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viewPromotersByGenes.blade.php
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viewPromotersByGenes.blade.php
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@php
include resource_path() . '/views/system/config.blade.php';
$organism = $info['organism'];
$result_arr = $info['result_arr'];
@endphp
<head>
<title>{{ $config_organism }}-KB</title>
<link rel="shortcut icon" href="{{ asset('css/images/Header/kbcommons_icon.ico') }}">
<script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
</head>
<body>
<!-- Back button -->
<a href="{{ route('system.tools.GenVarX', ['organism'=>$organism]) }}"><button> < Back </button></a>
<br />
<br />
@php
for ($i = 0; $i < count($result_arr); $i++) {
echo "<b>Queried Gene: </b>" . $result_arr[$i]->Name . " (" . $result_arr[$i]->Chromosome . ":" . $result_arr[$i]->Start . "-" . $result_arr[$i]->End . ") (" . $result_arr[$i]->Strand . ")";
echo "<br /><br />";
echo "<b>Promoter Region: </b>" . $result_arr[$i]->Promoter_Start . "-" . $result_arr[$i]->Promoter_End;
echo "<br /><br />";
if (count($result_arr[$i]->Motif_Data) > 0) {
echo "<div style=\"width:auto; height:auto; border:3px solid #000; max-height:1000px; overflow:scroll;\">";
echo "<table style=\"text-align:center; width:100%;\">";
// Table header
echo "<tr>";
foreach ($result_arr[$i]->Motif_Data[0] as $key => $value) {
echo "<th style=\"border:1px solid black; text-align:center; min-width:80px;\">" . $key . "</th>";
}
echo "</tr>";
// Table row
for ($j = 0; $j < count($result_arr[$i]->Motif_Data); $j++) {
// Table row
echo "<tr bgcolor=\"" . ($j % 2 ? "#FFFFFF" : "#DDFDD") . "\">";
foreach ($result_arr[$i]->Motif_Data[$j] as $key => $value) {
if ($key == "Binding_TF") {
echo "<td style=\"border:1px solid black; min-width:80px;\">";
echo "<a href=\"javascript:void(0);\" onclick=\"getMotifWeblogo('" . $organism . "', '" . $value . "', '" . $result_arr[$i]->Name . "', '" . $result_arr[$i]->Motif_Data[$j]->Chromosome . "', '" . $result_arr[$i]->Motif_Data[$j]->Start . "', '" . $result_arr[$i]->Motif_Data[$j]->End . "', '" . $result_arr[$i]->Motif_Data[$j]->Gene_Binding_Sequence . "')\">";
echo $value;
echo "</a>";
echo "</td>";
} else {
echo "<td style=\"border:1px solid black; min-width:80px;\">" . $value . "</td>";
}
}
echo "</tr>";
}
echo "</table>";
echo "</div>";
echo "<br />";
// Div tags for selected motif, weblogo, and motif sequence table
echo "<div id=\"" . $result_arr[$i]->Name . "_b\" style='width:auto; height:auto; overflow:visible; max-height:1000px;'></div>";
echo "<div id=\"" . $result_arr[$i]->Name . "_weblogo\" style='width:auto; height:auto; overflow:visible; max-height:1000px;'></div>";
echo "<div id=\"" . $result_arr[$i]->Name . "_detail_table\" style='width:auto; height:auto; overflow:visible; max-height:1000px;'></div>";
echo "<br /><br />";
} else {
echo "<p>No binding TF found in our database!!!</p><br /><br />";
}
}
@endphp
</body>
<script type="text/javascript">
function getMotifWeblogo(organism, motif, gene, chromosome, motif_start, motif_end, motif_sequence) {
// Clear data appended to the div tags, if there is any
if (document.getElementById(gene+"_b").innerHTML) {
document.getElementById(gene+"_b").innerHTML = null;
}
if (document.getElementById(gene+"_weblogo").innerHTML) {
document.getElementById(gene+"_weblogo").innerHTML = null;
}
if (document.getElementById(gene+"_detail_table").innerHTML) {
document.getElementById(gene+"_detail_table").innerHTML = null;
}
// Create b tag for motif
var motif_b = document.createElement("b");
motif_b.innerHTML = "Selected TF: " + motif;
document.getElementById(gene+"_b").appendChild(motif_b);
// Load Ceqlogo / Weblogo image
var weblogo = document.createElement("img");
if (organism === "Osativa") {
weblogo.setAttribute("src", "{{ asset('system/home/GenVarX/assets/mViz_Rice_Japonica_motif_weblogos')}}" + "/" + motif + ".png");
document.getElementById(gene+"_weblogo").appendChild(weblogo);
} else if(organism === "Athaliana") {
weblogo.setAttribute("src", "{{ asset('system/home/GenVarX/assets/mViz_Arabidopsis_motif_weblogos')}}" + "/" + motif + ".png");
document.getElementById(gene+"_weblogo").appendChild(weblogo);
} else if(organism === "Zmays") {
weblogo.setAttribute("src", "{{ asset('system/home/GenVarX/assets/mViz_Maize_motif_weblogos') }}" + "/" + motif + ".png");
document.getElementById(gene+"_weblogo").appendChild(weblogo);
}
// Create motif sequence table
let detail_table = document.createElement("table");
detail_table.setAttribute("style", "text-align:center; border:3px solid #000;");
