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| | library(shiny) |
| | library(shinyWidgets) |
| | library(colourpicker) |
| | library(shinyjs) |
| | library(bslib) |
| |
|
| | |
| | |
| | |
| |
|
| | sci_fi_css <- tags$style(HTML(" |
| | /* 基础字体 - 添加微妙渐变背景 */ |
| | body { |
| | font-family: -apple-system, BlinkMacSystemFont, 'SF Pro Text', 'Segoe UI', Roboto, sans-serif; |
| | background: linear-gradient(135deg, #F5F5F7 0%, #EFEFF4 50%, #F5F5F7 100%); /* 🔥 添加微妙渐变 */ |
| | margin: 0; |
| | padding: 0; |
| | font-size: 14px; |
| | min-height: 100vh; /* 🔥 确保背景覆盖整个视口 */ |
| | } |
| | |
| | /* 响应式字体大小 */ |
| | @media (max-width: 1200px) { |
| | body { |
| | font-size: 13px; |
| | } |
| | } |
| | |
| | @media (max-width: 768px) { |
| | body { |
| | font-size: 12px; |
| | } |
| | } |
| | |
| | @media (max-width: 480px) { |
| | body { |
| | font-size: 11px; |
| | } |
| | } |
| | |
| | /* 开发者页脚链接 */ |
| | .xseq-developer-footer a { |
| | color: #0d6efd; |
| | text-decoration: none; |
| | } |
| | .xseq-developer-footer a:hover { |
| | text-decoration: underline; |
| | } |
| | .dark-mode .xseq-developer-footer a { |
| | color: #6ea8fe; |
| | } |
| | |
| | /* 夜间模式 - 添加微妙渐变背景 */ |
| | .dark-mode { |
| | background: linear-gradient(135deg, #1C1C1E 0%, #252528 50%, #1C1C1E 100%) !important; /* 🔥 深色模式渐变 */ |
| | color: #FFFFFF !important; |
| | min-height: 100vh; |
| | } |
| | |
| | /* 夜间模式下的所有元素 */ |
| | .dark-mode, |
| | .dark-mode body, |
| | .dark-mode .navbar, |
| | .dark-mode .sidebar-panel, |
| | .dark-mode .main-panel, |
| | .dark-mode .well-panel, |
| | .dark-mode .tab-pane, |
| | .dark-mode .shiny-html-output, |
| | .dark-mode .container-fluid, |
| | .dark-mode .shiny-text-output, |
| | .dark-mode .form-group, |
| | .dark-mode .control-label, |
| | .dark-mode .help-block, |
| | .dark-mode .text-muted, |
| | .dark-mode .radio, |
| | .dark-mode .checkbox, |
| | .dark-mode .well, |
| | .dark-mode .panel, |
| | .dark-mode .panel-body { |
| | color: #FFFFFF !important; |
| | background-color: #1C1C1E !important; |
| | } |
| | |
| | /* 所有文本元素强制白色 */ |
| | .dark-mode h1, |
| | .dark-mode h2, |
| | .dark-mode h3, |
| | .dark-mode h4, |
| | .dark-mode h5, |
| | .dark-mode h6, |
| | .dark-mode p, |
| | .dark-mode span, |
| | .dark-mode div, |
| | .dark-mode label { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* 文件上传组件 */ |
| | .dark-mode .shiny-input-container, |
| | .dark-mode .form-group, |
| | .dark-mode .control-label { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | .dark-mode .shiny-file-input-label, |
| | .dark-mode .input-group-addon { |
| | color: #FFFFFF !important; |
| | background-color: #2C2C2E !important; |
| | border-color: #444444 !important; |
| | } |
| | |
| | /* 按钮组 */ |
| | .dark-mode .btn-group, |
| | .dark-mode .btn-group .btn { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* 下载按钮 */ |
| | .dark-mode .download-button, |
| | .dark-mode .shiny-download-link { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* 文件浏览区域 */ |
| | .dark-mode .file-input, |
| | .dark-mode .shiny-bound-input { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* 进度条 */ |
| | .dark-mode .progress, |
| | .dark-mode .progress-bar { |
| | background-color: #2C2C2E !important; |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* Shiny特定组件 */ |
| | .dark-mode .shiny-bound-output, |
| | .dark-mode .shiny-html-output, |
| | .dark-mode .shiny-text-output, |
| | .dark-mode .shiny-plot-output, |
| | .dark-mode .shiny-table-output { |
| | color: #FFFFFF !important; |
| | background-color: #1C1C1E !important; |
| | } |
| | |
| | /* 文件上传进度 */ |
| | .dark-mode .shiny-file-input-progress, |
| | .dark-mode .progress-text { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* 文件上传按钮 */ |
| | .dark-mode .btn-file { |
| | color: #FFFFFF !important; |
| | background-color: #2C2C2E !important; |
| | border-color: #444444 !important; |
| | } |
| | |
| | /* 文件上传区域 */ |
| | .dark-mode .file-input-wrapper, |
| | .dark-mode .file-input-name { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* 下载链接 */ |
| | .dark-mode a[download], |
| | .dark-mode .shiny-download-link a { |
| | color: #0A84FF !important; |
| | } |
| | |
| | |
| | /* 输入框特殊处理 */ |
| | .dark-mode .form-control, |
| | .dark-mode .selectize-input { |
| | color: #000000 !important; |
| | background-color: #FFFFFF !important; |
| | } |
| | |
| | .dark-mode select { |
| | color: #000000 !important; |
| | background-color: #FFFFFF !important; |
| | } |
| | |
| | /* 下拉菜单选项样式 */ |
| | .dark-mode select option { |
| | color: #000000 !important; |
| | background-color: #FFFFFF !important; |
| | } |
| | |
| | /* Selectize下拉菜单选项样式 */ |
| | .dark-mode .selectize-dropdown { |
| | background-color: #FFFFFF !important; |
| | border: 1px solid #444444 !important; |
| | } |
| | |
| | .dark-mode .selectize-dropdown .option { |
| | color: #000000 !important; |
| | background-color: #FFFFFF !important; |
| | } |
| | |
| | .dark-mode .selectize-dropdown .option:hover { |
| | background-color: #F0F0F0 !important; |
| | color: #000000 !important; |
| | } |
| | |
| | .dark-mode .selectize-dropdown .active { |
| | background-color: #007AFF !important; |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* 按钮 */ |
