Spaces:
Running
Running
File size: 34,702 Bytes
3211546 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 |
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Bioinformatics Toolkit</title>
<script src="https://cdn.tailwindcss.com"></script>
<script src="https://cdn.jsdelivr.net/npm/chart.js"></script>
<style>
.tool-card:hover {
transform: translateY(-5px);
box-shadow: 0 10px 20px rgba(0, 0, 0, 0.1);
}
.file-upload {
border: 2px dashed #cbd5e0;
transition: all 0.3s ease;
}
.file-upload:hover {
border-color: #4f46e5;
}
.file-upload.dragover {
border-color: #4f46e5;
background-color: #f0f7ff;
}
#volcanoPlot {
width: 100%;
height: 500px;
}
.gene-item:hover {
background-color: #f3f4f6;
}
</style>
</head>
<body class="bg-gray-50 min-h-screen">
<!-- Navigation -->
<nav class="bg-indigo-600 text-white shadow-lg">
<div class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8">
<div class="flex justify-between h-16 items-center">
<div class="flex items-center">
<div class="flex-shrink-0 flex items-center">
<svg class="h-8 w-8" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" fill="currentColor">
<path d="M20.5 11H19V7c0-1.1-.9-2-2-2h-4V3.5a2.5 2.5 0 00-5 0V5H4c-1.1 0-1.99.9-1.99 2v3.8H3.5c1.49 0 2.7 1.21 2.7 2.7 0 1.49-1.21 2.7-2.7 2.7H2V20c0 1.1.9 2 2 2h3.8v-1.5c0-1.49 1.21-2.7 2.7-2.7 1.49 0 2.7 1.21 2.7 2.7V22H17c1.1 0 2-.9 2-2v-4h1.5a2.5 2.5 0 000-5z" />
</svg>
<span class="ml-2 text-xl font-bold">BioTools</span>
</div>
</div>
<div>
<button id="homeBtn" class="px-3 py-2 rounded-md text-sm font-medium bg-indigo-700">Home</button>
</div>
</div>
</div>
</nav>
<!-- Main Content -->
<main class="max-w-7xl mx-auto px-4 sm:px-6 lg:px-8 py-8">
<!-- Home Page -->
<div id="homePage" class="space-y-8">
<div class="text-center">
<h1 class="text-4xl font-bold text-gray-900 mb-2">Bioinformatics Toolkit</h1>
<p class="text-xl text-gray-600">A collection of tools for biological data analysis</p>
</div>
<div class="grid grid-cols-1 md:grid-cols-2 gap-6">
<!-- Volcano Plot Tool Card -->
<div class="bg-white rounded-lg shadow-md overflow-hidden tool-card transition-all duration-300 cursor-pointer" id="volcanoToolCard">
<div class="p-6">
<div class="flex items-center">
<div class="flex-shrink-0 bg-indigo-100 p-3 rounded-lg">
<svg class="h-8 w-8 text-indigo-600" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 19v-6a2 2 0 00-2-2H5a2 2 0 00-2 2v6a2 2 0 002 2h2a2 2 0 002-2zm0 0V9a2 2 0 012-2h2a2 2 0 012 2v10m-6 0a2 2 0 002 2h2a2 2 0 002-2m0 0V5a2 2 0 012-2h2a2 2 0 012 2v14a2 2 0 01-2 2h-2a2 2 0 01-2-2z" />
</svg>
</div>
<div class="ml-4">
<h3 class="text-lg font-medium text-gray-900">Volcano Plot</h3>
<p class="text-gray-500">Visualize differential gene expression</p>
</div>
</div>
</div>
</div>
<!-- Enrichment Tool Card -->
<div class="bg-white rounded-lg shadow-md overflow-hidden tool-card transition-all duration-300 cursor-pointer" id="enrichmentToolCard">
<div class="p-6">
<div class="flex items-center">
<div class="flex-shrink-0 bg-green-100 p-3 rounded-lg">
<svg class="h-8 w-8 text-green-600" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M13 7h8m0 0v8m0-8l-8 8-4-4-6 6" />
</svg>
</div>
<div class="ml-4">
<h3 class="text-lg font-medium text-gray-900">Gene Enrichment</h3>
<p class="text-gray-500">Analyze DEGs for pathway enrichment</p>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Volcano Plot Tool -->
<div id="volcanoToolPage" class="hidden bg-white rounded-lg shadow-md p-6 space-y-6">
<div class="flex items-center">
