footerTagList <- list(
)
tags$script(src="fileInput_text.js")
shinyUI(fluidPage(
tweaks,
use_waiter(),
# useShinyjs(),
tags$head(
tags$link(rel = "icon", type = "image/png", sizes = "64x64", href = "IASbreeding_logo1.png"),
# Google Analytics 4 (GA4) 直接嵌入
tags$script(HTML("
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-456537467'); // 替换成你的 GA4 Measurement ID
")),
# 引入 GA4 脚本
tags$script(
async = TRUE,
src = "https://www.googletagmanager.com/gtag/js?id=G-456537467"
)
),
titlePanel(
div(
img(src = "IASbreeding_logo1.png",height = "70px"),
span("IASBreeding", style = "font-size:40px; color:#2d6a4f; margin-left: 10px;"),
span("智慧农业育种平台", style = "font-size:30px; color:#6a994e; margin-left: 16px;"),
style = "background-color:#e8f5e9; padding:10px; text-align: center;"
),
windowTitle = "智慧农业育种平台"
),
tags$head(
tags$link(rel = "stylesheet", href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0-beta3/css/all.min.css"),
includeCSS("www/custom_style.css") # 如果有自定义 CSS
),
shinydisconnect::disconnectMessage(
text = "您的会话超时，请刷新此网站!",
refresh = "Reload now",
background = "lightblue",
colour = "white",
overlayColour = "grey",
overlayOpacity = 0.75,
top = 250,
refreshColour = "brown"
),
navbarPage(
title = "",
windowTitle = "IAS-breeding",
theme = shinytheme("flatly"),
tags$div(
style = "position: absolute; top: 10px; right: 20px; z-index: 10;",
tags$a("中文网站|", style = "margin-right: 10px; color: #2d6a4f; text-decoration: none;"),
tags$a(href = "https://IASbreeding.cn/en", "English Website", style = "color: #2d6a4f; text-decoration: none;")
),
tabPanel(
"简介",
icon = icon("circle-info"),
dashboardPage(
dashboardHeader(disable = T),
dashboardSidebar(disable = T),
dashboardBody(
column(
width = 12,
offset = -1,
textBox(
width = 12,
p("智慧农业育种平台（Intelligent Agricultural Solutions of Breeding，简称IASBreeding） 是一个专门用于动物和农作物育种服务的分析平台。目前该平台功能包括了包括线性混合模型IASBLUP、机器学习非线性模型IASML、选配决策IASmating、基因型填充IASimpute四个功能模块。IASBLUP软件提供三种分析版本：C++软件、R语言软件包、云平台分析；IASML软件提供了python软件和云平台服务。选配决策IASmating提供了软件和云平台服务、IASimpute只提供了云平台服务。")
, style = "font-size:18px;color:black")
),
column(
width = 12,
offset = -1,
fluidRow(
tags$style(HTML("
.box.box-solid.box-primary>.box-header {
color:#ccccd6;
background:#ccccd6
}
.box.box-solid.box-primary{
border-bottom-color:#666666;
border-left-color:#666666;
border-right-color:#666666;
border-top-color:#666666;
}
")),
box(title = tags$p(tags$i(class = "fa-solid fa-thumbs-up", style = "font-size: 100%; color: darkred; margin-right: 10px;"), "IAS-breeding特点:",style = "font-size: 120%; color: black;"),
fluidRow(column(12,bslib::value_box(title = tags$p("版本丰富", style = "font-size: 200%;"),
value = tags$p("Linux C++, R, 在线网页", style = "font-size: 140%;"),
showcase = tags$p(bsicons::bs_icon("ubuntu"),style = "font-size: 150%;"),showcase_layout = "left center",
theme = bslib::value_box_theme(bg = "white", fg = "#64483d"), width =6))),
fluidRow(column(12,bslib::value_box(title = tags$p("运算高效", style = "font-size: 200%;"),
value = tags$p("Fast C++ math library", style = "font-size: 140%;"),
showcase = bsicons::bs_icon("cpu-fill"),showcase_layout = "left center",
theme = bslib::value_box_theme(bg = "white", fg = "#cf4813"), width = 6))),
fluidRow(column(12,bslib::value_box(title = tags$p("用户友好", style = "font-size: 200%;"),
