuta',
'tax_id' => '50463',
'version' => 'v1.0'
),
'cpa' => array(
'species' => 'cpa',
'common_name' => 'Carica papaya',
'tax_id' => '3649',
'version' => 'JGI ASGPB0.4'
),
'cfa' => array(
'species' => 'cfa',
'common_name' => 'Carpinus fangiana',
'tax_id' => '176857',
'version' => 'v1.0'
),
'cil' => array(
'species' => 'cil',
'common_name' => 'Carya illinoinensis',
'tax_id' => '32201',
'version' => 'v1.1'
),
'cde' => array(
'species' => 'cde',
'common_name' => 'Ceratophyllum demersum',
'tax_id' => '4428',
'version' => 'v1.0'
),
'cbr' => array(
'species' => 'cbr',
'common_name' => 'Chara braunii',
'tax_id' => '69332',
'version' => 'Cbr1.0'
),
'cqu' => array(
'species' => 'cqu',
'common_name' => 'Chenopodium quinoa',
'tax_id' => '63459',
'version' => 'KAUST v1.0'
),
'cre' => array(
'species' => 'cre',
'common_name' => 'Chlamydomonas reinhardtii',
'tax_id' => '3055',
'version' => 'JGI v5.5'
),
'car' => array(
'species' => 'car',
'common_name' => 'Cicer arietinum L.',
'tax_id' => '3827',
'version' => 'v3.0'
),
'cla' => array(
'species' => 'cla',
'common_name' => 'Citrullus lanatus',
'tax_id' => '3654',
'version' => 'WCG v2.0'
),
'ccl' => array(
'species' => 'ccl',
'common_name' => 'Citrus clementina',
'tax_id' => '85681',
'version' => 'JGI v1.0'
),
'ccan' => array(
'species' => 'ccan',
'common_name' => 'Coffea canephora',
'tax_id' => '49390',
'version' => 'Coffee Genome Hub v1'
),
'col' => array(
'species' => 'col',
'common_name' => 'Corchorus olitorius',
'tax_id' => '93759',
'version' => 'GenBank v1.0'
),
'cav' => array(
'species' => 'cav',
'common_name' => 'Corylus avellana',
'tax_id' => '13451',
'version' => 'v1.0'
),
'cme' => array(
'species' => 'cme',
'common_name' => 'Cucumis melo',
'tax_id' => '3656',
'version' => 'Melonomics v3.6.1'
),
'csa' => array(
'species' => 'csa',
'common_name' => 'Cucumis sativus L.',
'tax_id' => '3659',
'version' => 'v3.0'
),
'dca' => array(
'species' => 'dca',
'common_name' => 'Daucus carota',
'tax_id' => '4039',
'version' => 'JGI v2.0'
),
'din' => array(
'species' => 'din',
'common_name' => 'Davidia involucrata',
'tax_id' => '16924',
'version' => 'v1.0'
),
'dzi' => array(
'species' => 'dzi',
'common_name' => 'Durio zibethinus',
'tax_id' => '66656',
'version' => 'Duzib1.0'
),
'eca' => array(
'species' => 'eca',
'common_name' => 'Erigeron canadensis',
'tax_id' => '72917',
'version' => 'V1.0'
),
'egut' => array(
'species' => 'egut',
'common_name' => 'Erythranthe guttata',
'tax_id' => '4155',
'version' => 'v2.0'
),
'egr' => array(
'species' => 'egr',
'common_name' => 'Eucalyptus grandis',
'tax_id' => '71139',
'version' => 'v2.0'
),
'esa' => array(
'species' => 'esa',
'common_name' => 'Eutrema salsugineum',
'tax_id' => '72664',
'version' => 'v1.0'
),
'fve' => array(
'species' => 'fve',
'common_name' => 'Fragaria vesca',
'tax_id' => '57918',
'version' => 'V4.0.a2'
),
'fan' => array(
'species' => 'fan',
'common_name' => 'Fragaria x ananassa',
'tax_id' => '3747',
'version' => 'V1.0.a1'
),
'gma' => array(
'species' => 'gma',
'common_name' => 'Glycine max',
'tax_id' => '3847',
'version' => 'JGI Wm82.a4.v1'
),
'ghi' => array(
'species' => 'ghi',
'common_name' => 'Gossypium hirsutum',
'tax_id' => '3635',
'version' => 'v2.1'
),
'gra' => array(
'species' => 'gra',
'common_name' => 'Gossypium raimondii',
'tax_id' => '29730',
'version' => 'v2.1'
),
'han' => array(
'species' => 'han',