| | .dark-mode .btn { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | /* 表格 */ |
| | .dark-mode table, |
| | .dark-mode th, |
| | .dark-mode td { |
| | color: #FFFFFF !important; |
| | background-color: #2C2C2E !important; |
| | } |
| | |
| | /* 标签页 */ |
| | .dark-mode .nav-tabs .nav-link { |
| | color: #CCCCCC !important; |
| | } |
| | |
| | .dark-mode .nav-tabs .nav-link.active { |
| | color: #0A84FF !important; |
| | } |
| | |
| | .dark-mode .nav-tabs .nav-link:hover { |
| | color: #FFFFFF !important; |
| | } |
| | |
| | a { color: #007AFF; } |
| | .dark-mode a { color: #0A84FF; } |
| | |
| | |
| | /* 导航栏 - 简化效果提升速度 */ |
| | .navbar { |
| | background-color: rgba(255,255,255,0.95) !important; |
| | border-bottom: 1px solid rgba(0,0,0,0.05); |
| | } |
| | .dark-mode .navbar { |
| | background-color: rgba(28,28,30,0.95) !important; |
| | border-bottom: 1px solid rgba(255,255,255,0.05); |
| | } |
| | .navbar-brand, .nav-link { |
| | color: #111 !important; |
| | font-weight: 500; |
| | } |
| | .dark-mode .navbar-brand, .dark-mode .nav-link { |
| | color: #F2F2F7 !important; |
| | } |
| | |
| | /* 面板 - 增强阴影效果提升视觉层次 */ |
| | .sidebar-panel, .main-panel, .well-panel, .tab-pane { |
| | background-color: #FFFFFF !important; |
| | border-radius: 14px; |
| | padding: 20px; |
| | border: 1px solid rgba(0,0,0,0.06); |
| | box-shadow: 0 4px 16px rgba(0,0,0,0.08); /* 🔥 增强阴影：更明显更有层次 */ |
| | transition: box-shadow 0.3s ease; /* 🔥 添加柔和过渡效果 */ |
| | } |
| | |
| | /* 面板hover效果 */ |
| | .sidebar-panel:hover, .main-panel:hover, .well-panel:hover { |
| | box-shadow: 0 6px 24px rgba(0,0,0,0.12); /* 🔥 hover时阴影更深 */ |
| | } |
| | |
| | .dark-mode .sidebar-panel, |
| | .dark-mode .main-panel, |
| | .dark-mode .well-panel, |
| | .dark-mode .tab-pane { |
| | background-color: #2C2C2E !important; |
| | border: 1px solid rgba(255,255,255,0.08); |
| | box-shadow: 0 4px 16px rgba(0,0,0,0.5); /* 🔥 增强深色模式阴影 */ |
| | transition: box-shadow 0.3s ease; |
| | } |
| | |
| | .dark-mode .sidebar-panel:hover, |
| | .dark-mode .main-panel:hover, |
| | .dark-mode .well-panel:hover { |
| | box-shadow: 0 6px 24px rgba(0,0,0,0.7); /* 🔥 深色模式hover效果 */ |
| | } |
| | |
| | /* 按钮 */ |
| | .btn { |
| | border-radius: 10px !important; |
| | padding: 8px 14px !important; |
| | font-weight: 500 !important; |
| | border: none !important; |
| | font-size: 14px !important; |
| | } |
| | |
| | /* 响应式按钮字体大小 */ |
| | @media (max-width: 1200px) { |
| | .btn { |
| | font-size: 13px !important; |
| | padding: 7px 12px !important; |
| | } |
| | } |
| | |
| | @media (max-width: 768px) { |
| | .btn { |
| | font-size: 12px !important; |
| | padding: 6px 10px !important; |
| | } |
| | } |
| | |
| | @media (max-width: 480px) { |
| | .btn { |
| | font-size: 11px !important; |
| | padding: 5px 8px !important; |
| | } |
| | } |
| | .btn-primary { background-color: #007AFF !important; color: white !important; } |
| | .dark-mode .btn-primary { background-color: #0A84FF !important; } |
| | |
| | .btn-success { background-color: #34C759 !important; color: white !important; } |
| | .btn-warning { background-color: #FF9F0A !important; } |
| | .btn-info { background-color: #5AC8FA !important; } |
| | |
| | /* 🔥 增强按钮hover效果 - 添加transform和阴影 */ |
| | .btn:hover { |
| | transform: translateY(-2px); /* 🔥 向上浮动 */ |
| | box-shadow: 0 4px 12px rgba(0,122,255,0.3); /* 🔥 添加阴影 */ |
| | opacity: 1; /* 🔥 不再降低opacity */ |
| | } |
| | |
| | .btn-primary:hover { |
| | box-shadow: 0 4px 12px rgba(0,122,255,0.4); |
| | } |
| | |
| | .btn-success:hover { |
| | box-shadow: 0 4px 12px rgba(52,199,89,0.4); |
| | } |
| | |
| | .btn-warning:hover { |
| | box-shadow: 0 4px 12px rgba(255,159,10,0.4); |
| | } |
| | |
| | .btn-info:hover { |
| | box-shadow: 0 4px 12px rgba(90,200,250,0.4); |
| | } |
| | |
| | /* 深色模式按钮hover */ |
| | .dark-mode .btn:hover { |
| | box-shadow: 0 4px 12px rgba(10,132,255,0.5); |
| | } |
| | |
| | .dark-mode .btn-primary:hover { |
| | box-shadow: 0 4px 12px rgba(10,132,255,0.6); |
| | } |
| | |
| | /* 输入框 - 移除过渡效果提升速度 */ |
| | .form-control, .selectize-input { |
| | background-color: #FAFAFC !important; |
| | border-radius: 10px !important; |
| | border: 1px solid rgba(0,0,0,0.08) !important; |
| | height: 38px; |
| | } |
| | |
| | /* 下拉菜单选项样式 */ |
| | select option { |
| | color: #000000 !important; |
| | background-color: #FFFFFF !important; |
| | } |
| | |
| | /* Selectize下拉菜单选项样式 */ |
| | .selectize-dropdown { |
| | background-color: #FFFFFF !important; |
| | border: 1px solid rgba(0,0,0,0.1) !important; |
| | } |
| | |
| | .selectize-dropdown .option { |
| | color: #000000 !important; |
| | background-color: #FFFFFF !important; |
| | } |
| | |
| | .selectize-dropdown .option:hover { |
| | background-color: #F0F0F0 !important; |
| | color: #000000 !important; |
| | } |
| | |
| | .selectize-dropdown .active { |
| | background-color: #007AFF !important; |
| | color: #FFFFFF !important; |
| | } |
| | .form-control:focus, .selectize-input.focus { |
| | border-color: #007AFF !important; |
| | box-shadow: 0 0 0 3px rgba(0,122,255,0.15); |
| | } |
| | .dark-mode .form-control, |
| | .dark-mode .selectize-input { |
| | background-color: #3A3A3C !important; |
