664 lines
25 KiB
TypeScript
664 lines
25 KiB
TypeScript
import React, { useState, useEffect } from "react";
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import axios from "axios";
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import { ResponsiveSankey } from "@nivo/sankey";
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import { ResponsiveLine } from "@nivo/line";
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import PointCloud from "../components/PointCloud";
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import "../style.css";
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const TemporalAnalysis: React.FC = () => {
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const [cellDataCS7, setCellDataCS7] = useState<any[]>([]);
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const [cellDataCS8, setCellDataCS8] = useState<any[]>([]);
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const [cellDataCS9, setCellDataCS9] = useState<any[]>([]);
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const [loadingCS7, setLoadingCS7] = useState(false);
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const [loadingCS8, setLoadingCS8] = useState(false);
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const [loadingCS9, setLoadingCS9] = useState(false);
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const [errorCS7, setErrorCS7] = useState("");
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const [errorCS8, setErrorCS8] = useState("");
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const [errorCS9, setErrorCS9] = useState("");
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const [sankeyData, setSankeyData] = useState<any>({ nodes: [], links: [] });
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const [sankeyLoading, setSankeyLoading] = useState(false);
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// 第三部分：基因时序分析相关状态
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const [availableGenes, setAvailableGenes] = useState<string[]>([]);
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const [selectedGene, setSelectedGene] = useState("");
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const [temporalData, setTemporalData] = useState<any[]>([]);
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const [temporalLoading, setTemporalLoading] = useState(false);
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const [temporalError, setTemporalError] = useState("");
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// 生成细胞类型颜色映射
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const generateCellTypeColors = (cellTypes: string[]) => {
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const colorMap = new Map<string, string>();
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const colors = [
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'#FF6B6B', '#4ECDC4', '#45B7D1', '#96CEB4', '#FFEAA7',
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'#DDA0DD', '#98D8C8', '#F7DC6F', '#BB8FCE', '#85C1E9',
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'#F8C471', '#82E0AA', '#F1948A', '#85CDCE', '#D7BDE2',
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'#A9DFBF', '#F9E79F', '#D5A6BD', '#AED6F1', '#E8DAEF'
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];
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cellTypes.forEach((type, index) => {
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colorMap.set(type, colors[index % colors.length]);
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});
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return colorMap;
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};
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// 获取可用基因列表（从CS7阶段获取）
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useEffect(() => {
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axios
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.get("http://localhost:5000/api/genes", {
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params: { stage: "CS7" },
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})
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.then((res) => setAvailableGenes(res.data))
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.catch(() => setAvailableGenes([]));
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}, []);
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// 获取基因时序分析数据
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const fetchTemporalAnalysis = async (gene: string) => {
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if (!gene) return;
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setTemporalLoading(true);
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setTemporalError("");
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setTemporalData([]);
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try {
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const response = await axios.get("http://localhost:5000/api/gene_temporal_analysis", {
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params: { gene: gene.trim() }
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});
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// 转换数据为线图格式
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const stagesData = response.data.stages_data;
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const allCellTypes = new Set<string>();
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// 收集所有细胞类型
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stagesData.forEach((stageData: any) => {
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Object.keys(stageData.cell_types).forEach(cellType => {
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allCellTypes.add(cellType);
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});
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});
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const cellTypesArray = Array.from(allCellTypes).sort();
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const colorMap = generateCellTypeColors(cellTypesArray);