'common_name' => 'Helianthus annuus',
'tax_id' => '4232',
'version' => 'r1.2'
),
'hma' => array(
'species' => 'hma',
'common_name' => 'Hydrangea macrophylla',
'tax_id' => '23110',
'version' => 'v2.1'
),
'lsa' => array(
'species' => 'lsa',
'common_name' => 'Lactuca sativa',
'tax_id' => '4236',
'version' => 'v8.0'
),
'lonja' => array(
'species' => 'lonja',
'common_name' => 'Lonicera japonica',
'tax_id' => '105884',
'version' => 'v1.0'
),
'lja' => array(
'species' => 'lja',
'common_name' => 'Lotus japonicus',
'tax_id' => '34305',
'version' => 'Lj1.0v1'
),
'lal' => array(
'species' => 'lal',
'common_name' => 'Lupinus albus',
'tax_id' => '3870',
'version' => 'v1.0'
),
'mbi' => array(
'species' => 'mbi',
'common_name' => 'Magnolia biondii',
'tax_id' => '86725',
'version' => 'v1.0'
),
'mdo' => array(
'species' => 'mdo',
'common_name' => 'Malus domestica',
'tax_id' => '3750',
'version' => 'GDDH13 v1.1'
),
'mes' => array(
'species' => 'mes',
'common_name' => 'Manihot esculenta',
'tax_id' => '3983',
'version' => 'v8.1'
),
'mpo' => array(
'species' => 'mpo',
'common_name' => 'Marchantia polymorpha',
'tax_id' => '3197',
'version' => 'JGI v3.1'
),
'mtr' => array(
'species' => 'mtr',
'common_name' => 'Medicago truncatula',
'tax_id' => '3880',
'version' => 'JGI Mt4.0v1'
),
'mco' => array(
'species' => 'mco',
'common_name' => 'Micromonas commoda',
'tax_id' => '296587',
'version' => 'JGI v3.0'
),
'nnu' => array(
'species' => 'nnu',
'common_name' => 'Nelumbo nucifera',
'tax_id' => '4432',
'version' => 'v2.0'
),
'nta' => array(
'species' => 'nta',
'common_name' => 'Nicotiana tabacum',
'tax_id' => '4097',
'version' => 'Edwards2017'
),
'oeu' => array(
'species' => 'oeu',
'common_name' => 'Olea europaea',
'tax_id' => '4146',
'version' => 'v1.0'
),
'osa' => array(
'species' => 'osa',
'common_name' => 'Oryza sativa ssp. japonica',
'tax_id' => '39947',
'version' => 'IRGSP-1.0-2021-05-10'
),
'pso' => array(
'species' => 'pso',
'common_name' => 'Papaver somniferum',
'tax_id' => '3469',
'version' => 'ASM357369v1'
),
'pax' => array(
'species' => 'pax',
'common_name' => 'Petunia axillaris',
'tax_id' => '33119',
'version' => 'Sol Genomics v1.6.2'
),
'pvu' => array(
'species' => 'pvu',
'common_name' => 'Phaseolus vulgaris',
'tax_id' => '3885',
'version' => 'v2.1'
),
'ppa' => array(
'species' => 'ppa',
'common_name' => 'Physcomitrium patens',
'tax_id' => '3218',
'version' => 'JGI v3.3'
),
'psa' => array(
'species' => 'psa',
'common_name' => 'Pisum sativum',
'tax_id' => '3888',
'version' => 'V1.0a'
),
'ptr' => array(
'species' => 'ptr',
'common_name' => 'Populus trichocarpa',
'tax_id' => '3694',
'version' => 'JGI v4.1'
),
'pco' => array(
'species' => 'pco',
'common_name' => 'Prasinoderma coloniale',
'tax_id' => '156133',
'version' => 'v1.0'
),
'ppe' => array(
'species' => 'ppe',
'common_name' => 'Prunus persica',
'tax_id' => '3760',
'version' => 'v2.1'
),
'pgr' => array(
'species' => 'pgr',
'common_name' => 'Punica granatum',
'tax_id' => '22663',
'version' => 'ASM765513v2'
),
'qlo' => array(
'species' => 'qlo',
'common_name' => 'Quercus lobata',
'tax_id' => '97700',
'version' => 'v3.0'
),
'rsi' => array(
'species' => 'rsi',
'common_name' => 'Rhododendron simsii',
'tax_id' => '118357',
'version' => 'v1.0'
),
'rch' => array(
'species' => 'rch',
'common_name' => 'Rosa chinensis',
'tax_id' => '74649',
'version' => 'v2.0'
),