let detail_tr_index = document.createElement("tr");
let detail_tr_position = document.createElement("tr");
let detail_tr_nucleotide = document.createElement("tr");
let detail_tr_genotype_count = document.createElement("tr");
for (let i = 0; i < (motif_end-motif_start+1); i++) {
var detail_th = document.createElement("th");
detail_th.setAttribute("style", "border:1px solid black; min-width:80px; height:18.5px;");
detail_th.innerHTML = Number(i)+1;
detail_tr_index.appendChild(detail_th);
var detail_th = document.createElement("th");
detail_th.setAttribute("style", "border:1px solid black; min-width:80px; height:18.5px;");
detail_th.innerHTML = Number(motif_start)+Number(i);
detail_tr_position.appendChild(detail_th);
var detail_td = document.createElement("td");
detail_td.setAttribute("style", "border:1px solid black; min-width:80px; height:18.5px;");
detail_td.innerHTML = motif_sequence[i];
detail_tr_nucleotide.appendChild(detail_td);
var detail_td = document.createElement("td");
detail_td.id = "genotype_count_"+(Number(motif_start)+Number(i)).toString();
detail_tr_genotype_count.appendChild(detail_td);
}
detail_table.appendChild(detail_tr_index);
detail_table.appendChild(detail_tr_position);
detail_table.appendChild(detail_tr_nucleotide);
detail_table.appendChild(detail_tr_genotype_count);
document.getElementById(gene+"_detail_table").appendChild(detail_table);
$.ajax({
url: 'queryGenotypeCount/'+organism,
type: 'GET',
contentType: 'application/json',
data: {
Organism: organism,
Chromosome: chromosome,
Start: motif_start,
End: motif_end
},
success: function (response) {
let res = JSON.parse(response);
for (let i = 0; i < res.length; i++) {
var genotype_count_element = document.getElementById("genotype_count_"+(res[i]['Position']).toString());
if (genotype_count_element.innerHTML === null || genotype_count_element.innerHTML == '') {
// Construct table with header
genotype_count_element.setAttribute("style", "border:1px solid black; min-width:80px; height:18.5px;");
var genotype_count_table = document.createElement("table");
genotype_count_table.id = "genotype_count_"+(res[i]['Position']).toString()+"_table";
var genotype_count_tr_index = document.createElement("tr");
var detail_th = document.createElement("th");
detail_th.setAttribute("style", "border:1px solid black; min-width:20px; height:18.5px;");
detail_th.innerHTML = "Genotype";
genotype_count_tr_index.appendChild(detail_th);
var detail_th = document.createElement("th");
detail_th.setAttribute("style", "border:1px solid black; min-width:20px; height:18.5px;");
detail_th.innerHTML = "Category";
genotype_count_tr_index.appendChild(detail_th);
var detail_th = document.createElement("th");
detail_th.setAttribute("style", "border:1px solid black; min-width:20px; height:18.5px;");
detail_th.innerHTML = "Count";
genotype_count_tr_index.appendChild(detail_th);
genotype_count_table.appendChild(genotype_count_tr_index);
genotype_count_element.appendChild(genotype_count_table);
}
}
for (let i = 0; i < res.length; i++) {
var genotype_count_element_table = document.getElementById("genotype_count_"+(res[i]['Position']).toString()+"_table");
var genotype_count_tr_index = document.createElement("tr");
var detail_td = document.createElement("td");
detail_td.setAttribute("style", "border:1px solid black; min-width:20px; height:18.5px;");
detail_td.innerHTML = res[i]['Genotype'];
genotype_count_tr_index.appendChild(detail_td);
var detail_td = document.createElement("td");
detail_td.setAttribute("style", "border:1px solid black; min-width:20px; height:18.5px;");
detail_td.innerHTML = res[i]['Category'];
genotype_count_tr_index.appendChild(detail_td);
var detail_td = document.createElement("td");
detail_td.setAttribute("style", "border:1px solid black; min-width:20px; height:18.5px;");
var position_a = document.createElement("a");
position_a.href = "../viewVariantAndPhenotype/"+organism+"?Chromosome="+res[i]['Chromosome']+"&Position="+res[i]['Position']+"&Genotype="+res[i]['Genotype'];
position_a.target = "_blank";
position_a.innerHTML = res[i]['Count']
detail_td.appendChild(position_a);
genotype_count_tr_index.appendChild(detail_td);
genotype_count_element_table.appendChild(genotype_count_tr_index);
}
},
error: function (xhr, status, error) {
console.log('Error with code ' + xhr.status + ': ' + xhr.statusText);
}
});
// Change the overflow style of the div to scroll
document.getElementById(gene+"_b").style.overflow = 'scroll';
document.getElementById(gene+"_weblogo").style.overflow = 'scroll';
document.getElementById(gene+"_detail_table").style.overflow = 'scroll';
}
</script>