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// 构建线图数据 - 每个细胞类型一条线
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const lineData = cellTypesArray.map(cellType => {
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const linePoints = stagesData.map((stageData: any) => {
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const cellTypeData = stageData.cell_types[cellType];
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return {
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x: stageData.stage,
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y: cellTypeData ? cellTypeData.proportion : 0
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};
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});
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return {
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id: cellType,
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color: colorMap.get(cellType) || '#CCCCCC',
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data: linePoints
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};
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});
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setTemporalData(lineData);
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console.log('Temporal analysis data:', lineData);
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} catch (err: any) {
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if (err.response && err.response.data?.error) {
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setTemporalError(err.response.data.error);
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} else {
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setTemporalError("Failed to fetch temporal analysis data.");
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}
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} finally {
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setTemporalLoading(false);
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}
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};
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// 构建桑基图数据
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const buildSankeyData = (dataCS7: any[], dataCS8: any[], dataCS9: any[]) => {
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setSankeyLoading(true);
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try {
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// 统计各阶段的细胞类型数量
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const countCellTypes = (data: any[]) => {
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const counts: { [key: string]: number } = {};
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data.forEach(cell => {
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const cellType = cell.value || 'Unknown'; // 修正：细胞类型存储在value字段中
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counts[cellType] = (counts[cellType] || 0) + 1;
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});
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return counts;
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};
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const countsCS7 = countCellTypes(dataCS7);
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const countsCS8 = countCellTypes(dataCS8);
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const countsCS9 = countCellTypes(dataCS9);
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// 调试信息
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console.log('Cell type counts CS7:', countsCS7);
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console.log('Cell type counts CS8:', countsCS8);
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console.log('Cell type counts CS9:', countsCS9);
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// 获取所有细胞类型
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const allCellTypes = new Set([
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...Object.keys(countsCS7),
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...Object.keys(countsCS8),
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...Object.keys(countsCS9)
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]);
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const cellTypeArray = Array.from(allCellTypes).sort();
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const colorMap = generateCellTypeColors(cellTypeArray);
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// 计算总数
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const totalCS7 = Object.values(countsCS7).reduce((sum, count) => sum + count, 0);
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const totalCS8 = Object.values(countsCS8).reduce((sum, count) => sum + count, 0);
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const totalCS9 = Object.values(countsCS9).reduce((sum, count) => sum + count, 0);
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// 构建节点
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const nodes: any[] = [];
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cellTypeArray.forEach(cellType => {
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const color = colorMap.get(cellType) || '#CCCCCC';
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// CS7 节点
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if (countsCS7[cellType]) {
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const percentage = ((countsCS7[cellType] / totalCS7) * 100).toFixed(1);
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nodes.push({
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id: `CS7_${cellType}`,
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nodeColor: color,
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label: `${cellType} (${percentage}%)`
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});
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}
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// CS8 节点
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if (countsCS8[cellType]) {
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const percentage = ((countsCS8[cellType] / totalCS8) * 100).toFixed(1);