'sbr' => array(
'species' => 'sbr',
'common_name' => 'Salix brachista',
'tax_id' => '2182728',
'version' => 'v1.0'
),
'sbo' => array(
'species' => 'sbo',
'common_name' => 'Salvia bowleyana',
'tax_id' => '424416',
'version' => 'v1.0'
),
'shi' => array(
'species' => 'shi',
'common_name' => 'Sapria himalayana',
'tax_id' => '289637',
'version' => 'v1.0'
),
'spa' => array(
'species' => 'spa',
'common_name' => 'Schrenkiella parvula',
'tax_id' => '98039',
'version' => 'v2.2'
),
'sed' => array(
'species' => 'sed',
'common_name' => 'Sechium edule',
'tax_id' => '184140',
'version' => 'v1.0'
),
'smo' => array(
'species' => 'smo',
'common_name' => 'Selaginella moellendorffii',
'tax_id' => '88036',
'version' => 'v1.0'
),
'sun' => array(
'species' => 'sun',
'common_name' => 'Selenicereus undatus',
'tax_id' => '176265',
'version' => 'v1.0'
),
'sgi' => array(
'species' => 'sgi',
'common_name' => 'Sequoiadendron giganteum',
'tax_id' => '99814',
'version' => 'V2.0'
),
'sci' => array(
'species' => 'sci',
'common_name' => 'Simmondsia chinensis',
'tax_id' => '3999',
'version' => 'sc1'
),
'sly' => array(
'species' => 'sly',
'common_name' => 'Solanum lycopersicum',
'tax_id' => '4081',
'version' => 'ITAG4.0'
),
'spe' => array(
'species' => 'spe',
'common_name' => 'Solanum pennellii',
'tax_id' => '28526',
'version' => 'V2.0'
),
'stu' => array(
'species' => 'stu',
'common_name' => 'Solanum tuberosum',
'tax_id' => '4113',
'version' => 'JGI v4.03'
),
'sas' => array(
'species' => 'sas',
'common_name' => 'Striga asiatica',
'tax_id' => '4170',
'version' => 'v2.02'
),
'tha' => array(
'species' => 'tha',
'common_name' => 'Tarenaya hassleriana',
'tax_id' => '28532',
'version' => 'RefSeq v1'
),
'tca' => array(
'species' => 'tca',
'common_name' => 'Theobroma cacao',
'tax_id' => '3641',
'version' => 'V2.1'
),
'tpr' => array(
'species' => 'tpr',
'common_name' => 'Trifolium pratense',
'tax_id' => '57577',
'version' => 'V2.0'
),
'twi' => array(
'species' => 'twi',
'common_name' => 'Tripterygium wilfordii',
'tax_id' => '458696',
'version' => 'ASM1340144v1'
),
'tar' => array(
'species' => 'tar',
'common_name' => 'Trochodendron aralioides',
'tax_id' => '4407',
'version' => 'v1.0'
),
'ugi' => array(
'species' => 'ugi',
'common_name' => 'Utricularia gibba',
'tax_id' => '13748',
'version' => 'v1.1F'
),
'vma' => array(
'species' => 'vma',
'common_name' => 'Vaccinium macrocarpon',
'tax_id' => '13750',
'version' => 'V1.0'
),
'vpl' => array(
'species' => 'vpl',
'common_name' => 'Vanilla planifolia',
'tax_id' => '51239',
'version' => 'Elo Vpla-A Principal v1.0'
),
'vmu' => array(
'species' => 'vmu',
'common_name' => 'Vigna mungo',
'tax_id' => '3915',
'version' => 'ASM1342719v1'
),
'vvi' => array(
'species' => 'vvi',
'common_name' => 'Vitis vinifera',
'tax_id' => '29760',
'version' => 'Genoscope.12x'
),
'zma' => array(
'species' => 'zma',
'common_name' => 'Zea mays',
'tax_id' => '4577',
'version' => 'NAM v5.0'
)
)
$multiplicon_data = array(
(int) 1933599 => array(
'species' => 'sly',
'chromosome' => 'SL4.0ch02',
'data' => array(
(int) 0 => array(
[maximum depth reached]
),
(int) 1 => array(
[maximum depth reached]
),
(int) 2 => array(
[maximum depth reached]
),
(int) 3 => array(
[maximum depth reached]
),
(int) 4 => array(
[maximum depth reached]
),
(int) 5 => array(
[maximum depth reached]
),
(int) 6 => array(
[maximum depth reached]
),