value = tags$p("交互网页和R版本", style = "font-size: 140%;"),
showcase = bsicons::bs_icon("Person-hearts"),showcase_layout = "left center",
theme = bslib::value_box_theme(bg = "white", fg = "#1491a8"), width = 6))),
fluidRow(column(12,bslib::value_box(title = tags$p("功能丰富", style = "font-size: 200%;"),
value = tags$p("遗传力估计, 育种值估计", style = "font-size: 140%;"),
showcase = bsicons::bs_icon("palette-fill"),showcase_layout = "left center",
theme = bslib::value_box_theme(bg = "white", fg = "#f2ce2b"), width = 6))
),width = 4,height=410,solidHeader = TRUE, status = "primary", collapsible = TRUE),
box( title = tags$p(tags$i(class = "fa-solid fa-gifts", style = "font-size: 120%; color: darkred; margin-right: 10px;"), "IASBLUP 功能:",
style = "font-size: 120%; color: black;"),
# icon = tags$i(class = "fa-solid fa-house", style="font-size: 20px"),
fluidRow(column(12,bslib::value_box(title = tags$p("方差组分计算", style = "font-size: 200%;"),
value = tags$p("AI-REML", style = "font-size: 150%;", style = "font-size: 150%;"),
showcase = tags$p(bsicons::bs_icon("shuffle"),style = "font-size: 140%;"),showcase_layout = "left center",
theme = "text-purple", width = 2))),
fluidRow(column(12,bslib::value_box(title = tags$p("遗传参数估计", style = "font-size: 200%;"),
value = tags$p("遗传力和遗传相关", style = "font-size: 140%;"),
showcase = bsicons::bs_icon("calculator"),
showcase_layout = "left center",
theme = bslib::value_box_theme(bg = "white", fg = "#2775b6"), width = 2))
),
fluidRow(
column(12,bslib::value_box(title = tags$p("基于系谱亲缘关系矩阵 BLUP方法", style = "font-size: 200%;"),
value = tags$p("线性混合模型" ,style = "font-size: 140%;"),
showcase = bsicons::bs_icon("list-ol"),
showcase_layout = "left center",
theme = bslib::value_box_theme(bg = "white", fg = "#ce5777"), width = 2))
),
fluidRow(
column(12,bslib::value_box(title = tags$p("基因组预测", style = "font-size: 200%;"),
value = tags$p("基因组亲缘关系矩阵，线性混合模型", style = "font-size: 150%;"),
showcase = bsicons::bs_icon("graph-up-arrow"),
showcase_layout = "left center",theme = "text-success", width = 2))
),width = 4,height=410,solidHeader = TRUE, status = "primary", collapsible = TRUE
),
box(
title = tags$p(tags$i(class = "fa-brands fa-connectdevelop", style = "font-size: 120%; color: darkred; margin-right: 10px;"), "机器学习预测IASML软件",
style = "font-size: 120%; color: black;"),
# icon = tags$i(class = "fa-solid fa-house", style="font-size: 20px"),
fluidRow(
column(12,bslib::value_box(
tags$div(
style = "display: flex; justify-content: center;margin-top: -20px;",
#img(src="logo.jpg", height="60%", width="100%",style="text-align: center;",
img(src = "IASMLlogo.png", width = "395px", height = "230px",
style = "cursor: pointer;",
onclick = "window.location='https://iasbreeding.cn/IASML_zh/'")),
value = tags$p(
tags$a("IASML是一个基于多种机器学习算法预测表型的育种分析平台，提供SVM、 Ridge、 Lasso、 Elastic net、 Decision_tree、 Random_forest、LightGBM、 XGBoost、 Linear、PLS、GBM、CNN、MLP共13种机器学习算法用于表型预测。",
href = "https://iasbreeding.cn/IASML_zh/",
style = "font-size: 135%; text-decoration: none; color: #5e9fb3 ;"),
style = "font-size: 135%;margin-top: 10px;text-align: justify;"
),
showcase_layout = "center",
theme = bslib::value_box_theme(bg = "white", fg = "#b40373"),
width = 2
))#ad9e5f
),width = 4,height=410,solidHeader = TRUE, status = "primary", collapsible = TRUE
