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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Interactive Cell Type Visualization</title>
<style>
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</style>
</head>
<body><article>
<h1>Cell type abundance for niche analysis</h1>
<p class="subtitle">Nikolay Markov, May 2025</p>
<p>
In spatial transcriptomics we can discover spatial niches and quantify the contribution of
different cell types to these niches. How exactly to perform statistical testing of these
contributions between two groups of samples is an open question. Here is an interactive
exploration of the data and the two simple statistical tests that can be used for this
comparison.
</p>
<p>
Drag the bars to change the cell counts and proportions of cell types. The boxplots
will update automatically, and the results of Mann-Whitney U test will be shown below.
</p>
<div class="container">
<div class="chart-container">
<h2>Cell numbers per sample</h2>
<p>
Drag the bars to change cell counts in samples.
</p>
<div class="bar-chart" id="cellCountChart" style="height: 250px;">
<div class="sample-group" style="height: 200px;">
<!-- Group 1 cell count bars -->
<div class="sample">
<div class="cell-count-bar" id="cellCount-0" style="height: 150px;"></div>
<div>S1</div>
</div>
<div class="sample">
<div class="cell-count-bar" id="cellCount-1" style="height: 180px;"></div>
<div>S2</div>
</div>
<div class="sample">
<div class="cell-count-bar" id="cellCount-2" style="height: 120px;"></div>
<div>S3</div>
</div>
<div class="sample">
<div class="cell-count-bar" id="cellCount-3" style="height: 200px;"></div>
<div>S4</div>
</div>
<div class="sample">
<div class="cell-count-bar" id="cellCount-4" style="height: 160px;"></div>
<div>S5</div>
</div>
<div class="sample">
<div class="cell-count-bar" id="cellCount-5" style="height: 140px;"></div>
<div>S6</div>
</div>
</div>
<div class="group-separator"></div>
<div class="sample-group" style="height: 200px;">
<!-- Group 2 cell count bars -->
<div class="sample">
<div class="cell-count-bar" id="cellCount-6" style="height: 170px;"></div>
<div>S7</div>
</div>
<div class="sample">
<div class="cell-count-bar" id="cellCount-7" style="height: 190px;"></div>
<div>S8</div>
</div>
<div class="sample">
<div class="cell-count-bar" id="cellCount-8" style="height: 130px;"></div>
<div>S9</div>
</div>
<div class="sample">
<div class="cell-count-bar" id="cellCount-9" style="height: 155px;"></div>
<div>S10</div>
</div>
</div>
</div>
<h2>Cell type proportions</h2>
<p>
Drag the dividers to change the proportions of cell types in each sample.
</p>
<div class="bar-chart" id="proportionChart" style="height: 250px;">
<div class="sample-group">
<!-- Group 1 stacked bars -->
<div class="sample">
<div class="proportion-bar" id="proportion-0">
<div class="cell-type cell-type-0" style="height: 25%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 30%; top: 25%;"></div>
<div class="cell-type cell-type-2" style="height: 20%; top: 55%;"></div>
<div class="cell-type cell-type-3" style="height: 25%; top: 75%;"></div>
<div class="handle" style="top: 25%;"></div>
<div class="handle" style="top: 55%;"></div>
<div class="handle" style="top: 75%;"></div>
</div>
<div>S1</div>
</div>
<div class="sample">
<div class="proportion-bar" id="proportion-1">
<div class="cell-type cell-type-0" style="height: 20%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 35%; top: 20%;"></div>
<div class="cell-type cell-type-2" style="height: 25%; top: 55%;"></div>
<div class="cell-type cell-type-3" style="height: 20%; top: 80%;"></div>
<div class="handle" style="top: 20%;"></div>
<div class="handle" style="top: 55%;"></div>