(int) 7 => array(
[maximum depth reached]
),
(int) 8 => array(
[maximum depth reached]
),
(int) 9 => array(
[maximum depth reached]
),
(int) 10 => array(
[maximum depth reached]
),
(int) 11 => array(
[maximum depth reached]
),
(int) 12 => array(
[maximum depth reached]
),
(int) 13 => array(
[maximum depth reached]
),
(int) 14 => array(
[maximum depth reached]
),
(int) 15 => array(
[maximum depth reached]
),
(int) 16 => array(
[maximum depth reached]
),
(int) 17 => array(
[maximum depth reached]
),
(int) 18 => array(
[maximum depth reached]
),
(int) 19 => array(
[maximum depth reached]
),
(int) 20 => array(
[maximum depth reached]
),
(int) 21 => array(
[maximum depth reached]
),
(int) 22 => array(
[maximum depth reached]
),
(int) 23 => array(
[maximum depth reached]
),
(int) 24 => array(
[maximum depth reached]
),
(int) 25 => array(
[maximum depth reached]
),
(int) 26 => array(
[maximum depth reached]
),
(int) 27 => array(
[maximum depth reached]
),
(int) 28 => array(
[maximum depth reached]
),
(int) 29 => array(
[maximum depth reached]
),
(int) 30 => array(
[maximum depth reached]
),
(int) 31 => array(
[maximum depth reached]
),
(int) 32 => array(
[maximum depth reached]
),
(int) 33 => array(
[maximum depth reached]
),
(int) 34 => array(
[maximum depth reached]
),
(int) 35 => array(
[maximum depth reached]
),
(int) 36 => array(
[maximum depth reached]
),
(int) 37 => array(
[maximum depth reached]
),
(int) 38 => array(
[maximum depth reached]
),
(int) 39 => array(
[maximum depth reached]
),
(int) 40 => array(
[maximum depth reached]
),
(int) 41 => array(
[maximum depth reached]
),
(int) 42 => array(
[maximum depth reached]
),
(int) 43 => array(
[maximum depth reached]
),
(int) 44 => array(
[maximum depth reached]
),
(int) 45 => array(
[maximum depth reached]
),
(int) 46 => array(
[maximum depth reached]
),
(int) 47 => array(
[maximum depth reached]
),
(int) 48 => array(
[maximum depth reached]
),
(int) 49 => array(
[maximum depth reached]
),
(int) 50 => array(
[maximum depth reached]
),
(int) 51 => array(
[maximum depth reached]
),
(int) 52 => array(
[maximum depth reached]
),
(int) 53 => array(
[maximum depth reached]
),
(int) 54 => array(
[maximum depth reached]
),
(int) 55 => array(
[maximum depth reached]
),
(int) 56 => array(
[maximum depth reached]
),
(int) 57 => array(
[maximum depth reached]
),
(int) 58 => array(
[maximum depth reached]
),
(int) 59 => array(
[maximum depth reached]
),
(int) 60 => array(
[maximum depth reached]
),
(int) 61 => array(
[maximum depth reached]
),
(int) 62 => array(
[maximum depth reached]
),
(int) 63 => array(
[maximum depth reached]
),
(int) 64 => array(
[maximum depth reached]
),
(int) 65 => array(
[maximum depth reached]
),
(int) 66 => array(
[maximum depth reached]
),
(int) 67 => array(
[maximum depth reached]
),
(int) 68 => array(
[maximum depth reached]
),
(int) 69 => array(
[maximum depth reached]
),
(int) 70 => array(
[maximum depth reached]
),
(int) 71 => array(
[maximum depth reached]
),
(int) 72 => array(
[maximum depth reached]
),
(int) 73 => array(
[maximum depth reached]
),
(int) 74 => array(
[maximum depth reached]
),
(int) 75 => array(
[maximum depth reached]
),
(int) 76 => array(
[maximum depth reached]
),
(int) 77 => array(
[maximum depth reached]
),
(int) 78 => array(
[maximum depth reached]
),
(int) 79 => array(
[maximum depth reached]
),
