新增.hintrc配置文件，更新多个h5ad文件的大小和哈希值，修改FakeEmbryo.py中的细胞层参数，调整前端页面中细胞位置和大小的计算，优化TemporalAnalysis.tsx中的数据连接逻辑以确保细胞类型流动的平衡性。
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.hintrc
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8
.hintrc
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{
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"extends": [
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"development"
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],
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"hints": {
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"no-inline-styles": "off"
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}
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}
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BIN
embryo-backend/Data/CS7.5.h5ad
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embryo-backend/Data/CS7.5.h5ad
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embryo-backend/Data/CS7.h5ad
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embryo-backend/Data/CS7.h5ad
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embryo-backend/Data/CS8.h5ad
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embryo-backend/Data/CS8.h5ad
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embryo-backend/Data/CS9.h5ad
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embryo-backend/Data/CS9.h5ad
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@ -6,12 +6,12 @@ import os
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np.random.seed(42)
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# 参数配置
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stages = [("CS7", 500), ("CS8", 1000), ("CS9", 1500)]
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stages = [("CS7", 500), ("CS7.5", 750), ("CS8", 1000), ("CS9", 1500)]
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genes = ["SOX2", "NANOG", "T", "POU5F1", "OTX2", "ZIC2", "FOXA2", "LEFTY1"]
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layers = {
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"Ectoderm": 1.0, # 外层
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"Mesoderm": 0.85, # 中层
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"Endoderm": 0.7, # 内层
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"Ectoderm": 0.1, # 外层
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"Mesoderm": 0.085, # 中层
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"Endoderm": 0.07, # 内层
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}
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notochord_ratio = 0.05 # 脊索/原条占总细胞数的比例
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@ -21,17 +21,23 @@ script_path = os.path.dirname(os.path.realpath(__file__))
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for stage, total_cells in stages:
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n_noto = int(total_cells * notochord_ratio)
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n_layer = total_cells - n_noto
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n_per_layer = n_layer // len(layers)
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num_layers = len(layers)
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# 使用 Dirichlet 生成随机且不相等的概率，再用多项分布采样；若计数仍相等则重采样
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for _ in range(100):
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probs = np.random.dirichlet(np.ones(num_layers))
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n_per_layer = np.random.multinomial(n_layer, probs)
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if len(set(n_per_layer)) == num_layers:
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break
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positions = []
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cell_types = []
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ids = []
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# 椭球比例参数
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a, b, c = 10, 8, 5
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a, b, c = 1, 0.8, 0.5
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for i, (layer_name, scale) in enumerate(layers.items()):
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N = n_per_layer
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N = n_per_layer[i]
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phi = np.random.uniform(0, np.pi, N)
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theta = np.random.uniform(0, 2*np.pi, N)
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r = scale # 层的半径比例
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@ -46,9 +52,9 @@ for stage, total_cells in stages:
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ids.append(f"{stage}_{layer_name}_{len(ids)}")
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# 添加脊索/原条样结构（Z轴中间偏下的细胞）
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x = np.random.normal(0, 0.5, n_noto)
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y = np.random.normal(0, 0.5, n_noto)
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z = np.linspace(-3, 3, n_noto)
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x = np.random.normal(0, 0.01, n_noto)
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y = np.random.normal(0, 0.01, n_noto)
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z = np.linspace(-0.1, 0.1, n_noto)
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for xi, yi, zi in zip(x, y, z):
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positions.append([xi, yi, zi])
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@ -258,10 +258,10 @@ const UnifiedEmbryoAnimation: React.FC<UnifiedEmbryoAnimationProps> = ({ cs7Data
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// 计算所有点的包围盒，自动居中和缩放
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let allPositions: number[] = [];
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cs7Data.forEach(p => { allPositions.push(p.x - 40, p.y, p.z); });
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cs8Data.forEach(p => { allPositions.push(p.x + 40, p.y, p.z); });
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cs7Data.forEach(p => { allPositions.push(p.x - 0.5, p.y, p.z); });
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cs8Data.forEach(p => { allPositions.push(p.x + 0.5,p.y, p.z); });
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cs75Data.forEach((p, i) => {
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const fromX = i % 2 === 0 ? p.x - 40 : p.x + 40;
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const fromX = i % 2 === 0 ? p.x - 0.5 : p.x + 0.5;
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allPositions.push(fromX, p.y, p.z);
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allPositions.push(p.x, p.y, p.z);
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});
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@ -285,7 +285,7 @@ const UnifiedEmbryoAnimation: React.FC<UnifiedEmbryoAnimationProps> = ({ cs7Data
