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viewCNVAndPhenotypeFigures.blade.php
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viewCNVAndPhenotypeFigures.blade.php
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@php
include resource_path() . '/views/system/config.blade.php';
$organism = $info['organism'];
$chromosome = $info['chromosome'];
$position_start = $info['position_start'];
$position_end = $info['position_end'];
$width = $info['width'];
$strand = $info['strand'];
$cnv_data_option = $info['cnv_data_option'];
$cn_array = $info['cn_array'];
$phenotype = $info['phenotype'];
@endphp
<head>
<title>{{ $config_organism }}-KB</title>
<link rel="shortcut icon" href="{{ asset('css/images/Header/kbcommons_icon.ico') }}">
<script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
<script src="https://cdn.plot.ly/plotly-2.12.1.min.js"></script>
</head>
<body>
<h3>Queried CNV and Phenotype:</h3>
<div style='width:auto; height:auto; overflow:visible; max-height:1000px;'>
<table style='text-align:center; border:3px solid #000;'>
<tr>
<th style="border:1px solid black; min-width:80px;">Chromsome</th>
<th style="border:1px solid black; min-width:80px;">Position Start</th>
<th style="border:1px solid black; min-width:80px;">Position End</th>
<th style="border:1px solid black; min-width:80px;">Width</th>
<th style="border:1px solid black; min-width:80px;">Strand</th>
<th style="border:1px solid black; min-width:80px;">Data Option</th>
<th style="border:1px solid black; min-width:80px;">CN</th>
<th style="border:1px solid black; min-width:80px;">Phenotype</th>
</tr>
<tr bgcolor="#DDFFDD">
<td style="border:1px solid black; min-width:80px;">{{$chromosome}}</td>
<td style="border:1px solid black; min-width:80px;">{{$position_start}}</td>
<td style="border:1px solid black; min-width:80px;">{{$position_end}}</td>
<td style="border:1px solid black; min-width:80px;">{{$width}}</td>
<td style="border:1px solid black; min-width:80px;">{{$strand}}</td>
<td style="border:1px solid black; min-width:80px;">{{$cnv_data_option}}</td>
<td style="border:1px solid black; min-width:80px;">{{implode(',', $cn_array)}}</td>
<td style="border:1px solid black; min-width:80px;">{{$phenotype}}</td>
</tr>
</table>
</div>
<br /><br />
<h3>Figures:</h3>
<div id="cn_section_div">
<div id="cn_figure_div">Loading CN plot...</div>
<div id="cn_summary_table_div">Loading CN summary table...</div>
</div>
<hr />
<div id="improvement_status_summary_figure_div"></div>
<!-- <div id="status_figure_div">Loading status plot...</div> -->
</body>
<script src="{{ asset('system/home/GenVarX/js/viewCNVAndPhenotypeFigures.js') }}" type="text/javascript"></script>
<script type="text/javascript" language="javascript">
var organism = <?php if(isset($organism)) {echo json_encode($organism, JSON_INVALID_UTF8_IGNORE);} else {echo "";}?>;
var chromosome = <?php if(isset($chromosome)) {echo json_encode($chromosome, JSON_INVALID_UTF8_IGNORE);} else {echo "";}?>;
var position_start = <?php if(isset($position_start)) {echo json_encode($position_start, JSON_INVALID_UTF8_IGNORE);} else {echo "";}?>;
var position_end = <?php if(isset($position_end)) {echo json_encode($position_end, JSON_INVALID_UTF8_IGNORE);} else {echo "";}?>;
var cnv_data_option = <?php if(isset($cnv_data_option)) {echo json_encode($cnv_data_option, JSON_INVALID_UTF8_IGNORE);} else {echo "";}?>;
var phenotype = <?php if(isset($phenotype)) {echo json_encode($phenotype, JSON_INVALID_UTF8_IGNORE);} else {echo "";}?>;
var cn_array = <?php if(isset($cn_array) && is_array($cn_array) && !empty($cn_array)) {echo json_encode($cn_array, JSON_INVALID_UTF8_IGNORE);} else {echo "";}?>;
if (organism == "Osativa") {
document.getElementById('improvement_status_summary_figure_div').innerHTML = "Loading subpopulation summary plot...";
summaryPhenotype = "Subpopulation";
} else if (organism == "Athaliana") {
document.getElementById('improvement_status_summary_figure_div').innerHTML = "Loading admixture group summary plot...";
summaryPhenotype = "Admixture_Group";
} else if (organism == "Zmays") {