<button id="volcanoBackBtn" class="mr-4 p-2 rounded-full hover:bg-gray-100">
<svg class="h-6 w-6 text-gray-600" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M10 19l-7-7m0 0l7-7m-7 7h18" />
</svg>
</button>
<h2 class="text-2xl font-bold text-gray-900">Volcano Plot Tool</h2>
</div>
<div class="grid grid-cols-1 lg:grid-cols-3 gap-6">
<div class="lg:col-span-1 space-y-4">
<div class="file-upload p-8 rounded-lg text-center cursor-pointer" id="volcanoFileUpload">
<input type="file" id="volcanoFileInput" class="hidden" accept=".csv,.tsv,.txt">
<svg class="mx-auto h-12 w-12 text-gray-400" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M7 16a4 4 0 01-.88-7.903A5 5 0 1115.9 6L16 6a5 5 0 011 9.9M15 13l-3-3m0 0l-3 3m3-3v12" />
</svg>
<h3 class="mt-2 text-sm font-medium text-gray-900">Upload your data</h3>
<p class="mt-1 text-sm text-gray-500">CSV, TSV or TXT file with gene expression data</p>
<p class="mt-1 text-xs text-gray-500">(symbol, log2FoldChange, padj columns required)</p>
</div>
<div class="bg-gray-50 p-4 rounded-lg">
<h3 class="text-sm font-medium text-gray-900 mb-2">Plot Settings</h3>
<div class="space-y-3">
<div>
<label for="logFCCutoff" class="block text-sm font-medium text-gray-700">logFC Cutoff</label>
<input type="number" id="logFCCutoff" value="1" step="0.1" class="mt-1 block w-full rounded-md border-gray-300 shadow-sm focus:border-indigo-500 focus:ring-indigo-500 sm:text-sm">
</div>
<div>
<label for="pValueCutoff" class="block text-sm font-medium text-gray-700">p-value Cutoff</label>
<input type="number" id="pValueCutoff" value="0.05" step="0.01" min="0" max="1" class="mt-1 block w-full rounded-md border-gray-300 shadow-sm focus:border-indigo-500 focus:ring-indigo-500 sm:text-sm">
</div>
<button id="generateVolcanoBtn" class="w-full bg-indigo-600 text-white py-2 px-4 rounded-md hover:bg-indigo-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-indigo-500">
Generate Plot
</button>
</div>
</div>
</div>
<div class="lg:col-span-2">
<div class="bg-gray-50 p-4 rounded-lg h-full">
<h3 class="text-sm font-medium text-gray-900 mb-2">Volcano Plot</h3>
<div id="volcanoPlotContainer">
<canvas id="volcanoPlot"></canvas>
</div>
</div>
</div>
</div>
</div>
<!-- Enrichment Tool -->
<div id="enrichmentToolPage" class="hidden bg-white rounded-lg shadow-md p-6 space-y-6">
<div class="flex items-center">
<button id="enrichmentBackBtn" class="mr-4 p-2 rounded-full hover:bg-gray-100">
<svg class="h-6 w-6 text-gray-600" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M10 19l-7-7m0 0l7-7m-7 7h18" />
</svg>
</button>
<h2 class="text-2xl font-bold text-gray-900">Gene Enrichment Tool</h2>
</div>
<div class="grid grid-cols-1 lg:grid-cols-3 gap-6">
<div class="lg:col-span-1 space-y-4">
<div class="file-upload p-8 rounded-lg text-center cursor-pointer" id="enrichmentFileUpload">
<input type="file" id="enrichmentFileInput" class="hidden" accept=".csv,.tsv,.txt">
<svg class="mx-auto h-12 w-12 text-gray-400" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M7 16a4 4 0 01-.88-7.903A5 5 0 1115.9 6L16 6a5 5 0 011 9.9M15 13l-3-3m0 0l-3 3m3-3v12" />
</svg>
<h3 class="mt-2 text-sm font-medium text-gray-900">Upload your DEGs</h3>
<p class="mt-1 text-sm text-gray-500">CSV, TSV or TXT file with gene list</p>
<p class="mt-1 text-xs text-gray-500">(One gene per line or GeneID column)</p>
</div>
<div class="bg-gray-50 p-4 rounded-lg">
<h3 class="text-sm font-medium text-gray-900 mb-2">Enrichment Settings</h3>
<div class="space-y-3">
<div>
<label for="databaseSelect" class="block text-sm font-medium text-gray-700">Database</label>