<div class="handle" style="top: 80%;"></div>
</div>
<div>S2</div>
</div>
<div class="sample">
<div class="proportion-bar" id="proportion-2">
<div class="cell-type cell-type-0" style="height: 30%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 25%; top: 30%;"></div>
<div class="cell-type cell-type-2" style="height: 15%; top: 55%;"></div>
<div class="cell-type cell-type-3" style="height: 30%; top: 70%;"></div>
<div class="handle" style="top: 30%;"></div>
<div class="handle" style="top: 55%;"></div>
<div class="handle" style="top: 70%;"></div>
</div>
<div>S3</div>
</div>
<div class="sample">
<div class="proportion-bar" id="proportion-3">
<div class="cell-type cell-type-0" style="height: 15%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 30%; top: 15%;"></div>
<div class="cell-type cell-type-2" style="height: 35%; top: 45%;"></div>
<div class="cell-type cell-type-3" style="height: 20%; top: 80%;"></div>
<div class="handle" style="top: 15%;"></div>
<div class="handle" style="top: 45%;"></div>
<div class="handle" style="top: 80%;"></div>
</div>
<div>S4</div>
</div>
<div class="sample">
<div class="proportion-bar" id="proportion-4">
<div class="cell-type cell-type-0" style="height: 10%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 25%; top: 10%;"></div>
<div class="cell-type cell-type-2" style="height: 40%; top: 35%;"></div>
<div class="cell-type cell-type-3" style="height: 25%; top: 75%;"></div>
<div class="handle" style="top: 10%;"></div>
<div class="handle" style="top: 35%;"></div>
<div class="handle" style="top: 75%;"></div>
</div>
<div>S5</div>
</div>
<div class="sample">
<div class="proportion-bar" id="proportion-5">
<div class="cell-type cell-type-0" style="height: 35%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 20%; top: 35%;"></div>
<div class="cell-type cell-type-2" style="height: 15%; top: 55%;"></div>
<div class="cell-type cell-type-3" style="height: 30%; top: 70%;"></div>
<div class="handle" style="top: 35%;"></div>
<div class="handle" style="top: 55%;"></div>
<div class="handle" style="top: 70%;"></div>
</div>
<div>S6</div>
</div>
</div>
<div class="group-separator"></div>
<div class="sample-group">
<!-- Group 2 stacked bars -->
<div class="sample">
<div class="proportion-bar" id="proportion-6">
<div class="cell-type cell-type-0" style="height: 40%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 20%; top: 40%;"></div>
<div class="cell-type cell-type-2" style="height: 10%; top: 60%;"></div>
<div class="cell-type cell-type-3" style="height: 30%; top: 70%;"></div>
<div class="handle" style="top: 40%;"></div>
<div class="handle" style="top: 60%;"></div>
<div class="handle" style="top: 70%;"></div>
</div>
<div>S7</div>
</div>
<div class="sample">
<div class="proportion-bar" id="proportion-7">
<div class="cell-type cell-type-0" style="height: 45%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 15%; top: 45%;"></div>
<div class="cell-type cell-type-2" style="height: 20%; top: 60%;"></div>
<div class="cell-type cell-type-3" style="height: 20%; top: 80%;"></div>
<div class="handle" style="top: 45%;"></div>
<div class="handle" style="top: 60%;"></div>
<div class="handle" style="top: 80%;"></div>
</div>
<div>S8</div>
</div>
<div class="sample">
<div class="proportion-bar" id="proportion-8">
<div class="cell-type cell-type-0" style="height: 35%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 25%; top: 35%;"></div>
<div class="cell-type cell-type-2" style="height: 15%; top: 60%;"></div>
<div class="cell-type cell-type-3" style="height: 25%; top: 75%;"></div>
<div class="handle" style="top: 35%;"></div>
<div class="handle" style="top: 60%;"></div>
<div class="handle" style="top: 75%;"></div>