| | border: 1px solid rgba(255,255,255,0.1) !important; |
| | color: #F2F2F7 !important; |
| | } |
| | .dark-mode .form-control:focus { |
| | border-color: #0A84FF !important; |
| | box-shadow: 0 0 0 3px rgba(10,132,255,0.2); |
| | } |
| | |
| | /* 标签页 */ |
| | .nav-tabs .nav-link { |
| | border: none !important; |
| | padding: 10px 16px !important; |
| | color: #6E6E73; |
| | } |
| | .nav-tabs .nav-link.active { |
| | color: #007AFF !important; |
| | border-bottom: 3px solid #007AFF !important; |
| | background: transparent !important; |
| | font-weight: 600; |
| | } |
| | .dark-mode .nav-tabs .nav-link.active { |
| | color: #0A84FF !important; |
| | border-bottom: 3px solid #0A84FF !important; |
| | } |
| | |
| | /* DataTable */ |
| | .dataTables_wrapper { color: #111 !important; } |
| | .dark-mode .dataTables_wrapper { color: #F2F2F7 !important; } |
| | |
| | ")) |
| |
|
| | |
| | |
| | |
| |
|
| | theme_js <- tags$script(HTML(" |
| | Shiny.addCustomMessageHandler('toggle-darkmode', function(is_dark){ |
| | if(is_dark){ |
| | document.body.classList.add('dark-mode'); |
| | } else { |
| | document.body.classList.remove('dark-mode'); |
| | } |
| | }); |
| | |
| | ")) |
| |
|
| | |
| |
|
| | |
| | |
| | |
| |
|
| | landing_ui <- tagList( |
| | |
| | wellPanel( |
| | id = "landing_panel", |
| | |
| | |
| | tags$div(class="text-center", style="margin-bottom: 20px; min-height: 300px; display: flex; flex-direction: column; align-items: center; justify-content: center;", |
| | |
| | tags$img(src="logo.png", |
| | alt="YuanSeq", |
| | style="max-height: 300px; width: auto; object-fit: contain; margin-bottom: 20px;", |
| | class="img-responsive", |
| | id="main-logo" |
| | ), |
| | |
| | tags$h1(id="text-title", |
| | class="text-center", |
| | style="font-size: 28px; margin: 0; display: none;", |
| | span(style="color: #007AFF;", "YuanSeq"), |
| | span(style="color: #6E6E73; font-weight: normal;", " v1") |
| | ), |
| | |
| | tags$script(HTML(" |
| | document.addEventListener('DOMContentLoaded', function() { |
| | var img = document.getElementById('main-logo'); |
| | var textTitle = document.getElementById('text-title'); |
| | if (img && textTitle) { |
| | // 图片加载成功时隐藏文字标题 |
| | img.onload = function() { |
| | textTitle.style.display = 'none'; |
| | img.style.display = 'block'; |
| | }; |
| | // 图片加载失败时显示文字标题 |
| | img.onerror = function() { |
| | img.style.display = 'none'; |
| | textTitle.style.display = 'block'; |
| | }; |
| | } |
| | }); |
| | |
| | // 🔥 论文展开/折叠函数 |
| | function toggleOldPapers() { |
| | var oldPapers = document.getElementById('old-papers'); |
| | var btn = document.getElementById('toggle-papers'); |
| | if (oldPapers.style.display === 'none') { |
| | oldPapers.style.display = 'block'; |
| | btn.innerHTML = '📕 收起早期论文 ▲'; |
| | } else { |
| | oldPapers.style.display = 'none'; |
| | btn.innerHTML = '📖 查看早期论文 ▼'; |
| | } |
| | } |
| | ")) |
| | ), |
| | |
| | |
| | tags$div(class="text-center", style="margin-bottom: 35px; color: #6E6E73;", |
| | tags$p("R/Shiny 转录组与芯片数据分析平台", style="font-size: 18px; margin-bottom: 12px;"), |
| | tags$p("差异表达、KEGG/GO/GSEA 富集、通路与转录因子活性推断、交互可视化", style="font-size: 16px; margin-bottom: 0;") |
| | ), |
| |
|
| | tags$hr(style="margin: 30px 0;"), |
| |
|
| | |
| | tags$div(style="margin-bottom: 35px;", |
| | tags$h4("ℹ️ 项目信息", style="color: #007AFF; margin-bottom: 20px; font-size: 22px;"), |
| | tags$p("• 版本：1", style="margin-bottom: 12px; font-size: 18px;"), |
| | tags$p("• 更新日期：2025年12月26日", style="margin-bottom: 0; font-size: 18px;") |
| | ), |
| |
|
| | tags$hr(style="margin: 30px 0;"), |
| |
|
| | |
| | tags$div(class="text-center", style="margin: 10px 0 30px; color: #6E6E73;", |
| | tags$p("已移除登录与用户管理功能，直接进入分析工作台。", style="font-size: 16px; margin-bottom: 0;") |
| | ), |
| | |
| | |
| | tags$div(style="margin-bottom: 10px;") |
| | ) |
| | ) |
| |
|
| | |
| | |
| | |
| |
|
| | main_app_ui <- function(initial_theme) { |
| |
|
| | tagList( |
| | navbarPage( |
| | title = tagList( |
| | |
| | tags$img(src="logo.png", |
| | alt="YuanSeq", |
| | style="height: 60px; margin-right: 15px; vertical-align: middle;", |
| | class="img-responsive", |
| | id="navbar-logo", |
| | onerror = "this.style.display='none'; document.getElementById('navbar-title').style.display='inline';" |
| | ), |
| | |
| | tags$span(id="navbar-title", |
| | style="vertical-align: middle; display: none; color: #007AFF;", |
| | "YuanSeq") |
| | ), |
| | id = "navbar", |
| | theme = bslib::bs_theme(version = 5), |
| | header = tagList( |
| | sci_fi_css, |
| | theme_js, |
| | useShinyjs() |
| | ), |
| | collapsible = TRUE, |
| | |
| | tabPanel("分析工作台", |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | |
| | materialSwitch( |
| | inputId = "theme_toggle", |
| | label = span("🌙 夜间模式"), |
| | value = FALSE, |
| | status = "primary" |
| | ), |
| | |
| | tags$hr(), |
| | |
| | h4("数据设置"), |
| | radioButtons("data_source", "数据来源", |
| | choices = c("原始Counts矩阵" = "counts", |
| | "差异基因结果" = "deg", |
| | "芯片差异结果" = "chip"), |
| | inline = TRUE), |
| | |
| | conditionalPanel( |
| | condition = "input.data_source == 'counts'", |
| | fileInput("file", "上传 Counts Matrix (CSV)", accept = c(".csv")), |