<select id="databaseSelect" class="mt-1 block w-full rounded-md border-gray-300 py-2 pl-3 pr-10 text-base focus:border-indigo-500 focus:outline-none focus:ring-indigo-500 sm:text-sm">
<option>GO Biological Process</option>
<option>GO Molecular Function</option>
<option>GO Cellular Component</option>
<option>KEGG Pathways</option>
<option>Reactome Pathways</option>
</select>
</div>
<div>
<label for="pValueEnrichCutoff" class="block text-sm font-medium text-gray-700">p-value Cutoff</label>
<input type="number" id="pValueEnrichCutoff" value="0.05" step="0.01" min="0" max="1" class="mt-1 block w-full rounded-md border-gray-300 shadow-sm focus:border-indigo-500 focus:ring-indigo-500 sm:text-sm">
</div>
<button id="runEnrichmentBtn" class="w-full bg-green-600 text-white py-2 px-4 rounded-md hover:bg-green-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-green-500">
Run Enrichment
</button>
</div>
</div>
</div>
<div class="lg:col-span-2">
<div class="bg-gray-50 p-4 rounded-lg h-full">
<h3 class="text-sm font-medium text-gray-900 mb-2">Enrichment Results</h3>
<div id="enrichmentResults" class="overflow-auto max-h-96">
<div class="text-center text-gray-500 py-8">
<svg class="mx-auto h-12 w-12 text-gray-400" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 12h6m-6 4h6m2 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z" />
</svg>
<p class="mt-2">Upload your DEGs and run enrichment analysis to see results</p>
</div>
</div>
</div>
</div>
</div>
</div>
</main>
<script>
// DOM Elements
const homePage = document.getElementById('homePage');
const volcanoToolPage = document.getElementById('volcanoToolPage');
const enrichmentToolPage = document.getElementById('enrichmentToolPage');
const volcanoToolCard = document.getElementById('volcanoToolCard');
const enrichmentToolCard = document.getElementById('enrichmentToolCard');
const homeBtn = document.getElementById('homeBtn');
const volcanoBackBtn = document.getElementById('volcanoBackBtn');
const enrichmentBackBtn = document.getElementById('enrichmentBackBtn');
// File upload elements
const volcanoFileUpload = document.getElementById('volcanoFileUpload');
const volcanoFileInput = document.getElementById('volcanoFileInput');
const enrichmentFileUpload = document.getElementById('enrichmentFileUpload');
const enrichmentFileInput = document.getElementById('enrichmentFileInput');
// Buttons
const generateVolcanoBtn = document.getElementById('generateVolcanoBtn');
const runEnrichmentBtn = document.getElementById('runEnrichmentBtn');
// Results containers
const enrichmentResults = document.getElementById('enrichmentResults');
// Chart variables
let volcanoChart = null;
let enrichmentChart = null;
// Event Listeners
volcanoToolCard.addEventListener('click', () => {
homePage.classList.add('hidden');
volcanoToolPage.classList.remove('hidden');
enrichmentToolPage.classList.add('hidden');
});
enrichmentToolCard.addEventListener('click', () => {
homePage.classList.add('hidden');
enrichmentToolPage.classList.remove('hidden');
volcanoToolPage.classList.add('hidden');
});
homeBtn.addEventListener('click', () => {
homePage.classList.remove('hidden');
volcanoToolPage.classList.add('hidden');
enrichmentToolPage.classList.add('hidden');
});
volcanoBackBtn.addEventListener('click', () => {
homePage.classList.remove('hidden');
volcanoToolPage.classList.add('hidden');
});
enrichmentBackBtn.addEventListener('click', () => {
homePage.classList.remove('hidden');
enrichmentToolPage.classList.add('hidden');
});