document.getElementById('improvement_status_summary_figure_div').innerHTML = "Loading improvement status summary plot...";
summaryPhenotype = "Improvement_Status";
}
if (organism && chromosome && position_start && position_end && cnv_data_option && phenotype && cn_array.length > 0) {
$.ajax({
url: 'queryCNVAndPhenotypeFigures/'+organism,
type: 'GET',
contentType: 'application/json',
data: {
Organism: organism,
Chromosome: chromosome,
Start: position_start,
End: position_end,
Data_Option: cnv_data_option,
CN: cn_array,
Phenotype: phenotype
},
success: function (response) {
res = JSON.parse(response);
if (res && phenotype) {
document.getElementById("cn_figure_div").style.minHeight = "800px";
document.getElementById("improvement_status_summary_figure_div").style.minHeight = "800px";
// document.getElementById("status_figure_div").style.minHeight = "800px";
// Summarize data
var result_dict = summarizeQueriedData(
JSON.parse(JSON.stringify(res)),
phenotype,
'CN'
);
var result_arr = result_dict['Data'];
var summary_array = result_dict['Summary'];
var cnData = collectDataForFigure(result_arr, phenotype, 'CN');
var cnAndImprovementStatusData = collectDataForFigure(result_arr, summaryPhenotype, 'CN');
// var statusData = collectDataForFigure(result_arr, phenotype, 'Status');
plotFigure(cnData, 'CN', 'CN', 'cn_figure_div');
plotFigure(cnAndImprovementStatusData, 'CN', summaryPhenotype+'_Summary', 'improvement_status_summary_figure_div');
// plotFigure(statusData, 'Status', 'Status', 'status_figure_div');
// Render summarized data
document.getElementById('cn_summary_table_div').innerText = "";
document.getElementById('cn_summary_table_div').innerHTML = "";
document.getElementById('cn_summary_table_div').appendChild(
constructInfoTable(summary_array)
);
document.getElementById('cn_summary_table_div').style.overflow = 'scroll';
}
},
error: function (xhr, status, error) {
console.log('Error with code ' + xhr.status + ': ' + xhr.statusText);
document.getElementById('cn_figure_div').innerText="";
document.getElementById('cn_summary_table_div').innerHTML="";
document.getElementById('improvement_status_summary_figure_div').innerHTML="";
// document.getElementById('status_figure_div').innerHTML="";
var p_tag = document.createElement('p');
p_tag.innerHTML = "CN distribution figure is not available due to lack of data!!!";
document.getElementById('cn_figure_div').appendChild(p_tag);
var p_tag = document.createElement('p');
p_tag.innerHTML = "CN summary table is not available due to lack of data!!!";
document.getElementById('cn_summary_table_div').appendChild(p_tag);
var p_tag = document.createElement('p');
p_tag.innerHTML = summaryPhenotype + " summary figure is not available due to lack of data!!!";
document.getElementById('improvement_status_summary_figure_div').appendChild(p_tag);
// var p_tag = document.createElement('p');
// p_tag.innerHTML = "Status distribution figure is not available due to lack of data!!!";
// document.getElementById('status_figure_div').appendChild(p_tag);
}
});
} else {
document.getElementById('cn_figure_div').innerText="";
document.getElementById('cn_summary_table_div').innerHTML="";
document.getElementById('improvement_status_summary_figure_div').innerHTML="";
// document.getElementById('status_figure_div').innerHTML="";
var p_tag = document.createElement('p');
p_tag.innerHTML = "CN distribution figure is not available due to lack of data!!!";
document.getElementById('cn_figure_div').appendChild(p_tag);
var p_tag = document.createElement('p');
p_tag.innerHTML = "CN summary table is not available due to lack of data!!!";
document.getElementById('cn_summary_table_div').appendChild(p_tag);
var p_tag = document.createElement('p');
p_tag.innerHTML = summaryPhenotype + " summary figure is not available due to lack of data!!!";
document.getElementById('improvement_status_summary_figure_div').appendChild(p_tag);
// var p_tag = document.createElement('p');
// p_tag.innerHTML = "Status distribution figure is not available due to lack of data!!!";
// document.getElementById('status_figure_div').appendChild(p_tag);
}
</script>