</div>
<div>S9</div>
</div>
<div class="sample">
<div class="proportion-bar" id="proportion-9">
<div class="cell-type cell-type-0" style="height: 30%; top: 0%;"></div>
<div class="cell-type cell-type-1" style="height: 30%; top: 30%;"></div>
<div class="cell-type cell-type-2" style="height: 20%; top: 60%;"></div>
<div class="cell-type cell-type-3" style="height: 20%; top: 80%;"></div>
<div class="handle" style="top: 30%;"></div>
<div class="handle" style="top: 60%;"></div>
<div class="handle" style="top: 80%;"></div>
</div>
<div>S10</div>
</div>
</div>
</div>
<div class="legend">
<div class="legend-item">
<div class="legend-color cell-type-0"></div>
<div>Cell Type A</div>
</div>
<div class="legend-item">
<div class="legend-color cell-type-1"></div>
<div>Cell Type B</div>
</div>
<div class="legend-item">
<div class="legend-color cell-type-2"></div>
<div>Cell Type C</div>
</div>
<div class="legend-item">
<div class="legend-color cell-type-3"></div>
<div>Cell Type D</div>
</div>
</div>
</div>
<div class="stats-container">
<h2>Cell type proportions within sample</h2>
<div class="boxplot-container" id="group-boxplots">
<!-- Boxplots will be generated here -->
</div>
<h2>Cell type proportions of total number of cells</h2>
<div class="boxplot-container" id="overall-boxplots">
<!-- Boxplots will be generated here -->
</div>
</div>
</div></article>
<script>
// Initial data
const samples = 10;
const cellTypes = 4;
const group1Size = 6;
const group2Size = 4;
// Cell count data (adjustable)
let cellCounts = [150, 180, 120, 200, 160, 140, 170, 190, 130, 155];
const minCellCount = 10;
const maxCellCount = 1000;
const cellCountBarHeight = 200; // Fixed height for the bar chart container
// Store data point positions for all box plots
const dataPointPositions = {
group: {}, // Will store left positions for each group and cell type
overall: {}
};
// Cell proportion data
let proportions = [
[0.25, 0.30, 0.20, 0.25], // Sample 1
[0.20, 0.35, 0.25, 0.20], // Sample 2
[0.30, 0.25, 0.15, 0.30], // Sample 3
[0.15, 0.30, 0.35, 0.20], // Sample 4
[0.10, 0.25, 0.40, 0.25], // Sample 5
[0.35, 0.20, 0.15, 0.30], // Sample 6
[0.40, 0.20, 0.10, 0.30], // Sample 7
[0.45, 0.15, 0.20, 0.20], // Sample 8
[0.35, 0.25, 0.15, 0.25], // Sample 9
[0.30, 0.30, 0.20, 0.20] // Sample 10
]; // Function to update all cell count bar heights based on current cellCounts array
function updateCellCountBars() {
// Find the maximum cell count
const currentMaxCount = Math.max(...cellCounts);
// Scale factor to convert counts to pixel heights (max height = cellCountBarHeight)
const scaleFactor = cellCountBarHeight / currentMaxCount;
// Update all bars
for (let i = 0; i < samples; i++) {
const bar = document.getElementById(`cellCount-${i}`);
const scaledHeight = Math.round(cellCounts[i] * scaleFactor);
bar.style.height = scaledHeight + 'px';
// Update the count display text
const cellCountNode = bar.parentNode.querySelector('.cell-number');
if (cellCountNode) {
cellCountNode.innerText = cellCounts[i];
}
}
// Make sure both groups have the same container height
document.querySelectorAll('.sample-group').forEach(group => {
group.style.height = cellCountBarHeight + 'px';
});
}
// Function to make cell count bars draggable
function setupCellCountDrag() {
// Add mousedown event to prevent text selection during dragging
document.addEventListener('mousedown', function(e) {
if (e.target.classList.contains('cell-count-bar') ||
e.target.classList.contains('handle')) {
e.preventDefault();
document.body.style.userSelect = 'none';
}
});
// Add mouseup event to restore text selection
document.addEventListener('mouseup', function() {
document.body.style.userSelect = '';