// File upload handling
volcanoFileUpload.addEventListener('click', () => volcanoFileInput.click());
enrichmentFileUpload.addEventListener('click', () => enrichmentFileInput.click());
// Drag and drop for file uploads
[volcanoFileUpload, enrichmentFileUpload].forEach(uploadArea => {
uploadArea.addEventListener('dragover', (e) => {
e.preventDefault();
uploadArea.classList.add('dragover');
});
uploadArea.addEventListener('dragleave', () => {
uploadArea.classList.remove('dragover');
});
uploadArea.addEventListener('drop', (e) => {
e.preventDefault();
uploadArea.classList.remove('dragover');
const fileInput = uploadArea === volcanoFileUpload ? volcanoFileInput : enrichmentFileInput;
if (e.dataTransfer.files.length) {
fileInput.files = e.dataTransfer.files;
updateFileUploadUI(uploadArea, e.dataTransfer.files[0].name);
}
});
});
volcanoFileInput.addEventListener('change', () => {
if (volcanoFileInput.files.length) {
updateFileUploadUI(volcanoFileUpload, volcanoFileInput.files[0].name);
}
});
enrichmentFileInput.addEventListener('change', () => {
if (enrichmentFileInput.files.length) {
updateFileUploadUI(enrichmentFileUpload, enrichmentFileInput.files[0].name);
}
});
function updateFileUploadUI(uploadArea, fileName) {
uploadArea.innerHTML = `
<svg class="mx-auto h-12 w-12 text-green-500" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7" />
</svg>
<h3 class="mt-2 text-sm font-medium text-gray-900">File ready</h3>
<p class="mt-1 text-sm text-gray-500">${fileName}</p>
<p class="mt-1 text-xs text-gray-500">Click to change file</p>
`;
}
// Generate Volcano Plot
generateVolcanoBtn.addEventListener('click', () => {
if (!volcanoFileInput.files.length) {
alert('Please upload a file first');
return;
}
// In a real app, you would parse the file here
// For demo purposes, we'll use mock data
const mockData = generateMockVolcanoData();
createVolcanoPlot(mockData);
});
// Run Enrichment Analysis
runEnrichmentBtn.addEventListener('click', () => {
if (!enrichmentFileInput.files.length) {
alert('Please upload a file first');
return;
}
// In a real app, you would parse the file and run enrichment
// For demo purposes, we'll use mock results
const mockResults = generateMockEnrichmentResults();
displayEnrichmentResults(mockResults);
});
// Helper functions
function generateMockVolcanoData() {
// Generate mock data for the volcano plot
const data = [];
const geneNames = ['TP53', 'BRCA1', 'EGFR', 'MYC', 'AKT1', 'PTEN', 'CDKN2A', 'RB1', 'NF1', 'APC'];
// Generate non-significant points
for (let i = 0; i < 1000; i++) {
const log2FoldChange = (Math.random() - 0.5) * 4;
const padj = Math.pow(10, -Math.random() * 5);
data.push({
symbol: i < 10 ? geneNames[i] : `Gene_${i}`,
log2FoldChange: log2FoldChange,
padj: padj
});
}
// Add significant points (more dramatic fold changes)
for (let i = 0; i < 20; i++) {
const log2FoldChange = (Math.random() > 0.5 ? 1 : -1) * (1.5 + Math.random() * 3);
const padj = Math.pow(10, -(3 + Math.random() * 4));
data.push({
symbol: `SigGene_${i}`,
log2FoldChange: log2FoldChange,
padj: padj
});
}
return data;
}
function createVolcanoPlot(data) {
const ctx = document.getElementById('volcanoPlot').getContext('2d');
const logFCCutoff = parseFloat(document.getElementById('logFCCutoff').value);
const pValueCutoff = parseFloat(document.getElementById('pValueCutoff').value);
// Prepare data for Chart.js
const plotData = {
datasets: [{
label: 'Not significant',
data: data.filter(d =>
Math.abs(d.log2FoldChange) < logFCCutoff || d.padj > pValueCutoff
).map(d => ({
x: d.log2FoldChange,