)
),
fluidRow(
tags$style(HTML("
.box.box-solid.box-primary>.box-header {
color:#ccccd6;
background:#ccccd6
}
.box.box-solid.box-primary{
border-bottom-color:#666666;
border-left-color:#666666;
border-right-color:#666666;
border-top-color:#666666;
}
")),
box(
title = tags$p(tags$i(class = "fa-brands fa-connectdevelop", style = "font-size: 120%; color: darkred; margin-right: 10px;"), "分子表型MPtools处理软件",
style = "font-size: 120%; color: black;"),
# icon = tags$i(class = "fa-solid fa-house", style="font-size: 20px"),
fluidRow(
column(12,bslib::value_box(
tags$div(
style = "display: flex; justify-content: center;",
#img(src="logo.jpg", height="60%", width="100%",style="text-align: center;",
img(src = "Mptools_logo_zh.png", width = "430px", height = "200px",
style = "cursor: pointer;",
onclick = "window.location='https://iasbreeding.cn/MPtools/'")),
value = tags$p(
tags$a("MPtools 全称是Molecular Phenotypic Tools，是一款专门用于分子表型数据处理的工具。它包括分子表型的数据处理、过滤、校正、分子系谱构建等功能。该软件是基于C++开发。",
href = "https://iasbreeding.cn/MPtools/",
style = "font-size: 135%; text-decoration: none; color: inherit;"),
style = "font-size: 135%;line-height: 1.6;margin-top: 20px;text-align: justify;"
),
showcase_layout = "center",
theme = bslib::value_box_theme(bg = "white", fg = "#ad9e5f"),
width = 2
))),width = 4,height=410,solidHeader = TRUE, status = "primary", collapsible = TRUE
),
box(
title = tags$p(tags$i(class = "fa-brands fa-connectdevelop", style = "font-size: 120%; color: darkred; margin-right: 10px;"), "基因型填充平台IASimpute",
style = "font-size: 120%; color: black;"),
# icon = tags$i(class = "fa-solid fa-house", style="font-size: 20px"),
fluidRow(
column(12,bslib::value_box(
tags$div(
style = "display: flex; justify-content: center;",
#img(src="logo.jpg", height="60%", width="100%",style="text-align: center;",
img(src = "imlogo.jpg", width = "430px", height = "220px",
style = "cursor: pointer;",
onclick = "window.location='https://iasbreeding.cn/IASimpute/'")),
value = tags$p(
tags$a("IASimpute 平台是一款基因型填充工具，支持多种基因型格式。通过填充算法，平台能够精准填充缺失的基因型数据，并进行数据质量控制。适用于牛、鸭等多个物种，帮助科学家加速基因组研究与育种改良。用户可轻松上传数据，快速获得填充结果。",
href = "https://iasbreeding.cn/IASimpute/",
style = "font-size: 135%; text-decoration: none; color: #075cca;"),
style = "font-size: 135%;text-align: justify;"
),
showcase_layout = "center",
theme = bslib::value_box_theme(bg = "white", fg = "#ad9e5f"),
width = 2
))),width = 4,height=410,solidHeader = TRUE, status = "primary", collapsible = TRUE
),
box(
title = tags$p(tags$i(class = "fa-brands fa-connectdevelop", style = "font-size: 120%; color: darkred; margin-right: 10px;"), "育种选配IASmating软件",
style = "font-size: 120%; color: black;"),
# icon = tags$i(class = "fa-solid fa-house", style="font-size: 20px"),
fluidRow(
column(12,bslib::value_box(
tags$div(
style = "display: flex; justify-content: center;",
img(src = "IASmating.jpg", width = "400px", height = "200px",
style = "cursor: pointer;")),
value = tags$p(
tags$a("IASmating 平台是一个育种选配工具，旨在优化农畜繁殖策略。它支持多种选配策略，帮助用户自定义世代避免近交，提高种群的遗传多样性。IASmating 还提供近交系数计算，辅助育种决策，推动智慧农业可持续发展，提升农业生产的质量和效率。GBM、CNN、MLP共13种机器学习算法用于表型预测。",
# href = "https://iasbreeding.cn/IASML_zh/",
style = "font-size: 135%; text-decoration: none; color: inherit;"),
style = "font-size: 135%;"
),
showcase_layout = "center",