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const positions: number[] = [];
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const colors: number[] = [];
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cs7Data.forEach((p) => {
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positions.push(p.x - 40, p.y, p.z);
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positions.push(p.x - 0.5, p.y, p.z);
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const c = colorMap.get(p.value as string) || new THREE.Color('#CCCCCC');
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colors.push(c.r, c.g, c.b);
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});
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@ -293,7 +293,7 @@ const UnifiedEmbryoAnimation: React.FC<UnifiedEmbryoAnimationProps> = ({ cs7Data
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geometry.setAttribute("color", new THREE.Float32BufferAttribute(colors, 3));
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const material = new THREE.PointsMaterial({
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vertexColors: true,
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size: 0.8,
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size: 0.4,
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sizeAttenuation: true,
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transparent: true,
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alphaTest: 0.5,
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@ -327,7 +327,7 @@ const UnifiedEmbryoAnimation: React.FC<UnifiedEmbryoAnimationProps> = ({ cs7Data
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const positions: number[] = [];
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const colors: number[] = [];
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cs8Data.forEach((p) => {
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positions.push(p.x + 40, p.y, p.z);
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positions.push(p.x + 0.5, p.y, p.z);
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const c = colorMap.get(p.value as string) || new THREE.Color('#CCCCCC');
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colors.push(c.r, c.g, c.b);
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});
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@ -335,7 +335,7 @@ const UnifiedEmbryoAnimation: React.FC<UnifiedEmbryoAnimationProps> = ({ cs7Data
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geometry.setAttribute("color", new THREE.Float32BufferAttribute(colors, 3));
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const material = new THREE.PointsMaterial({
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vertexColors: true,
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size: 0.8,
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size: 0.4,
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sizeAttenuation: true,
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transparent: true,
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alphaTest: 0.5,
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@ -408,7 +408,7 @@ const UnifiedEmbryoAnimation: React.FC<UnifiedEmbryoAnimationProps> = ({ cs7Data
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const sourcePoint = cs7PointsOfType.length > 0
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? cs7PointsOfType[sourceIndex]
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: cs7Data[i % cs7Data.length];
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fromX = sourcePoint.x - 40;
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fromX = sourcePoint.x - 0.5;
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fromY = sourcePoint.y;
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fromZ = sourcePoint.z;
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} else {
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@ -418,7 +418,7 @@ const UnifiedEmbryoAnimation: React.FC<UnifiedEmbryoAnimationProps> = ({ cs7Data
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const sourcePoint = cs8PointsOfType.length > 0
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? cs8PointsOfType[sourceIndex]
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: cs8Data[i % cs8Data.length];
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fromX = sourcePoint.x + 40;
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fromX = sourcePoint.x + 0.5;
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fromY = sourcePoint.y;
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fromZ = sourcePoint.z;
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}
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@ -466,7 +466,7 @@ const UnifiedEmbryoAnimation: React.FC<UnifiedEmbryoAnimationProps> = ({ cs7Data
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vAlpha = alpha;
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vColor = color;
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gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0);
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gl_PointSize = 10.0;
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gl_PointSize = 5.0;
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}
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`;
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@ -184,39 +184,79 @@ const TemporalAnalysis: React.FC = () => {
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}
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});
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// 构建连接
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const links: any[] = [];
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cellTypeArray.forEach(cellType => {
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const color = colorMap.get(cellType) || '#CCCCCC';
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// 构建连接：使用最小百分比作为同类连线，并将剩余部分匹配到有缺口的目标细胞类型，保证各阶段总量守恒
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const buildBalancedLinks = (
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sourceCounts: Record<string, number>,
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sourceTotal: number,
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targetCounts: Record<string, number>,
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targetTotal: number,
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sourceStage: string,
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targetStage: string
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) => {
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const types = Array.from(
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new Set([
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...Object.keys(sourceCounts),
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...Object.keys(targetCounts)