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nodes.push({
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id: `CS8_${cellType}`,
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nodeColor: color,
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label: `${cellType} (${percentage}%)`
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});
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}
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// CS9 节点
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if (countsCS9[cellType]) {
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const percentage = ((countsCS9[cellType] / totalCS9) * 100).toFixed(1);
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nodes.push({
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id: `CS9_${cellType}`,
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nodeColor: color,
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label: `${cellType} (${percentage}%)`
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});
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}
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});
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// 构建连接
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const links: any[] = [];
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cellTypeArray.forEach(cellType => {
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const color = colorMap.get(cellType) || '#CCCCCC';
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// CS7 -> CS8 连接
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if (countsCS7[cellType] && countsCS8[cellType]) {
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const cs7Percentage = (countsCS7[cellType] / totalCS7) * 100;
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const cs8Percentage = (countsCS8[cellType] / totalCS8) * 100;
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const avgPercentage = (cs7Percentage + cs8Percentage) / 2;
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links.push({
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source: `CS7_${cellType}`,
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target: `CS8_${cellType}`,
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value: Math.max(avgPercentage, 0.1), // 确保有最小值以显示连接
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color: color + '80' // 添加透明度
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});
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}
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// CS8 -> CS9 连接
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if (countsCS8[cellType] && countsCS9[cellType]) {
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const cs8Percentage = (countsCS8[cellType] / totalCS8) * 100;
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const cs9Percentage = (countsCS9[cellType] / totalCS9) * 100;
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const avgPercentage = (cs8Percentage + cs9Percentage) / 2;
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links.push({
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source: `CS8_${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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});
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}
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});
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setSankeyData({ nodes, links });
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} catch (error) {
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console.error('Error building Sankey data:', error);
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setSankeyData({ nodes: [], links: [] });
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} finally {
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setSankeyLoading(false);
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}
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};
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// 获取CS7阶段细胞类型数据
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useEffect(() => {
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setLoadingCS7(true);
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setErrorCS7("");
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setCellDataCS7([]);
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axios
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.get("http://localhost:5000/api/cell", {
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params: { stage: "CS7" },
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})
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.then((res) => {
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setCellDataCS7(res.data.cells);
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})
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.catch((err) => {
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if (err.response && err.response.data?.error) {
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setErrorCS7(err.response.data.error);
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} else {
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setErrorCS7("Failed to fetch CS7 cell type data.");
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}
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})
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.finally(() => {
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setLoadingCS7(false);
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});
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}, []);
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// 获取CS8阶段细胞类型数据
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useEffect(() => {
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setLoadingCS8(true);
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setErrorCS8("");
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setCellDataCS8([]);
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axios