| | selectInput("species_select", "物种", choices = c("Mouse (org.Mm.eg.db)" = "Mm", "Human (org.Hs.eg.db)" = "Hs")), |
| | uiOutput("group_selector"), |
| |
|
| | |
| | uiOutput("sample_count_display"), |
| |
|
| | tags$hr(), |
| | h4("差异参数"), |
| | selectInput("pval_type", "显著性指标", choices = c("padj", "pvalue")), |
| | splitLayout( |
| | numericInput("pval_cutoff", "P阈值", 0.05, step = 0.01), |
| | numericInput("log2fc_cutoff", "FC阈值", 1, step = 0.5) |
| | ), |
| |
|
| | numericInput("edgeR_dispersion", "edgeR 离散度 (Dispersion^0.5)", |
| | value = 0.1, min = 0, max = 1, step = 0.01), |
| | helpText(class="text-muted", "注：分析方法将根据样本数量自动选择。每组样本数≥3时使用limma-voom，<3时使用edgeR。"), |
| |
|
| | |
| | hidden(selectInput("method", "方法", choices = c("limma-voom", "edgeR"), selected = "limma-voom")) |
| | ), |
| |
|
| | conditionalPanel( |
| | condition = "input.data_source == 'deg'", |
| | fileInput("deg_file", "上传差异基因 (CSV)", accept = c(".csv")), |
| | selectInput("deg_species", "物种", choices = c("Mouse (org.Mm.eg.db)" = "Mm", "Human (org.Hs.eg.db)" = "Hs")), |
| |
|
| | helpText(class="text-muted", |
| | "CSV文件应包含以下列：p_val, avg_log2FC, pct.1, pct.2, p_val_adj, gene"), |
| |
|
| | tags$hr(), |
| | h4("差异参数"), |
| | selectInput("deg_pval_type", "显著性指标", |
| | choices = c("调整P值" = "p_val_adj", "原始P值" = "p_val")), |
| | splitLayout( |
| | numericInput("deg_pval_cutoff", "P阈值", 0.05, step = 0.01), |
| | numericInput("deg_log2fc_cutoff", "FC阈值", 0.25, step = 0.1) |
| | ), |
| |
|
| | tags$hr(), |
| | actionButton("load_deg", "加载差异基因", class = "btn-info", width = "100%") |
| | ), |
| |
|
| | |
| | conditionalPanel( |
| | condition = "input.data_source == 'chip'", |
| | fileInput("chip_file", "上传芯片差异结果 (CSV)", accept = c(".csv")), |
| | selectInput("chip_species", "物种", choices = c("Mouse (org.Mm.eg.db)" = "mmu", "Human (org.Hs.eg.db)" = "hsa")), |
| |
|
| | helpText(class="text-info", |
| | "CSV文件应包含以下列：logFC, AveExpr, t, P.Value, adj.P.Val, B, SYMBOL, ID", |
| | br(), |
| | "这是从芯片分析模块导出的limma差异分析结果。"), |
| |
|
| | tags$hr(), |
| | h4("差异参数"), |
| | selectInput("chip_pval_type", "显著性指标", |
| | choices = c("调整P值" = "adj.P.Val", "原始P值" = "P.Value")), |
| | splitLayout( |
| | numericInput("chip_pval_cutoff", "P阈值", 0.05, step = 0.01), |
| | numericInput("chip_log2fc_cutoff", "FC阈值", 1, step = 0.5) |
| | ), |
| |
|
| | tags$hr(), |
| | actionButton("load_chip", "加载芯片差异结果", class = "btn-primary", width="100%") |
| | ), |
| | |
| | tags$hr(), |
| | actionButton("analyze", "开始分析", class="btn-success", width="100%"), |
| | br(), br(), |
| | downloadButton("download_results", "下载结果", class="btn-info", style="width:100%") |
| | ), |
| | |
| | mainPanel( |
| | class="main-panel", |
| | tabsetPanel( |
| | tabPanel("📊 数据概览", icon = icon("table"), |
| | br(), |
| | uiOutput("deg_summary"), |
| | tags$hr(), |
| | DT::dataTableOutput("deg_table") |
| | ), |
| |
|
| | tabPanel("🌋 火山图", icon = icon("chart-area"), |
| | fluidRow( |
| | column(9, |
| | plotlyOutput("interactive_volcano", height = "600px"), |
| | tags$br(), |
| | wellPanel( |
| | h4("📤 导出火山图"), |
| | splitLayout( |
| | numericInput("export_width", "宽度 (英寸)", 10, min = 5, max = 20), |
| | numericInput("export_height", "高度 (英寸)", 8, min = 5, max = 20) |
| | ), |
| | radioButtons("export_format", "导出格式", |
| | choices = c("PNG" = "png", "PDF" = "pdf", "SVG" = "svg"), |
| | selected = "png", inline = TRUE), |
| | downloadButton("download_volcano", "📥 下载火山图", |
| | class = "btn-success", style = "width:100%") |
| | ), |
| | tags$br(), |
| | ), |
| | column(3, |
| | wellPanel( |
| | h4("🎨 火山图设置"), |
| |
|
| | tags$hr(), |
| | h4("🔍 基因标签设置"), |
| | textInput("custom_genes_input", "自定义显示基因 (逗号分隔)", |
| | placeholder = "例如: TP53, MYC, EGFR"), |
| | actionButton("show_custom_genes", "显示自定义基因", |
| | class = "btn-primary", style = "width:100%"), |
| | actionButton("clear_custom_genes", "清除自定义基因", |
| | class = "btn-warning", style = "width:100%; margin-top: 5px;"), |
| |
|
| | tags$hr(), |
| | h4("🔧 标签样式设置"), |
| | sliderInput("gene_label_size", "标签字体大小", 8, 16, 10), |
| | checkboxInput("gene_label_bold", "标签加粗", value = FALSE), |
| | colourInput("gene_label_color", "标签颜色", "#2c3e50"), |
| |
|
| | tags$hr(), |
| | h4("🔧 点样式设置"), |
| | sliderInput("point_size", "点大小", 5, 15, 6), |
| | sliderInput("point_alpha", "点透明度", 0.1, 1, 0.7), |
| |
|
| | tags$hr(), |
| | h4("📊 坐标轴设置"), |
| | selectInput("y_axis_type", "Y轴类型", |
| | choices = c("-log10(pvalue)" = "pvalue", |
| | "-log10(padj)" = "padj"), |
| | selected = "pvalue"), |
| | splitLayout( |
| | numericInput("x_axis_min", "X轴最小值", -10), |
| | numericInput("x_axis_max", "X轴最大值", 15) |
| | ), |
| | sliderInput("axis_label_size", "坐标轴标签大小", 10, 20, 14), |
| | sliderInput("axis_title_size", "坐标轴标题大小", 12, 24, 16), |
| |
|
| | tags$hr(), |
| | h4("🎨 颜色设置"), |
| | colourInput("up_color", "上调颜色", "#e74c3c"), |
| | colourInput("down_color", "下调颜色", "#3498db"), |
| |
|
| | tags$hr(), |
| | checkboxInput("show_grid", "显示背景方格", value = TRUE) |
| | ) |
| | ) |
| | ) |
| | ), |
| |
|
| | tabPanel("🧬 KEGG富集", icon = icon("project-diagram"), |
| | tabsetPanel( |
| | tabPanel("基于差异基因", |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | h4("🔧 分析设置"), |