(int) 80 => array(
[maximum depth reached]
),
(int) 81 => array(
[maximum depth reached]
),
(int) 82 => array(
[maximum depth reached]
),
(int) 83 => array(
[maximum depth reached]
),
(int) 84 => array(
[maximum depth reached]
),
(int) 85 => array(
[maximum depth reached]
),
(int) 86 => array(
[maximum depth reached]
),
(int) 87 => array(
[maximum depth reached]
),
(int) 88 => array(
[maximum depth reached]
),
(int) 89 => array(
[maximum depth reached]
),
(int) 90 => array(
[maximum depth reached]
),
(int) 91 => array(
[maximum depth reached]
),
(int) 92 => array(
[maximum depth reached]
),
(int) 93 => array(
[maximum depth reached]
),
(int) 94 => array(
[maximum depth reached]
),
(int) 95 => array(
[maximum depth reached]
)
)
),
(int) 1933600 => array(
'species' => 'camsi',
'chromosome' => 'Chr2',
'data' => array(
(int) 0 => array(
[maximum depth reached]
),
(int) 1 => array(
[maximum depth reached]
),
(int) 2 => array(
[maximum depth reached]
),
(int) 3 => array(
[maximum depth reached]
),
(int) 4 => array(
[maximum depth reached]
),
(int) 5 => array(
[maximum depth reached]
),
(int) 6 => array(
[maximum depth reached]
),
(int) 7 => array(
[maximum depth reached]
),
(int) 8 => array(
[maximum depth reached]
),
(int) 9 => array(
[maximum depth reached]
),
(int) 10 => array(
[maximum depth reached]
),
(int) 11 => array(
[maximum depth reached]
),
(int) 12 => array(
[maximum depth reached]
),
(int) 13 => array(
[maximum depth reached]
),
(int) 14 => array(
[maximum depth reached]
),
(int) 15 => array(
[maximum depth reached]
),
(int) 16 => array(
[maximum depth reached]
),
(int) 17 => array(
[maximum depth reached]
),
(int) 18 => array(
[maximum depth reached]
),
(int) 19 => array(
[maximum depth reached]
),
(int) 20 => array(
[maximum depth reached]
),
(int) 21 => array(
[maximum depth reached]
),
(int) 22 => array(
[maximum depth reached]
),
(int) 23 => array(
[maximum depth reached]
),
(int) 24 => array(
[maximum depth reached]
),
(int) 25 => array(
[maximum depth reached]
),
(int) 26 => array(
[maximum depth reached]
),
(int) 27 => array(
[maximum depth reached]
),
(int) 28 => array(
[maximum depth reached]
),
(int) 29 => array(
[maximum depth reached]
),
(int) 30 => array(
[maximum depth reached]
),
(int) 31 => array(
[maximum depth reached]
),
(int) 32 => array(
[maximum depth reached]
),
(int) 33 => array(
[maximum depth reached]
),
(int) 34 => array(
[maximum depth reached]
),
(int) 35 => array(
[maximum depth reached]
),
(int) 36 => array(
[maximum depth reached]
),
(int) 37 => array(
[maximum depth reached]
),
(int) 38 => array(
[maximum depth reached]
),
(int) 39 => array(
[maximum depth reached]
),
(int) 40 => array(
[maximum depth reached]
),
(int) 41 => array(
[maximum depth reached]
),
(int) 42 => array(
[maximum depth reached]
),
(int) 43 => array(
[maximum depth reached]
),
(int) 44 => array(
[maximum depth reached]
),
(int) 45 => array(
[maximum depth reached]
),
(int) 46 => array(
[maximum depth reached]
),
(int) 47 => array(
[maximum depth reached]
),
(int) 48 => array(
[maximum depth reached]
),
(int) 49 => array(
[maximum depth reached]
),
(int) 50 => array(
[maximum depth reached]
),
(int) 51 => array(
[maximum depth reached]
),
(int) 52 => array(
[maximum depth reached]
),
(int) 53 => array(
[maximum depth reached]
),
(int) 54 => array(
[maximum depth reached]
),
(int) 55 => array(