y: -Math.log10(d.padj),
symbol: d.symbol
})),
backgroundColor: 'rgba(120, 120, 120, 0.3)',
borderColor: 'rgba(120, 120, 120, 0.5)',
borderWidth: 1,
pointRadius: 3,
pointHoverRadius: 5
}, {
label: 'Up-regulated',
data: data.filter(d =>
d.log2FoldChange >= logFCCutoff && d.padj <= pValueCutoff
).map(d => ({
x: d.log2FoldChange,
y: -Math.log10(d.padj),
symbol: d.symbol
})),
backgroundColor: 'rgba(220, 50, 50, 0.8)',
borderColor: 'rgba(180, 40, 40, 1)',
borderWidth: 1,
pointRadius: 4,
pointHoverRadius: 6
}, {
label: 'Down-regulated',
data: data.filter(d =>
d.log2FoldChange <= -logFCCutoff && d.padj <= pValueCutoff
).map(d => ({
x: d.log2FoldChange,
y: -Math.log10(d.padj),
symbol: d.symbol
})),
backgroundColor: 'rgba(50, 120, 220, 0.8)',
borderColor: 'rgba(40, 90, 180, 1)',
borderWidth: 1,
pointRadius: 4,
pointHoverRadius: 6
}]
};
// Destroy previous chart if it exists
if (volcanoChart) {
volcanoChart.destroy();
}
// Create new chart
volcanoChart = new Chart(ctx, {
type: 'scatter',
data: plotData,
options: {
responsive: true,
maintainAspectRatio: false,
scales: {
x: {
title: {
display: true,
text: 'log2 Fold Change (log2FC)',
font: {
weight: 'bold'
}
},
grid: {
color: 'rgba(0, 0, 0, 0.05)'
}
},
y: {
title: {
display: true,
text: '-log10(adj. p-value)',
font: {
weight: 'bold'
}
},
grid: {
color: 'rgba(0, 0, 0, 0.05)'
}
}
},
plugins: {
tooltip: {
callbacks: {
title: function(context) {
return context[0].raw.symbol;
},
label: function(context) {
return [
`log2FC: ${context.parsed.x.toFixed(2)}`,
`adj. p-value: ${Math.pow(10, -context.parsed.y).toExponential(2)}`
];
}
}
},
legend: {
position: 'top',
}
},
onClick: (e) => {
const points = volcanoChart.getElementsAtEventForMode(
e, 'nearest', { intersect: true }, true
);
if (points.length) {
const point = points[0];
const symbol = volcanoChart.data.datasets[point.datasetIndex].data[point.index].symbol;
alert(`Selected gene: ${symbol}`);
}
}
}
});
}
function generateMockEnrichmentResults() {
const databases = [
'GO Biological Process',
'GO Molecular Function',
'GO Cellular Component',
'KEGG Pathways',
'Reactome Pathways'
];
const selectedDB = document.getElementById('databaseSelect').value;
const results = [];
for (let i = 1; i <= 10; i++) {
results.push({
term: `${selectedDB} term ${i}`,
pValue: (Math.random() * 0.04).toFixed(4),
genes: Math.floor(Math.random() * 50) + 5,
overlap: `${Math.floor(Math.random() * 15) + 1}/${Math.floor(Math.random() * 20) + 5}`
});
}
// Sort by p-value
return results.sort((a, b) => parseFloat(a.pValue) - parseFloat(b.pValue));
}
function displayEnrichmentResults(results) {
const pValueCutoff = parseFloat(document.getElementById('pValueEnrichCutoff').value);
const filteredResults = results.filter(r => parseFloat(r.pValue) <= pValueCutoff);
// Destroy previous chart if exists
if (enrichmentChart) {
enrichmentChart.destroy();
}
if (filteredResults.length === 0) {
document.getElementById('enrichmentResults').innerHTML = `
<div class="text-center text-gray-500 py-8">
<svg class="mx-auto h-12 w-12 text-gray-400" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9.172 16.172a4 4 0 015.656 0M9 10h.01M15 10h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z" />
</svg>
<p class="mt-2">No significant enrichment results found</p>
<p class="text-sm">Try adjusting the p-value cutoff</p>
</div>
`;
return;
}
let html = `
<div class="overflow-x-auto">
<table class="min-w-full divide-y divide-gray-200">
<thead class="bg-gray-100">
<tr>
<th scope="col" class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Term</th>