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.get("http://localhost:5000/api/cell", {
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params: { stage: "CS8" },
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})
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.then((res) => {
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setCellDataCS8(res.data.cells);
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})
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.catch((err) => {
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if (err.response && err.response.data?.error) {
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setErrorCS8(err.response.data.error);
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} else {
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setErrorCS8("Failed to fetch CS8 cell type data.");
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}
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})
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.finally(() => {
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setLoadingCS8(false);
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});
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}, []);
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// 获取CS9阶段细胞类型数据
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useEffect(() => {
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setLoadingCS9(true);
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setErrorCS9("");
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setCellDataCS9([]);
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axios
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.get("http://localhost:5000/api/cell", {
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params: { stage: "CS9" },
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})
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.then((res) => {
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setCellDataCS9(res.data.cells);
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})
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.catch((err) => {
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if (err.response && err.response.data?.error) {
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setErrorCS9(err.response.data.error);
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} else {
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setErrorCS9("Failed to fetch CS9 cell type data.");
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}
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})
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.finally(() => {
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setLoadingCS9(false);
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});
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}, []);
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// 当所有数据加载完成后构建桑基图数据
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useEffect(() => {
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if (cellDataCS7.length > 0 && cellDataCS8.length > 0 && cellDataCS9.length > 0) {
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buildSankeyData(cellDataCS7, cellDataCS8, cellDataCS9);
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}
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}, [cellDataCS7, cellDataCS8, cellDataCS9]);
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return (
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<div className="page-container">
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<div className="page-header">
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<h1>时间序列分析</h1>
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<p className="page-description">
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通过对比不同发育阶段的细胞类型分布，分析胚胎发育过程中细胞类型的变化和演进模式。
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</p>
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</div>
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<div className="page-content">
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{/* 第一部分：三个发育阶段的细胞类型分布 */}
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<div className="section">
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<h2>发育阶段对比</h2>
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<p className="flat-section-description">
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下方展示了CS7、CS8、CS9三个发育阶段的细胞类型3D分布图。通过对比可以观察细胞类型在发育过程中的空间分布变化。
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</p>
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<div
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className="three-column-grid visualization-grid"
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style={{
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display: "grid",
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gridTemplateColumns: "repeat(3, minmax(400px, 1fr))",
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gap: "2rem",
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minHeight: "600px",
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width: "100%",
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marginBottom: "3rem"
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}}
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>
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{/* CS7阶段细胞类型分布 */}
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<div className="visualization-container">
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<h3 style={{ marginBottom: "1rem", textAlign: "center" }}>CS7 - 早期发育阶段</h3>
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{errorCS7 && <div className="error-message">{errorCS7}</div>}
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{cellDataCS7.length > 0 ? (
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<PointCloud data={cellDataCS7} isCategorical={true} />
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) : (
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<div className="no-data-message">
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{loadingCS7 ? (