| | radioButtons("kegg_direction", "方向", |
| | choices = c("上调" = "Up", "下调" = "Down", "全部" = "All"), |
| | selected = "Up"), |
| | selectInput("kegg_species", "物种代码", choices = c("hsa", "mmu")), |
| | numericInput("kegg_p", "P Cutoff", 0.05), |
| | actionButton("run_kegg", "运行 KEGG", class = "btn-warning"), |
| |
|
| | tags$hr(), |
| | h4("🎨 绘图样式"), |
| | selectInput("kegg_x_axis", "X轴显示", |
| | choices = c("基因数量" = "Count", |
| | "富集倍数" = "FoldEnrichment"), |
| | selected = "Count"), |
| | sliderInput("kegg_font_size", "字体大小", 10, 20, 12), |
| | checkboxInput("kegg_bold", "字体加粗", value = FALSE), |
| | colourInput("kegg_low_col", "低显著颜色 (Low)", "#3498db"), |
| | colourInput("kegg_high_col", "高显著颜色 (High)", "#e74c3c"), |
| |
|
| | tags$hr(), |
| | h5("📤 导出图表"), |
| | radioButtons("kegg_export_format", "导出格式", |
| | choices = c("PNG" = "png", "PDF" = "pdf", "SVG" = "svg"), |
| | selected = "png", inline = TRUE), |
| | downloadButton("download_kegg_plot", "下载KEGG图表", class="btn-sm btn-success"), |
| | tags$hr(), |
| | downloadButton("download_kegg", "下载结果表", class="btn-sm btn-light"), |
| |
|
| | ), |
| | mainPanel( |
| | class = "main-panel", |
| | plotOutput("kegg_dotplot", height = "600px"), |
| | tags$br(), |
| | h4("详细结果表 (ID已转Symbol)"), |
| | DT::dataTableOutput("kegg_table"), |
| |
|
| | ) |
| | ) |
| | ), |
| |
|
| | tabPanel("基于基因列表", |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | h4("🔧 单列基因 KEGG 分析"), |
| | fileInput("single_gene_file", "上传基因列表 (CSV)", |
| | accept = c(".csv"), |
| | placeholder = "包含 SYMBOL 列的文件"), |
| | helpText(class="text-muted", |
| | "CSV 文件应包含一列名为 'SYMBOL' 的基因符号"), |
| |
|
| | selectInput("single_gene_species", "物种代码", |
| | choices = c("Human" = "hsa", "Mouse" = "mmu")), |
| | numericInput("single_gene_kegg_p", "P Cutoff", 0.05), |
| | actionButton("run_single_gene_kegg", "运行 KEGG", class = "btn-primary"), |
| |
|
| | tags$hr(), |
| | h4("🎨 绘图样式"), |
| | selectInput("single_gene_kegg_x_axis", "X轴显示", |
| | choices = c("基因数量" = "Count", |
| | "富集倍数" = "FoldEnrichment"), |
| | selected = "Count"), |
| | sliderInput("single_gene_kegg_font_size", "字体大小", 10, 20, 12), |
| | checkboxInput("single_gene_kegg_bold", "字体加粗", value = FALSE), |
| | colourInput("single_gene_kegg_low_col", "低显著颜色 (Low)", "#3498db"), |
| | colourInput("single_gene_kegg_high_col", "高显著颜色 (High)", "#e74c3c"), |
| |
|
| | tags$hr(), |
| | h5("📤 导出图表"), |
| | radioButtons("single_gene_kegg_export_format", "导出格式", |
| | choices = c("PNG" = "png", "PDF" = "pdf", "SVG" = "svg"), |
| | selected = "png", inline = TRUE), |
| | downloadButton("download_single_gene_kegg_plot", "下载KEGG图表", class="btn-sm btn-success"), |
| | tags$hr(), |
| | downloadButton("download_single_gene_kegg", "下载结果表", class="btn-sm btn-light") |
| | ), |
| | mainPanel( |
| | class = "main-panel", |
| | plotOutput("single_gene_kegg_dotplot", height = "600px"), |
| | tags$br(), |
| | h4("详细结果表 (ID已转Symbol)"), |
| | DT::dataTableOutput("single_gene_kegg_table") |
| | ) |
| | ) |
| | ) |
| | ) |
| | ), |
| |
|
| | tabPanel("🧬 GO分析", icon = icon("dna"), |
| | tabsetPanel( |
| | tabPanel("基于差异基因", |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | h4("🔧 分析设置"), |
| | radioButtons("go_direction", "方向", |
| | choices = c("上调" = "Up", "下调" = "Down", "全部" = "All"), |
| | selected = "Up"), |
| | selectInput("go_species", "物种代码", choices = c("hsa", "mmu")), |
| | selectInput("go_ontology", "GO类别", |
| | choices = c("生物过程" = "BP", |
| | "分子功能" = "MF", |
| | "细胞组分" = "CC"), |
| | selected = "BP"), |
| | numericInput("go_p", "P Cutoff", 0.05), |
| | numericInput("go_top_n", "显示Top N", 20, min = 5, max = 50), |
| | actionButton("run_go", "运行 GO分析", class = "btn-warning"), |
| |
|
| | tags$hr(), |
| | h4("🎨 绘图样式"), |
| | selectInput("go_x_axis", "X轴属性", |
| | choices = c("Gene Ratio" = "GeneRatio", |
| | "Background Ratio" = "BgRatio", |
| | "Gene Count" = "Count", |
| | "Fold Enrichment" = "FoldEnrichment"), |
| | selected = "GeneRatio"), |
| | sliderInput("go_font_size", "字体大小", 10, 20, 12), |
| | checkboxInput("go_bold", "字体加粗", value = FALSE), |
| | colourInput("go_low_col", "低显著颜色 (Low)", "#3498db"), |
| | colourInput("go_high_col", "高显著颜色 (High)", "#e74c3c"), |
| |
|
| | tags$hr(), |
| | h5("📤 导出图表"), |
| | radioButtons("go_export_format", "导出格式", |
| | choices = c("PNG" = "png", "PDF" = "pdf", "SVG" = "svg"), |
| | selected = "png", inline = TRUE), |
| | downloadButton("download_go_plot", "下载GO图表", class="btn-sm btn-success"), |
| | tags$hr(), |
| | downloadButton("download_go", "下载结果表", class="btn-sm btn-light"), |
| |
|
| | ), |
| | mainPanel( |
| | class = "main-panel", |
| | plotOutput("go_dotplot", height = "600px"), |
| | tags$br(), |
| | h4("详细结果表"), |
| | DT::dataTableOutput("go_table"), |
| |
|
| | ) |
| | ) |
| | ), |
| |
|
| | tabPanel("基于基因列表", |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | h4("🔧 单列基因 GO 分析"), |
| | fileInput("single_gene_go_file", "上传基因列表 (CSV)", |
| | accept = c(".csv"), |
| | placeholder = "包含 SYMBOL 列的文件"), |
| | helpText(class="text-muted", |
| | "CSV 文件应包含一列名为 'SYMBOL' 的基因符号"), |
| |
|
| | selectInput("single_gene_species_go", "物种代码", |
| | choices = c("Human" = "hsa", "Mouse" = "mmu")), |