<th scope="col" class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">p-value</th>
<th scope="col" class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Genes</th>
<th scope="col" class="px-6 py-3 text-left text-xs font-medium text-gray-500 uppercase tracking-wider">Overlap</th>
</tr>
</thead>
<tbody class="bg-white divide-y divide-gray-200">
`;
filteredResults.forEach(result => {
const pValueColor = parseFloat(result.pValue) < 0.01 ? 'text-red-600' : 'text-yellow-600';
html += `
<tr class="hover:bg-gray-50 cursor-pointer gene-item" onclick="alert('${result.term}')">
<td class="px-6 py-4 whitespace-nowrap text-sm font-medium text-gray-900">${result.term}</td>
<td class="px-6 py-4 whitespace-nowrap text-sm ${pValueColor}">${result.pValue}</td>
<td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">${result.genes}</td>
<td class="px-6 py-4 whitespace-nowrap text-sm text-gray-500">${result.overlap}</td>
</tr>
`;
});
html += `
</tbody>
</table>
</div>
<div class="mt-4 text-sm text-gray-500">
Showing ${filteredResults.length} of ${results.length} terms (p-value ≤ ${pValueCutoff})
</div>
`;
document.getElementById('enrichmentResults').innerHTML = html;
// Create enrichment chart if we have results
if (filteredResults.length > 0) {
const ctx = document.getElementById('enrichmentChart').getContext('2d');
const labels = filteredResults.map(r => r.term);
const pValues = filteredResults.map(r => -Math.log10(parseFloat(r.pValue)));
const geneCounts = filteredResults.map(r => r.genes);
// Sort by p-value (most significant first)
const sortedIndices = [...Array(filteredResults.length).keys()]
.sort((a, b) => pValues[b] - pValues[a]);
enrichmentChart = new Chart(ctx, {
type: 'bar',
data: {
labels: sortedIndices.map(i => labels[i]),
datasets: [{
label: '-log10(p-value)',
data: sortedIndices.map(i => pValues[i]),
backgroundColor: 'rgba(75, 192, 192, 0.6)',
borderColor: 'rgba(75, 192, 192, 1)',
borderWidth: 1,
yAxisID: 'y'
}, {
label: 'Gene Count',
data: sortedIndices.map(i => geneCounts[i]),
backgroundColor: 'rgba(153, 102, 255, 0.6)',
borderColor: 'rgba(153, 102, 255, 1)',
borderWidth: 1,
type: 'line',
yAxisID: 'y1'
}]
},
options: {
responsive: true,
plugins: {
title: {
display: true,
text: 'Enrichment Results',
font: {
size: 16
}
},
tooltip: {
callbacks: {
label: function(context) {
let label = context.dataset.label || '';
if (label) {
label += ': ';
}
if (context.datasetIndex === 0) {
label += context.raw.toFixed(2);
} else {
label += context.raw;
}
return label;
}
}
}
},
scales: {
y: {
type: 'linear',
display: true,
position: 'left',
title: {
display: true,
text: '-log10(p-value)'
}
},
y1: {
type: 'linear',
display: true,
position: 'right',
title: {
display: true,
text: 'Gene Count'
},
grid: {
drawOnChartArea: false
}
}
}
}
});
}
}
</script>
<p style="border-radius: 8px; text-align: center; font-size: 12px; color: #fff; margin-top: 16px;position: fixed; left: 8px; bottom: 8px; z-index: 10; background: rgba(0, 0, 0, 0.8); padding: 4px 8px;">Made with <img src="https://enzostvs-deepsite.hf.space/logo.svg" alt="DeepSite Logo" style="width: 16px; height: 16px; vertical-align: middle;display:inline-block;margin-right:3px;filter:brightness(0) invert(1);"><a href="https://enzostvs-deepsite.hf.space" style="color: #fff;text-decoration: underline;" target="_blank" >DeepSite</a> - 🧬 <a href="https://enzostvs-deepsite.hf.space?remix=Dobator/bioinformatics" style="color: #fff;text-decoration: underline;" target="_blank" >Remix</a></p></body>
</html> |