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<div>
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<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>🔄</div>
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<p>正在加载CS7数据...</p>
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</div>
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) : (
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<div>
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<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>🧬</div>
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<p>CS7阶段细胞类型分布</p>
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<p style={{ fontSize: "0.9rem", color: "var(--text-secondary)" }}>
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早期发育阶段
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</p>
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</div>
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)}
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</div>
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)}
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</div>
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{/* CS8阶段细胞类型分布 */}
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<div className="visualization-container">
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<h3 style={{ marginBottom: "1rem", textAlign: "center" }}>CS8 - 中期发育阶段</h3>
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{errorCS8 && <div className="error-message">{errorCS8}</div>}
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{cellDataCS8.length > 0 ? (
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<PointCloud data={cellDataCS8} isCategorical={true} />
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) : (
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<div className="no-data-message">
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{loadingCS8 ? (
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<div>
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<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>🔄</div>
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<p>正在加载CS8数据...</p>
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</div>
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) : (
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<div>
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<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>🧬</div>
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<p>CS8阶段细胞类型分布</p>
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<p style={{ fontSize: "0.9rem", color: "var(--text-secondary)" }}>
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中期发育阶段
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</p>
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</div>
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)}
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</div>
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)}
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</div>
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{/* CS9阶段细胞类型分布 */}
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<div className="visualization-container">
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<h3 style={{ marginBottom: "1rem", textAlign: "center" }}>CS9 - 后期发育阶段</h3>
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{errorCS9 && <div className="error-message">{errorCS9}</div>}
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{cellDataCS9.length > 0 ? (
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<PointCloud data={cellDataCS9} isCategorical={true} />
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) : (
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<div className="no-data-message">
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{loadingCS9 ? (
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<div>
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<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>🔄</div>
|
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<p>正在加载CS9数据...</p>
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</div>
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) : (
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<div>
|
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<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>🧬</div>
|
||
<p>CS9阶段细胞类型分布</p>
|
||
<p style={{ fontSize: "0.9rem", color: "var(--text-secondary)" }}>
|
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后期发育阶段
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</p>
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||
</div>
|
||
)}
|
||
</div>
|
||
)}
|
||
</div>
|
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</div>
|
||
</div>
|
||
|
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{/* 第二部分和第三部分：并排显示 */}
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<div className="section">
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<h2>流动分析与基因时序</h2>
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||
<p className="flat-section-description">
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左侧桑基图展示细胞类型在发育阶段间的流动模式，右侧线图显示选定基因在各细胞类型中的占比变化。
|
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</p>
|
||
|
||
<div
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||
style={{
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display: "grid",
|
||
gridTemplateColumns: "1fr 1fr",
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gap: "2rem",
|
||
marginBottom: "3rem"
|
||
}}
|
||
>
|
||
{/* 桑基图部分 */}
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<div className="visualization-container">
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<h3 style={{ marginBottom: "1rem", textAlign: "center" }}>细胞类型演进流动图</h3>
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||
<div style={{ width: "100%", height: "500px", position: "relative" }}>
|
||
{sankeyData.nodes.length > 0 && sankeyData.links.length > 0 ? (
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||
<>
|
||