});
// Create tooltips container
const tooltipContainer = document.createElement('div');
tooltipContainer.id = 'tooltips-container';
document.body.appendChild(tooltipContainer);
for (let i = 0; i < samples; i++) {
const bar = document.getElementById(`cellCount-${i}`);
const cellCountNode = document.createElement('div');
cellCountNode.className = 'cell-number';
cellCountNode.innerText = cellCounts[i];
bar.parentNode.insertBefore(cellCountNode, bar);
// Create tooltip elements for this bar
const groupTooltip = document.createElement('div');
groupTooltip.className = 'data-tooltip';
groupTooltip.id = `group-tooltip-${i}`;
tooltipContainer.appendChild(groupTooltip);
const overallTooltip = document.createElement('div');
overallTooltip.className = 'data-tooltip';
overallTooltip.id = `overall-tooltip-${i}`;
tooltipContainer.appendChild(overallTooltip);
// Add hover events for highlighting
bar.addEventListener('mouseenter', function() {
highlightSample(i, true);
});
bar.addEventListener('mouseleave', function() {
highlightSample(i, false);
});
bar.addEventListener('mousedown', function(e) {
const startY = e.clientY;
const startHeight = parseInt(bar.style.height);
const startCount = cellCounts[i];
// Find the current maximum cell count for scaling
const currentMaxCount = Math.max(...cellCounts);
const heightToCountRatio = currentMaxCount / cellCountBarHeight;
function onMouseMove(e) {
// Calculate new height based on mouse movement
const heightDelta = startY - e.clientY;
const countDelta = Math.round(heightDelta * heightToCountRatio);
// Calculate new cell count and constrain to min/max
const newCount = Math.max(minCellCount, Math.min(maxCellCount, startCount + countDelta));
// Update the cell count
cellCounts[i] = newCount;
cellCountNode.innerText = newCount;
// Update all bars to maintain proper scaling
updateCellCountBars();
// Update stats
updateStats();
// Keep highlight during drag
highlightSample(i, true);
}
function onMouseUp(e) {
document.removeEventListener('mousemove', onMouseMove);
document.removeEventListener('mouseup', onMouseUp);
// Check if mouse is still over the bar after dragging ends
const barRect = bar.getBoundingClientRect();
const isOverBar = (
e.clientX >= barRect.left &&
e.clientX <= barRect.right &&
e.clientY >= barRect.top &&
e.clientY <= barRect.bottom
);
// Only keep highlighting if mouse is still over the bar
if (!isOverBar) {
highlightSample(i, false);
}
}
document.addEventListener('mousemove', onMouseMove);
document.addEventListener('mouseup', onMouseUp);
});
}
}
// Function to highlight a sample and its corresponding data points
function highlightSample(sampleIndex, highlight) {
// Highlight the cell count bar
const bar = document.getElementById(`cellCount-${sampleIndex}`);
if (highlight) {
bar.classList.add('highlight');
} else {
bar.classList.remove('highlight');
}
// Highlight Cell Type A in the proportion bar
const proportionBar = document.getElementById(`proportion-${sampleIndex}`);
if (proportionBar) {
const cellTypeA = proportionBar.querySelector('.cell-type-0');
if (cellTypeA) {
if (highlight) {
cellTypeA.classList.add('highlight');
} else {
cellTypeA.classList.remove('highlight');
}
}
}
// Highlight corresponding data points in boxplots and show tooltips
const dataPoints = document.querySelectorAll(`.data-point[data-sample-index="${sampleIndex}"]`);
dataPoints.forEach(point => {
if (highlight) {
point.classList.add('highlight');
// Get container info to determine if it's a group or overall boxplot
const boxplotArea = point.closest('.boxplot');
const isGroupBoxplot = boxplotArea && boxplotArea.closest('#group-boxplots');
// Show tooltip with value
const tooltipId = isGroupBoxplot ?