| | selectInput("single_gene_go_ontology", "GO类别", |
| | choices = c("生物过程" = "BP", |
| | "分子功能" = "MF", |
| | "细胞组分" = "CC"), |
| | selected = "BP"), |
| | numericInput("single_gene_go_p", "P Cutoff", 0.05), |
| | actionButton("run_single_gene_go", "运行 GO分析", class = "btn-primary"), |
| |
|
| | tags$hr(), |
| | h4("🎨 绘图样式"), |
| | selectInput("single_gene_go_x_axis", "X轴属性", |
| | choices = c("Gene Ratio" = "GeneRatio", |
| | "Background Ratio" = "BgRatio", |
| | "Gene Count" = "Count", |
| | "Fold Enrichment" = "FoldEnrichment"), |
| | selected = "GeneRatio"), |
| | sliderInput("single_gene_go_font_size", "字体大小", 10, 20, 12), |
| | checkboxInput("single_gene_go_bold", "字体加粗", value = FALSE), |
| | colourInput("single_gene_go_low_col", "低显著颜色 (Low)", "#3498db"), |
| | colourInput("single_gene_go_high_col", "高显著颜色 (High)", "#e74c3c"), |
| |
|
| | tags$hr(), |
| | h5("📤 导出图表"), |
| | radioButtons("single_gene_go_export_format", "导出格式", |
| | choices = c("PNG" = "png", "PDF" = "pdf", "SVG" = "svg"), |
| | selected = "png", inline = TRUE), |
| | downloadButton("download_single_gene_go_plot", "下载GO图表", class="btn-sm btn-success"), |
| | tags$hr(), |
| | downloadButton("download_single_gene_go", "下载结果表", class="btn-sm btn-light") |
| | ), |
| | mainPanel( |
| | class = "main-panel", |
| | plotOutput("single_gene_go_dotplot", height = "600px"), |
| | tags$br(), |
| | h4("详细结果表"), |
| | DT::dataTableOutput("single_gene_go_table") |
| | ) |
| | ) |
| | ) |
| | ) |
| | ), |
| |
|
| | tabPanel("🌊 GSEA分析", icon = icon("water"), |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | h4("🔧 GSEA 设置"), |
| | fileInput("gmt_file", "上传 GMT 文件", accept = c(".gmt")), |
| | helpText(class="text-muted", "支持大文件上传 (Max 100MB)"), |
| |
|
| | selectInput("gsea_id_type", "GMT中的ID类型", |
| | choices = c("Gene Symbol (推荐)" = "SYMBOL", |
| | "Entrez ID" = "ENTREZID"), |
| | selected = "SYMBOL"), |
| | helpText(class="text-info small", |
| | "💡 推荐使用Symbol以在图上显示基因名称（如Csf3）"), |
| |
|
| | numericInput("gsea_pvalue", "Pvalue Cutoff", 0.05), |
| | actionButton("run_gsea", "运行 GSEA", class = "btn-primary"), |
| | tags$div( |
| | class = "alert alert-info", |
| | style = "margin-top: 12px; margin-bottom: 0; padding: 10px; font-size: 0.9em;", |
| | tags$strong("💡 延伸分析：GPSA"), |
| | tags$p( |
| | style = "margin: 6px 0 8px 0;", |
| | "能做 GSEA 时，推荐在 ", |
| | tags$a(href = "https://www.gpsadb.com/", target = "_blank", rel = "noopener noreferrer", "GPSAdb"), |
| | " 上再做一次 ", |
| | tags$a(href = "https://www.gpsadb.com/", target = "_blank", rel = "noopener noreferrer", "fastGPSA"), |
| | " 分析：可发现「哪个基因的敲减/扰动会产生类似的下游转录组效应」，有助于发现分子伴侣与上下游调控分子。" |
| | ), |
| | tags$a( |
| | href = "https://www.gpsadb.com/", |
| | target = "_blank", |
| | rel = "noopener noreferrer", |
| | class = "btn btn-sm btn-outline-primary", |
| | style = "margin-top: 4px;", |
| | "打开 GPSAdb →" |
| | ) |
| | ), |
| | tags$hr(), |
| |
|
| | h4("🎨 绘图调整"), |
| | p(class="text-muted", "拖动滑块调整统计值位置"), |
| | sliderInput("gsea_stats_x", "统计值水平位置 (X)", min = 0, max = 1, value = 0.6, step = 0.05), |
| | sliderInput("gsea_stats_y", "统计值垂直位置 (Y)", min = 0, max = 1, value = 0.8, step = 0.05), |
| |
|
| | tags$hr(), |
| |
|
| | h4("🧬 基因展示设置"), |
| | p(class="text-muted", "在GSEA图上标记Leading Edge基因"), |
| | numericInput("gsea_top_genes", "自动标记Top N基因", value = 20, min = 5, max = 100, step = 5), |
| | selectInput("gsea_gene_order", "基因排序方式", |
| | choices = c("🔥 GSEA Leading Edge基因（顶峰基因）" = "leading_edge", |
| | "按log2FoldChange绝对值" = "abs_logFC", |
| | "按log2FoldChange值" = "logFC", |
| | "按基因在ranked list中的位置" = "rank"), |
| | selected = "leading_edge"), |
| | textInput("custom_gene_list", "自定义基因列表 (可选)", |
| | placeholder = "例如: Entpd8, Htr2a, Nt5e, Actn3"), |
| | helpText(class="text-muted small", |
| | "留空则自动显示Top N基因。支持逗号、分号或空格分隔。"), |
| |
|
| | tags$hr(), |
| |
|
| | h4("📊 多通路可视化"), |
| | p(class="text-muted", "使用gseaRidge展示多个通路的基因分布"), |
| | numericInput("gsea_ridge_pathways", "选择Top N通路", value = 10, min = 3, max = 20, step = 1), |
| | checkboxInput("show_gsea_ridge", "显示山脊图", value = FALSE), |
| |
|
| | tags$hr(), |
| |
|
| | h4("📤 GSEA结果导出"), |
| | div(class = "gsea-export-section", |
| | p(strong("导出选项:")), |
| | radioButtons("gsea_export_type", "导出内容", |
| | choices = c("完整结果表" = "full", |
| | "显著结果表 (P < 0.05)" = "significant", |
| | "Top 50 通路" = "top50"), |
| | selected = "full"), |
| | numericInput("gsea_export_topn", "Top N 通路 (仅Top N模式)", |
| | value = 50, min = 10, max = 200, step = 10), |
| | downloadButton("download_gsea_full", "📥 下载完整结果", |
| | class = "btn-success btn-sm", |
| | style = "width:100%; margin-bottom:5px;"), |
| | downloadButton("download_gsea_sig", "📥 下载显著结果", |
| | class = "btn-warning btn-sm", |
| | style = "width:100%; margin-bottom:5px;"), |
| | downloadButton("download_gsea_top", "📥 下载Top N结果", |
| | class = "btn-info btn-sm", |
| | style = "width:100%; margin-bottom:5px;"), |
| |
|
| | tags$hr(style = "margin: 10px 0;"), |
| |
|
| | |
| | p(class="text-primary", style="font-weight:bold", "📊 导出图表 (SVG格式)"), |
| | downloadButton("download_gsea_plot_svg", "📥 下载GSEA图 (SVG)", |
| | class = "btn-primary btn-sm", |
| | style = "width:100%; margin-bottom:5px;"), |