[maximum depth reached]
),
(int) 56 => array(
[maximum depth reached]
),
(int) 57 => array(
[maximum depth reached]
),
(int) 58 => array(
[maximum depth reached]
),
(int) 59 => array(
[maximum depth reached]
),
(int) 60 => array(
[maximum depth reached]
),
(int) 61 => array(
[maximum depth reached]
),
(int) 62 => array(
[maximum depth reached]
),
(int) 63 => array(
[maximum depth reached]
),
(int) 64 => array(
[maximum depth reached]
),
(int) 65 => array(
[maximum depth reached]
),
(int) 66 => array(
[maximum depth reached]
),
(int) 67 => array(
[maximum depth reached]
),
(int) 68 => array(
[maximum depth reached]
),
(int) 69 => array(
[maximum depth reached]
),
(int) 70 => array(
[maximum depth reached]
),
(int) 71 => array(
[maximum depth reached]
),
(int) 72 => array(
[maximum depth reached]
),
(int) 73 => array(
[maximum depth reached]
),
(int) 74 => array(
[maximum depth reached]
),
(int) 75 => array(
[maximum depth reached]
)
)
)
)
$children_multiplicon_information = array()
$parental_multiplicon_information = array()
$multiplicon_information = array(
'multiplicon_id' => '966800',
'exp_id' => '1',
'info' => array(
'parent' => '0',
'level' => '2',
'num_anchorpoints' => '16',
'profile_length' => '96',
'is_redundant' => '-1'
),
'profile' => array(
'num_segments' => '2',
'num_species' => '2',
'species' => array(
'aag' => '0',
'aar' => '0',
'acertr' => '0',
'ach' => '0',
'aly' => '0',
'ama' => '0',
'amhyb' => '0',
'aox' => '0',
'arhy' => '0',
'ath' => '0',
'atr' => '0',
'bca' => '0',
'bna' => '0',
'bol' => '0',
'bra' => '0',
'bvu' => '0',
'camsi' => '1',
'can' => '0',
'cansat' => '0',
'car' => '0',
'cav' => '0',
'cbr' => '0',
'ccan' => '0',
'ccl' => '0',
'cde' => '0',
'cfa' => '0',
'chi' => '0',
'cil' => '0',
'cla' => '0',
'cme' => '0',
'col' => '0',
'cpa' => '0',
'cqu' => '0',
'cre' => '0',
'cru' => '0',
'csa' => '0',
'dca' => '0',
'din' => '0',
'dzi' => '0',
'eca' => '0',
'egr' => '0',
'egut' => '0',
'esa' => '0',
'fan' => '0',
'fve' => '0',
'ghi' => '0',
'gma' => '0',
'gra' => '0',
'han' => '0',
'hma' => '0',
'lal' => '0',
'lja' => '0',
'lonja' => '0',
'lsa' => '0',
'mbi' => '0',
'mco' => '0',
'mdo' => '0',
'mes' => '0',
'mpo' => '0',
'mtr' => '0',
'nnu' => '0',
'nta' => '0',
'oeu' => '0',
'osa' => '0',
'pax' => '0',
'pco' => '0',
'pgr' => '0',
'ppa' => '0',
'ppe' => '0',
'psa' => '0',
'pso' => '0',
'ptr' => '0',
'pvu' => '0',
'qlo' => '0',
'rch' => '0',
'rsi' => '0',
'sas' => '0',
'sbo' => '0',
'sbr' => '0',
'sci' => '0',
'sed' => '0',
'sgi' => '0',
'shi' => '0',
'sly' => '1',
'smo' => '0',
'spa' => '0',
'spe' => '0',
'stu' => '0',
'sun' => '0',
'tar' => '0',
'tca' => '0',
'tha' => '0',
'tpr' => '0',
'twi' => '0',
'ugi' => '0',
'vma' => '0',
'vmu' => '0',
'vpl' => '0',
'vvi' => '0',
'zma' => '0'
)
)
)
$multiplicon_id = '966800'
$iadhore_exp_id = '1'
$title_for_layout = 'Dicots PLAZA 5.0 : Colinearity Data'
$content_for_layout = '<!-- Load the CSS files for this view -->
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/bootstrap-multiselect.min.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/multiplicon_svg.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/multiplicon_graph.css"/>
<link rel="stylesheet" type="text/css" href="/plaza.dev/_dev_instances/feedback/css/tipsy.css"/>
<!-- Load the JS files for this view -->
