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