| | downloadButton("download_gsea_ridge_svg", "📥 下载山脊图 (SVG)", |
| | class = "btn-primary btn-sm", |
| | style = "width:100%;") |
| | ), |
| |
|
| | tags$hr(), |
| | p(class="text-muted", "注：GSEA 基于 log2FoldChange 排序。SVG格式可无损缩放，适合出版。") |
| | ), |
| | mainPanel( |
| | class = "main-panel", |
| | fluidRow( |
| | column(12, |
| | h4("GseaVis 可视化"), |
| | p(class="text-muted", "点击下方表格中的某一行，即可显示对应的 GSEA 图，图中会自动标记Leading Edge基因（红色斜体标注）。"), |
| | p(class="text-info small", "💡 做完 GSEA 后，可到 ", |
| | tags$a(href = "https://www.gpsadb.com/", target = "_blank", rel = "noopener noreferrer", "GPSAdb"), " 使用 fastGPSA 上传同一排序基因列表，查找产生类似下游效应的敲减/扰动基因。"), |
| | plotOutput("gsea_plot", height = "600px") |
| | ) |
| | ), |
| | tags$hr(), |
| | |
| | conditionalPanel( |
| | condition = "input.show_gsea_ridge", |
| | fluidRow( |
| | column(12, |
| | h4("GseaRidge 多通路山脊图"), |
| | p(class="text-muted", "展示Top N个GSEA通路的基因分布山脊图"), |
| | plotOutput("gsea_ridge_plot", height = "800px") |
| | ) |
| | ), |
| | tags$hr() |
| | ), |
| | h4("GSEA 结果表"), |
| | DT::dataTableOutput("gsea_table") |
| | ) |
| | ) |
| | ), |
| |
|
| | tabPanel("🔬 转录因子活性", icon = icon("dna"), |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | h4("🧬 TF 活性推断"), |
| | helpText(class="text-muted", "使用 decoupleR 推断转录因子活性。"), |
| |
|
| | |
| | selectInput("tf_method", "推断算法", |
| | choices = c( |
| | "ULM (单变量线性模型)" = "ulm", |
| | "MLM (多变量线性模型)" = "mlm", |
| | "WMEAN (加权平均)" = "wmean", |
| | "WSUM (加权求和)" = "wsum" |
| | ), |
| | selected = "ulm"), |
| | helpText(class="text-muted small", "ULM: 快速准确 | MLM: 考虑共调控 | WMEAN/WSUM: 简单加权"), |
| |
|
| | numericInput("tf_min_size", "TF靶基因最小数量", 5, min = 1, step = 1), |
| |
|
| | tags$hr(), |
| | actionButton("run_tf_activity", "运行 TF 活性分析", class = "btn-info"), |
| | tags$hr(), |
| |
|
| | h4("🎨 绘图样式"), |
| | sliderInput("tf_top_n", "显示 Top N 个TF", 10, 50, 20), |
| | colourInput("tf_active_col", "激活颜色", "#e74c3c"), |
| | colourInput("tf_inactive_col", "失活颜色", "#3498db"), |
| |
|
| | tags$hr(), |
| | h5("🎯 网络图自定义"), |
| | sliderInput("tf_network_node_size", "节点大小倍数", 0.5, 3, 1, step = 0.1), |
| | sliderInput("tf_network_label_size", "标签大小", 2, 6, 3.5, step = 0.5), |
| | colourInput("tf_tf_node_col", "TF节点颜色", "#2ecc71"), |
| | colourInput("tf_consistent_act_col", "一致-激活节点", "#27ae60"), |
| | colourInput("tf_consistent_rep_col", "一致-抑制节点", "#2980b9"), |
| | colourInput("tf_inconsistent_act_col", "不一致-激活节点", "#c0392b"), |
| | colourInput("tf_inconsistent_rep_col", "不一致-抑制节点", "#2c3e50"), |
| | colourInput("tf_neutral_col", "未知节点", "#95a5a6"), |
| |
|
| | tags$hr(), |
| | h5("🎯 散点图自定义"), |
| | sliderInput("tf_scatter_point_size", "散点大小", 1, 6, 3, step = 0.5), |
| | sliderInput("tf_scatter_alpha", "散点透明度", 0.1, 1, 0.7, step = 0.1), |
| | sliderInput("tf_scatter_label_size", "标签大小", 2, 6, 3, step = 0.5), |
| | sliderInput("tf_scatter_n_labels", "显示标签数量", 0, 30, 15, step = 1), |
| |
|
| | tags$hr(), |
| | downloadButton("download_tf_results", "下载 TF 结果表", class="btn-sm btn-light") |
| | ), |
| | mainPanel( |
| | class = "main-panel", |
| | fluidRow( |
| | column(12, |
| | h4("TF 活性变化柱状图 (Treatment vs Control)"), |
| | plotOutput("tf_activity_bar_plot", height = "600px") |
| | ) |
| | ), |
| | tags$hr(), |
| | h4("转录因子活性结果表"), |
| | DT::dataTableOutput("tf_activity_table"), |
| |
|
| | tags$hr(), |
| | h4("所选 TF 靶基因调控一致性散点图"), |
| | p(class="text-muted", "图中的颜色显示了靶基因的实际差异表达方向与 TF 调控网络预设方向的匹配程度。"), |
| | |
| | uiOutput("tf_consistency_summary"), |
| | tags$br(), |
| | plotOutput("tf_target_plot", height = "600px"), |
| |
|
| | tags$hr(), |
| | h4("所选 TF 靶基因调控网络"), |
| | p(class="text-muted", "显示TF与其靶基因的调控关系。红色=激活，蓝色=抑制，实线=一致，虚线=不一致。"), |
| | |
| | plotlyOutput("tf_network_plot_interactive", height = "700px"), |
| | |
| | hidden(plotOutput("tf_network_plot_static", height = "700px")), |
| | tags$br(), |
| | checkboxInput("use_static_network", "使用静态图（用于SVG导出）", FALSE), |
| | |
| | downloadButton("download_tf_network_svg", "📥 下载网络图 (SVG)", class = "btn-sm btn-primary"), |
| | downloadButton("download_tf_scatter_svg", "📥 下载散点图 (SVG)", class = "btn-sm btn-primary"), |
| |
|
| | |
| | downloadButton("download_tf_scatter_data", "💾 导出靶基因数据 (CSV)", class = "btn-sm btn-success"), |
| |
|
| | tags$hr(), |
| | h4("所选 TF 的靶基因详细信息"), |
| | p(class="text-muted", "请在上方 '转录因子活性结果表' 中点击一行，查看其靶基因。"), |
| | DT::dataTableOutput("tf_target_table") |
| | ) |
| | ) |
| | ), |
| |
|
| | tabPanel("🔷 韦恩图", icon = icon("object-group"), |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | h4("🔷 韦恩图设置"), |
| |
|
| | numericInput("venn_sets", "集合数量", |
| | value = 2, min = 2, max = 5, step = 1), |
| |
|
| | uiOutput("venn_inputs"), |
| |
|
| | tags$hr(), |
| | h4("🎨 绘图样式"), |
| | colourInput("venn_color1", "集合1颜色", "#1f77b4"), |
| | colourInput("venn_color2", "集合2颜色", "#ff7f0e"), |
| | colourInput("venn_color3", "集合3颜色", "#2ca02c"), |
| | colourInput("venn_color4", "集合4颜色", "#d62728"), |
| | colourInput("venn_color5", "集合5颜色", "#9467bd"), |
| |
|
| | sliderInput("venn_alpha", "透明度", 0.3, 0.8, 0.5), |
| |
|
| | tags$hr(), |
| | actionButton("generate_venn", "生成韦恩图", |
| | class = "btn-primary btn-lg", |
| | width = "100%") |
| | ), |
| |
|
| | mainPanel( |
| | class = "main-panel", |