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/snap.svg-min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/bootstrap-multiselect.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/gf_colors.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/plaza/multiplicon_svg.js"></script>
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<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/dagre/dagre-d3.min.js"></script>
<script type="text/javascript" src="/plaza.dev/_dev_instances/feedback/js/dagre/tipsy.js"></script>
<h1>
Multiplicon view:
<strong>966800</strong>
(Experiment Id: 1)
<a href='https://bioinformatics.psb.ugent.be/plaza/documentation/tools#multiplicon_view' target='_blank' onclick='window.open("https://bioinformatics.psb.ugent.be/plaza/documentation/tools#multiplicon_view","HELP","width=1000,height=600,scrollbars=yes,toolbar=no,location=no");return false;'>
<span class="glyphicon glyphicon-question-sign documentation_link"></span>
</a></h1>
<div class="mb-4">
<p>
The Multiplicon view displays the aligned gene strings of a set of homologous segments.
</p>
</div>
<h2>Multiplicon Information</h2>
<div class="mb-4">
<table class='table'>
<thead>
<tr>
<th>Multiplicon Id</th>
<th>#Species</th>
<th>#Segments</th>
<th>#Anchorpoints</th>
<th>Profile Length</th>
</tr>
</thead>
<tbody>
<tr>
<td>966800</td>
<td>2</td>
<td>2</td>
<td>16</td>
<td>96</td>
</tr>
</tbody>
</table>
</div>
<div class="mb-4">
<h2>
Multiplicon Plot
</h2>
<!-- left panel: contains the multiplicon SVG -->
<div class="d-flex flex-row flex-wrap mt-3">
<div class="d-flex flex-column col-lg-9">
<!-- multiplicon itself -->
<div>
<div id="multiplicon_loading" class='loader'></div>
<div id="multiplicon_view_div">
<svg id="multiplicon_svg"></svg>
</div>
</div>
<!-- GF graph -->
<!-- <div>
<div id='multiplicon_gf_graph_div'>
<svg id="multiplicon_gf_graph_svg" height="200">
<g />
</svg>
</div>
</div> -->
</div>
<!-- right panels: contain the options etc -->
<div class="col-lg-3 ps-4">
<div style="display:none" id="gene_gf_info">
<div class="parameter_option_box mb-3">
<h5>Gene Information</h5>
<div id="gene_information"></div>
<hr>
<h5>Gene Family Information</h5>
<div id="gf_information"></div>
</div>
</div>
<div class="parameter_option_box mb-3">
<h3>Options</h3>
<span>Draw mode</span>
<select class="form form-select" name="draw_mode_form_select" id="draw_mode_form_select">
<option value='all' selected='selected'>Display all genes</option>
<option value='anchor'>Display only anchorpoints</option>
</select>
<span>Segment ordering</span>
<select class="form form-select" name="ordering_form_select" id="ordering_form_select">
<option value='standard' selected='selected'>Use standard order</option>
<option value='cluster'>Group species together</option>
</select>
<span>Species</span>
<select class="form form-select" name="species_form_select" id="species_form_select" multiple="multiple">
<option value='camsi' selected='selected'>Camellia sinensis var. sinensis</option>
<option value='sly' selected='selected'>Solanum lycopersicum</option>
</select>
</div>
</div>
</div>
<!-- JS code to load species & create multiplicon SVG -->
<script type="text/javascript">
//<![CDATA[
jQuery(document).ready(function() {
//Enable the multiselect
jQuery("#species_form_select").multiselect({
disableIfEmpty: true,
enableFiltering: false,
maxHeight: 300,
includeSelectAllOption: true,