<ResponsiveSankey
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||
data={sankeyData}
|
||
margin={{ top: 30, right: 100, bottom: 50, left: 100 }}
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||
align="justify"
|
||
colors={(node: any) => node.nodeColor}
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||
nodeOpacity={0.8}
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||
nodeHoverOpacity={1}
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||
nodeThickness={18}
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||
nodeSpacing={8}
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||
nodeBorderWidth={2}
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||
nodeBorderColor={{
|
||
from: 'color',
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||
modifiers: [['darker', 0.3]]
|
||
}}
|
||
linkOpacity={0.3}
|
||
linkHoverOpacity={0.6}
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||
linkContract={4}
|
||
enableLinkGradient={true}
|
||
labelPosition="outside"
|
||
labelOrientation="horizontal"
|
||
labelPadding={12}
|
||
labelTextColor={{
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||
from: 'color',
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||
modifiers: [['darker', 1]]
|
||
}}
|
||
legends={[]}
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||
motionConfig="gentle"
|
||
/>
|
||
{/* 发育阶段标签行 */}
|
||
<div
|
||
style={{
|
||
position: "absolute",
|
||
bottom: "15px",
|
||
left: "100px",
|
||
right: "100px",
|
||
display: "flex",
|
||
justifyContent: "space-between",
|
||
alignItems: "center",
|
||
fontSize: "13px",
|
||
fontWeight: "500",
|
||
color: "#666"
|
||
}}
|
||
>
|
||
<div style={{ textAlign: "left", flex: 1, paddingLeft: "20px" }}>
|
||
CS7 - 早期
|
||
</div>
|
||
<div style={{ textAlign: "center", flex: 1 }}>
|
||
CS8 - 中期
|
||
</div>
|
||
<div style={{ textAlign: "right", flex: 1, paddingRight: "20px" }}>
|
||
CS9 - 后期
|
||
</div>
|
||
</div>
|
||
</>
|
||
) : (
|
||
<div className="no-data-message">
|
||
{sankeyLoading || loadingCS7 || loadingCS8 || loadingCS9 ? (
|
||
<div>
|
||
<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>🔄</div>
|
||
<p>正在构建流动图...</p>
|
||
</div>
|
||
) : (
|
||
<div>
|
||
<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>📊</div>
|
||
<p>等待数据加载</p>
|
||
</div>
|
||
)}
|
||
</div>
|
||
)}
|
||
</div>
|
||
</div>
|
||
|
||
{/* 基因时序分析部分 */}
|
||
<div className="visualization-container">
|
||
<div style={{ display: "flex", justifyContent: "space-between", alignItems: "center", marginBottom: "1rem" }}>
|
||
<h3 style={{ margin: 0 }}>基因时序分析</h3>
|
||
<select
|
||
value={selectedGene}
|
||
onChange={(e) => {
|
||
setSelectedGene(e.target.value);
|
||
if (e.target.value) {
|
||
fetchTemporalAnalysis(e.target.value);
|
||
}
|
||
}}
|
||
title="选择基因进行时序分析"
|
||
style={{ padding: "0.5rem", borderRadius: "0.3rem", border: "1px solid #ccc", fontSize: "0.9rem" }}
|
||
>
|
||
<option value="">请选择基因</option>
|
||
{availableGenes.map((gene) => (
|
||
<option key={gene} value={gene}>
|
||
{gene}
|
||
</option>
|
||
))}
|
||
</select>
|
||
</div>
|
||
|
||
<div style={{ width: "100%", height: "450px" }}>
|
||
{temporalLoading ? (
|
||
<div className="no-data-message">
|
||
<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>🔄</div>
|
||
<p>正在加载时序数据...</p>
|
||
</div>
|
||
) : temporalError ? (
|
||
<div className="error-message">{temporalError}</div>
|
||
) : temporalData.length > 0 ? (
|
||
<ResponsiveLine
|
||
data={temporalData}
|
||
margin={{ top: 30, right: 70, bottom: 70, left: 70 }}
|
||
xScale={{ type: 'point' }}
|
||
yScale={{
|
||
type: 'linear',
|
||
min: 0,
|
||
max: 'auto',
|
||
stacked: false,
|
||
reverse: false
|
||
}}
|
||
yFormat=" >-.2f"
|
||
axisTop={null}
|
||
axisRight={null}
|
||
axisBottom={{
|
||
tickSize: 5,
|
||
tickPadding: 5,
|
||
tickRotation: 0,
|
||
legend: '发育阶段',
|
||
legendPosition: 'middle',
|
||
legendOffset: 40
|
||
}}
|
||
axisLeft={{
|
||
tickSize: 5,
|
||
tickPadding: 5,
|
||
tickRotation: 0,
|
||
legend: '占比 (%)',
|
||
legendPosition: 'middle',
|
||
legendOffset: -50
|
||
}}
|
||
colors={(line: any) => line.color}
|
||
pointSize={8}
|
||
pointColor={{ theme: 'background' }}
|
||
pointBorderWidth={3}
|
||
pointBorderColor={{ from: 'serieColor' }}
|
||
pointLabelYOffset={-12}
|
||
useMesh={true}
|
||
enableGridX={false}
|
||
enableGridY={true}
|
||
lineWidth={3}
|
||
legends={[
|
||
{
|
||
anchor: 'bottom-right',
|
||
direction: 'column',
|
||
justify: false,
|
||
translateX: 60,
|
||
translateY: 0,
|
||
itemsSpacing: 1,
|
||
itemWidth: 50,
|
||
itemHeight: 14,
|
||
itemDirection: 'left-to-right',
|
||
itemOpacity: 0.75,
|
||
symbolSize: 8,
|
||
symbolShape: 'circle',
|
||
effects: [
|
||
{
|
||
on: 'hover',
|
||
style: {
|
||
itemOpacity: 1
|
||
}
|
||
}
|
||
]
|
||
}
|
||
]}
|
||
/>
|
||
) : (
|
||
<div className="no-data-message">
|
||
<div style={{ fontSize: "2rem", marginBottom: "1rem" }}>📊</div>
|
||
<p>请选择基因查看时序变化</p>
|
||
</div>
|
||
)}
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div className="section">
|
||
<h2>使用说明</h2>
|
||
<div style={{ display: "grid", gridTemplateColumns: "repeat(auto-fit, minmax(300px, 1fr))", gap: "2rem", marginTop: "1.5rem" }}>
|
||
<div>
|
||
<h3>📅 时间序列对比</h3>
|
||
<p>三个3D图分别展示CS7、CS8、CS9三个发育阶段的细胞类型分布，可以直观地观察细胞类型随时间的变化。</p>
|
||
</div>
|
||
<div>
|
||
<h3>🌊 桑基图解读</h3>
|
||
<p>桑基图显示细胞类型的演进流动：节点大小表示占比，连接线显示相同细胞类型在不同阶段间的延续性，颜色保持一致便于追踪。</p>
|
||
</div>
|
||
<div>
|
||
<h3>📊 基因时序分析</h3>
|
||
<p>选择特定基因后，堆叠面积图显示该基因在各细胞类型中的占比变化，帮助理解基因在发育过程中的表达模式演进。</p>
|
||
</div>
|
||
<div>
|
||
<h3>🖱️ 交互操作</h3>
|
||
<p>在3D视图中使用鼠标拖拽旋转视角，滚轮缩放，点击数据点查看详细信息。在桑基图和堆叠图中悬停查看具体数值。</p>
|
||
</div>
|
||
<div>
|
||
<h3>🎨 颜色编码</h3>
|
||
<p>相同颜色代表相同的细胞类型，在所有图表中保持一致，便于追踪特定细胞类型的变化和流动模式。</p>
|
||
</div>
|
||
<div>
|
||
<h3>🔍 发育模式识别</h3>
|
||
<p>通过对比三个阶段和不同基因，可以识别细胞类型的出现、消失、迁移和分化模式，以及基因表达的动态变化。</p>
|
||
</div>
|
||
<div>
|
||
<h3>📈 百分比分析</h3>
|
||
<p>桑基图和堆叠图中的百分比表示各细胞类型在对应发育阶段中的相对丰度，帮助理解细胞类型组成的动态平衡。</p>
|
||
</div>
|
||
<div>
|
||
<h3>🧬 基因选择策略</h3>
|
||
<p>选择不同的发育相关基因（如SOX2、NANOG等），观察其在胚胎发育过程中的表达变化模式和细胞类型特异性。</p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
);
|
||
};
|
||
|
||
export default TemporalAnalysis;
|