| | fluidRow( |
| | column(12, |
| | h4("交互式韦恩图"), |
| | p(class="text-muted", |
| | "点击图中的交集区域查看详细信息，交集内容会自动复制到剪贴板。"), |
| |
|
| | plotOutput("venn_plot", |
| | click = "venn_click", |
| | height = "500px"), |
| |
|
| | tags$br(), |
| |
|
| | uiOutput("venn_result_ui"), |
| |
|
| | tags$hr(), |
| |
|
| | h4("详细交集数据"), |
| | DT::dataTableOutput("venn_table") |
| | ) |
| | ) |
| | ) |
| | ) |
| | ), |
| |
|
| | |
| | tabPanel("🛤️ 通路活性", icon = icon("project-diagram"), |
| | sidebarLayout( |
| | sidebarPanel( |
| | width = 3, |
| | class = "sidebar-panel", |
| | h4("🧬 KEGG 通路活性推断"), |
| | helpText(class="text-muted", "基于 KEGG 富集结果推断通路活性。"), |
| |
|
| | tags$hr(), |
| |
|
| | |
| | selectInput("pathway_method", "推断方法", |
| | choices = c( |
| | "ULM (推荐)" = "ulm", |
| | "WMEAN (加权平均)" = "wmean" |
| | |
| | |
| | ), |
| | selected = "ulm"), |
| |
|
| | |
| | uiOutput("pathway_method_info"), |
| |
|
| | |
| | helpText(class="text-muted", |
| | style = "color: #f39c12; font-size: 11px;", |
| | "⚠️ 注意: AUCell和GSVA方法需要原始表达矩阵，暂不可用。"), |
| |
|
| | tags$hr(), |
| |
|
| | |
| | numericInput("pathway_minsize", "最小基因集大小", |
| | value = 5, min = 3, max = 50), |
| |
|
| | helpText(class="text-muted", |
| | "通路至少包含的基因数量"), |
| |
|
| | tags$hr(), |
| |
|
| | |
| | sliderInput("pathway_top_n", "显示 Top N 通路", |
| | min = 5, max = 50, value = 20, step = 5), |
| |
|
| | tags$hr(), |
| |
|
| | |
| | colourInput("pathway_active_col", "激活通路颜色", |
| | value = "#e74c3c"), |
| | colourInput("pathway_inactive_col", "抑制通路颜色", |
| | value = "#3498db"), |
| |
|
| | tags$hr(), |
| |
|
| | |
| | numericInput("pathway_heatmap_fontsize", "热图字体大小", |
| | value = 10, min = 6, max = 20, step = 1), |
| |
|
| | helpText(class="text-muted", |
| | "调整热图中基因名和分数的字体大小"), |
| |
|
| | |
| | numericInput("pathway_bar_fontsize", "柱状图字体大小", |
| | value = 10, min = 6, max = 20, step = 1), |
| |
|
| | helpText(class="text-muted", |
| | "调整柱状图中的标题、轴标签和图例字体大小"), |
| |
|
| | tags$hr(), |
| |
|
| | |
| | actionButton("run_pathway_activity", "🚀 运行通路活性分析", |
| | class = "btn-primary btn-block", |
| | icon = icon("play"), |
| | style = "margin-top: 10px;"), |
| |
|
| | |
| | uiOutput("pathway_summary"), |
| |
|
| | tags$hr(), |
| |
|
| | |
| | downloadButton("download_pathway_results", "📥 下载结果", |
| | class = "btn-success btn-block"), |
| |
|
| | helpText(class="text-muted", |
| | "💡 提示：请先运行 KEGG 富集分析", |
| | style = "color: #f39c12; font-size: 11px;") |
| | ), |
| | mainPanel( |
| | class = "main-panel", |
| |
|
| | |
| | tabsetPanel( |
| | id = "pathway_tabs", |
| | type = "tabs", |
| |
|
| | |
| | tabPanel("📖 算法说明", |
| | h4("🧠 什么是通路活性分析？"), |
| | uiOutput("pathway_algorithm_intro"), |
| |
|
| | tags$hr(), |
| |
|
| | h4("🔬 ULM 方法原理"), |
| | uiOutput("pathway_ulm_explanation"), |
| |
|
| | tags$hr(), |
| |
|
| | h4("📊 结果解读指南"), |
| | uiOutput("pathway_result_guide"), |
| |
|
| | tags$hr(), |
| |
|
| | h4("💡 实际应用案例"), |
| | uiOutput("pathway_example_use_case"), |
| |
|
| | tags$hr(), |
| |
|
| | h4("❓ 常见问题"), |
| | uiOutput("pathway_faq") |
| | ), |
| |
|
| | |
| | tabPanel("柱状图", |
| | fluidRow( |
| | column(10, |
| | h4("通路活性排名") |
| | ), |
| | column(2, |
| | align = "right", |
| | downloadButton("download_pathway_bar_png", |
| | "📥 PNG", |
| | class = "btn-sm btn-primary"), |
| | downloadButton("download_pathway_bar_svg", |
| | "📥 SVG", |
| | class = "btn-sm btn-info") |
| | ) |
| | ), |
| | plotOutput("pathway_activity_bar_plot", |
| | height = "600px"), |
| | tags$br(), |
| | h4("详细结果表"), |
| | DT::dataTableOutput("pathway_activity_table") |
| | ), |
| |
|
| | |
| | tabPanel("热图", |
| | fluidRow( |
| | column(10, |
| | h4("通路活性热图") |
| | ), |
| | column(2, |
| | align = "right", |
| | downloadButton("download_pathway_heatmap_png", |
| | "📥 PNG", |
| | class = "btn-sm btn-primary"), |
| | downloadButton("download_pathway_heatmap_svg", |
| | "📥 SVG", |
| | class = "btn-sm btn-info") |
| | ) |
| | ), |
| | plotOutput("pathway_activity_heatmap", |
| | height = "600px") |
| | ) |
| | ) |
| | ) |
| | ) |
| | ), |
| |
|
| | |
| | tabPanel("🧬 芯片分析", icon = icon("microchip"), |
| | uiOutput("chip_analysis_ui_output") |
| | ) |
| | ) |
| | ) |
| | ) |
| | ), |
| | |
| | tags$div( |
| | class = "xseq-developer-footer", |
| | style = "padding: 12px 15px; text-align: center; font-size: 12px; color: #6c757d; border-top: 1px solid #dee2e6; margin-top: 8px; background: rgba(0,0,0,0.02);", |
| | tags$p(style = "margin: 0; font-weight: 600;", "开发者 Developer: 乔宇 Yu Qiao"), |
| | tags$p(style = "margin: 2px 0 0 0;", "上海交通大学药学院 · 药理学博士 | School of Pharmacy, Shanghai Jiao Tong University · PhD in Pharmacology"), |
| | tags$p(style = "margin: 4px 0 0 0;", |
| | "导师 Supervisors: ", |
| | tags$a(href = "https://pharm.sjtu.edu.cn/szdy/2862.html", target = "_blank", rel = "noopener noreferrer", "钱峰教授 Prof. Feng Qian"), |
| | "、", |
| | tags$a(href = "https://pharm.sjtu.edu.cn/szdy/2870.html", target = "_blank", rel = "noopener noreferrer", "孙磊教授 Prof. Lei Sun") |
| | ), |
| | tags$p(style = "margin: 6px 0 0 0; font-size: 11px; opacity: 0.9;", |
| | "饮水思源 · 致谢 R/Bioconductor 及本平台所集成的开源包 | Thanks to R, Bioconductor & all integrated packages") |
| | ) |
| | ) |
| | } |
| |
|
| |
|
| |
|