`group-tooltip-${sampleIndex}` :
`overall-tooltip-${sampleIndex}`;
const tooltip = document.getElementById(tooltipId);
if (tooltip) {
const isGroupA = sampleIndex < group1Size ? "Group 1" : "Group 2";
const sampleNumber = isGroupA == "Group 1" ? sampleIndex + 1 : sampleIndex - group1Size + 1;
// Show cell count and proportion information
const cellCount = cellCounts[sampleIndex];
const cellTypeProportion = proportions[sampleIndex][0]; // Cell Type A proportion
const cellTypeCount = Math.round(cellCount * cellTypeProportion);
tooltip.innerHTML = `
value: ${point.dataset.value}
`;
tooltip.style.visibility = 'visible';
// Position tooltip near the data point
const pointRect = point.getBoundingClientRect();
tooltip.style.left = (pointRect.left + pointRect.width/2) + 'px';
tooltip.style.top = (pointRect.top) + 'px';
}
} else {
point.classList.remove('highlight');
// Hide tooltips
document.getElementById(`group-tooltip-${sampleIndex}`).style.visibility = 'hidden';
document.getElementById(`overall-tooltip-${sampleIndex}`).style.visibility = 'hidden';
}
});
}
// Function to make proportion handles draggable
function setupProportionDrag() {
for (let i = 0; i < samples; i++) {
const bar = document.getElementById(`proportion-${i}`);
const handles = bar.querySelectorAll('.handle');
const cellTypeDivs = bar.querySelectorAll('.cell-type');
// Add hover events for cell type A (first cell type)
const cellTypeA = cellTypeDivs[0];
cellTypeA.addEventListener('mouseenter', function() {
// Highlight cell type div
cellTypeA.classList.add('highlight');
// Highlight sample in boxplots
highlightSample(i, true);
});
cellTypeA.addEventListener('mouseleave', function() {
// Remove highlight from cell type div
cellTypeA.classList.remove('highlight');
// Remove highlight from boxplots
highlightSample(i, false);
});
handles.forEach((handle, handleIndex) => {
handle.addEventListener('mousedown', function(e) {
e.preventDefault();
const startY = e.clientY;
const startTop = parseInt(handle.style.top);
const barRect = bar.getBoundingClientRect();
const barHeight = barRect.height;
function onMouseMove(e) {
const delta = e.clientY - startY;
let newTop = Math.max(0, Math.min(100, startTop + delta / barHeight * 100));
// Ensure handles don't cross each other
if (handleIndex > 0) {
const prevHandle = handles[handleIndex - 1];
const prevTop = parseFloat(prevHandle.style.top);
newTop = Math.max(newTop, prevTop);
}
if (handleIndex < handles.length - 1) {
const nextHandle = handles[handleIndex + 1];
const nextTop = parseFloat(nextHandle.style.top);
newTop = Math.min(newTop, nextTop);
}
handle.style.top = newTop + '%';
// Update the cell type divs
updateCellTypeHeights(i);
// Update proportions data
updateProportionData(i);
// Update stats
updateStats();
}
function onMouseUp() {
document.removeEventListener('mousemove', onMouseMove);
document.removeEventListener('mouseup', onMouseUp);
}
document.addEventListener('mousemove', onMouseMove);
document.addEventListener('mouseup', onMouseUp);
});
});
}
}
// Update cell type heights based on handle positions
function updateCellTypeHeights(sampleIndex) {
const bar = document.getElementById(`proportion-${sampleIndex}`);
const handles = Array.from(bar.querySelectorAll('.handle'));
const cellTypeDivs = bar.querySelectorAll('.cell-type');
// Get handle positions
const positions = [0, ...handles.map(h => parseFloat(h.style.top)), 100];
// Update cell type divs
for (let i = 0; i < cellTypes; i++) {
const height = positions[i + 1] - positions[i];
const top = positions[i];
cellTypeDivs[i].style.height = height + '%';
cellTypeDivs[i].style.top = top + '%';
}
}
// Update proportion data based on visual elements
function updateProportionData(sampleIndex) {
const bar = document.getElementById(`proportion-${sampleIndex}`);
const handles = Array.from(bar.querySelectorAll('.handle'));
// Get handle positions
const positions = [0, ...handles.map(h => parseFloat(h.style.top)), 100];
// Update proportions array
for (let i = 0; i < cellTypes; i++) {
proportions[sampleIndex][i] = (positions[i + 1] - positions[i]) / 100;
}
}
// Function to calculate Mann-Whitney U test
function mannWhitneyUTest(group1, group2) {
const combined = [];
// Create combined array with values and group info
for (let i = 0; i < group1.length; i++) {
combined.push({ value: group1[i], group: 1 });
}
for (let i = 0; i < group2.length; i++) {
combined.push({ value: group2[i], group: 2 });
}
// Sort by value
combined.sort((a, b) => a.value - b.value);