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])
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);
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// CS7 -> CS8 连接
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if (countsCS7[cellType] && countsCS8[cellType]) {
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const cs7Percentage = (countsCS7[cellType] / totalCS7) * 100;
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const cs8Percentage = (countsCS8[cellType] / totalCS8) * 100;
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const avgPercentage = (cs7Percentage + cs8Percentage) / 2;
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const sourcePct: Record<string, number> = {};
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const targetPct: Record<string, number> = {};
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types.forEach((t) => {
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sourcePct[t] = ((sourceCounts[t] || 0) / sourceTotal) * 100;
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targetPct[t] = ((targetCounts[t] || 0) / targetTotal) * 100;
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});
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links.push({
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source: `CS7_${cellType}`,
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target: `CS8_${cellType}`,
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value: Math.max(avgPercentage, 0.1), // 确保有最小值以显示连接
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color: color + '80' // 添加透明度
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const flows: any[] = [];
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// 同类对齐：取最小值
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const sourceResidual: Record<string, number> = {};
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const targetResidual: Record<string, number> = {};
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types.forEach((t) => {
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const direct = Math.min(sourcePct[t], targetPct[t]);
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if (direct > 0) {
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const color = (colorMap.get(t) || '#CCCCCC') + '80';
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flows.push({
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source: `${sourceStage}_${t}`,
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target: `${targetStage}_${t}`,
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value: direct,
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color
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});
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}
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// CS8 -> CS9 连接
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if (countsCS8[cellType] && countsCS9[cellType]) {
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const cs8Percentage = (countsCS8[cellType] / totalCS8) * 100;
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const cs9Percentage = (countsCS9[cellType] / totalCS9) * 100;
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const avgPercentage = (cs8Percentage + cs9Percentage) / 2;
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links.push({
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source: `CS8_${cellType}`,
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target: `CS9_${cellType}`,
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value: Math.max(avgPercentage, 0.1), // 确保有最小值以显示连接
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color: color + '80' // 添加透明度
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sourceResidual[t] = sourcePct[t] - direct; // >= 0
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targetResidual[t] = targetPct[t] - direct; // >= 0
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});
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// 将源阶段的剩余按目标阶段的缺口比例分配
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types.forEach((sType) => {
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let remaining = sourceResidual[sType];
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if (remaining <= 0) return;
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// 计算当前目标缺口总和
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let totalDeficit = types.reduce((sum, t) => sum + Math.max(targetResidual[t], 0), 0);
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if (totalDeficit <= 0) return;
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types.forEach((dType) => {
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if (targetResidual[dType] <= 0) return;
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const share = (remaining * targetResidual[dType]) / totalDeficit;
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if (share > 1e-6) {
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const color = (colorMap.get(sType) || '#CCCCCC') + '80';
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flows.push({
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source: `${sourceStage}_${sType}`,
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target: `${targetStage}_${dType}`,
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value: share,
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color
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});
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targetResidual[dType] -= share;
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}
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});
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});
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return flows;
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};
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const links: any[] = [
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...buildBalancedLinks(countsCS7, totalCS7, countsCS8, totalCS8, 'CS7', 'CS8'),
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...buildBalancedLinks(countsCS8, totalCS8, countsCS9, totalCS9, 'CS8', 'CS9')
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];
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setSankeyData({ nodes, links });
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} catch (error) {
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@ -6,6 +6,7 @@
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"module": "ESNext",
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"lib": ["ES2022", "DOM", "DOM.Iterable"],
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"skipLibCheck": true,
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"forceConsistentCasingInFileNames": true,
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/* Bundler mode */
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"moduleResolution": "bundler",
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