numberDisplayed: 2,
templates: {
button: '<button type="button" class="multiselect dropdown-toggle btn btn-light border" data-bs-toggle="dropdown" aria-expanded="false"><i class="bi bi-list-check me-2"></i><span class="multiselect-selected-text"></span></button>'
}
});
//setup the SVG for the graph to have a fixed width based on parental size
jQuery("#multiplicon_gf_graph_svg").attr("width", jQuery('#multiplicon_gf_graph_div').width());
//Hide the gene and gf info panel
jQuery("#gene_gf_info").hide();
//Create the multiplicon SVG
try {
let multiplicon_svg = new MultipliconSVG();
multiplicon_svg.options({
apiEndpointSpecies: '/plaza.dev/_dev_instances/feedback/api/list_species',
apiEndpointMultiplicon: '/plaza.dev/_dev_instances/feedback/collinearity/multiplicon_plot_data/1/966800',
apiEndpointGfFuncAnnotBase: '/plaza.dev/_dev_instances/feedback/api/gf_functional_annotation',
urlSpeciesBase: '/plaza.dev/_dev_instances/feedback/organism/view',
urlGeneBase: '/plaza.dev/_dev_instances/feedback/genes/view',
urlGeneFamilyBase: '/plaza.dev/_dev_instances/feedback/gene_families/view',
urlGoBase: '/plaza.dev/_dev_instances/feedback/go/view',
urlInterproBase: '/plaza.dev/_dev_instances/feedback/interpro/view',
urlMapmanBase: '/plaza.dev/_dev_instances/feedback/mapman/view',
idMain: 'multiplicon_svg',
idLoading: 'multiplicon_loading',
idPanelGene: 'gene_information',
idPanelGeneFamily: 'gf_information',
idPanelGeneGF: 'gene_gf_info',
idSelectDrawMode: 'draw_mode_form_select',
idSelectOrder: 'ordering_form_select',
idSelectSpecies: 'species_form_select',
idGraph: 'multiplicon_gf_graph_svg'
});
multiplicon_svg.render();
//Allow for the resizing of the view
jQuery(window).resize(multiplicon_svg.debouncer(function(e) {
multiplicon_svg.render();
}));
} catch (error) {
jQuery("#multiplicon_loading").hide();
jQuery("#multiplicon_view_div").show();
jQuery("#multiplicon_view_div").html("Error while loading multiplicon");
}
});
//]]>
</script>
</div>
<h2>Data Table</h2>
<div id="data_table_div">
<table class='table'>
<thead>
<tr>
<th>Species</th>
<th>Chromosome</th>
<th>First Gene</th>
<th>Last Gene</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/organism/view/Camellia%2Bsinensis%2Bvar.%2Bsinensis">Camellia sinensis var. sinensis</a></td>
<td>Chr2</td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/CSS0005295">CSS0005295</a></td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/CSS0012962">CSS0012962</a></td>
</tr>
<tr>
<td><a href="/plaza.dev/_dev_instances/feedback/organism/view/Solanum%2Blycopersicum">Solanum lycopersicum</a></td>
<td>SL4.0ch02</td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/Solyc02g088090.1">Solyc02g088090.1</a></td>
<td><a href="/plaza.dev/_dev_instances/feedback/genes/view/Solyc02g089200.4">Solyc02g089200.4</a></td>
</tr>
</tbody>
</table>
</div>
'
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Multiplicon view:
966800
(Experiment Id: 1)
The Multiplicon view displays the aligned gene strings of a set of homologous segments.
Multiplicon Information
Multiplicon Id
#Species
#Segments
#Anchorpoints
Profile Length
966800
2
2
16
96
Multiplicon Plot
Gene Information
Gene Family Information
Options
Draw mode
Display all genes
Display only anchorpoints
Segment ordering
Use standard order
Group species together
Species
Camellia sinensis var. sinensis
Solanum lycopersicum
Data Table