theme = bslib::value_box_theme(bg = "white", fg = "#b40373"),
width = 2
))#ad9e5f
),width = 4,height=410,solidHeader = TRUE, status = "primary", collapsible = TRUE
)
)
),
)
)),
#####################Run pedigree BLUP########################
tabPanel( "IASBLUP在线运行",
icon = icon("circle-play"),
sidebarLayout(
sidebarPanel(
fluidRow(
shinydashboard::box(
title = tags$p(tags$i(class = "fa fa-upload", style = "font-size: 100%; color: darkred; margin-right: 10px;"), "数据上传",
style = "font-size: 100%; color: black;"),status = "primary",solidHeader = TRUE,
fluidRow(column(width =8,
tags$script(src="fileInput_text.js"),
fileInput(c("phenotype"),
label = tags$div(HTML(' 上传表型文件 '),
bsButton("q1", label="", icon=icon("question"), style="info", size="small")),
accept = c(
"text/plain",
"text/comma-separated-values,text/plain",
".txt",
".csv",
".xlsx"
),
placeholder = "表型.txt",
buttonLabel = "上传...", # 关键修改：将浏览按钮改为中文
),
), bsPopover("q1", "表型文件需要有表头，表型文件需要包括个体ID号、影响因素（固定效应）、表型值",trigger = "focus"),
column(width = 1,downloadButton("Phenotype_exp", "示例",class = "btn btn-success btn-sm",style="color: #fff; background-color: #20894d; border-color: #20894d;"))),
column(width = 6,uiOutput('dropdown1')),
column(width = 6,uiOutput('dropdown2')),
column(width = 12,uiOutput('multi_select_ui')),
fluidRow(column(width = 8,fileInput(c("pedigree"),
label = tags$div(HTML(' 上传系谱文件'),
bsButton("q2", label="", icon=icon("question"), style="info", size="small")),
accept = c(
"text/plain",
"text/comma-separated-values,text/plain",
".txt",
".csv",
".xlsx"
),
placeholder = "系谱.txt",buttonLabel = "上传..."
)
),
bsPopover("q2", "系谱文件至少三列，前三列必须是个体ID，父亲ID，母亲ID",trigger = "focus"),
column(width = 1,downloadButton("Pedigree_exp", "示例",class = "btn btn-success btn-sm",style="color: #fff; background-color: #20894d; border-color: #20894d"))),
# radioButtons(inputId = "FileType", tags$div(HTML(' Select algorithms:'),
# bsButton("qg99", label="", icon=icon("question"), style="info", size="small")), choices = list("AI-REML"), selected = "AI-REML"),
# bsPopover("qg99", "Select REML algorithms",trigger = "focus"),
fluidRow(
column(width = 8,fileInput(c("genotype"),
label = tags$div(HTML(' 上传基因型文件'),
bsButton("q4", label="", icon=icon("question"), style="info", size="small")),
accept = c(
".bed",
".bim",
".fam"
), multiple = TRUE,
placeholder = "geno.bed, geno.bim, geno.fam", buttonLabel = "上传..."
)
),
bsPopover("q4", "基因型文件支持PLINK二进制文件 (.bed, .bim 和.fam)",trigger = "focus"),
column(width = 2,downloadButton("Genotype_exp", "示例",class = "btn btn-success btn-sm",style="color: #fff; background-color: #20894d; border-color: #20894d"))),width = 12),
shinydashboard::box(
title = tags$p(tags$i(class = "fa fa-bar-chart", style = "font-size: 100%; color: darkred; margin-right: 10px;"), "选择分析模块",
style = "font-size: 100%; color: black;"),status = "primary",solidHeader = TRUE,
h4("选择分析模块", style = "color:#2d6a4f;"),
selectInput("analysis_type", "选择分析类型:",
choices = c("表型汇总", "基于系谱的BLUP", "GBLUP", "ssGBLUP"),
selected = "表型汇总"),
hr(),
actionButton("run_analysis", "运行分析",
style = "color: white; background-color: #2d6a4f; border: none; padding: 10px 20px; font-size: 16px;"),
height = 270,width = 12
),
),width = 4),
mainPanel(
h4("分析结果", style = "color:#2d6a4f;"),
tabsetPanel(
tabPanel(
title = tags$p(tags$i(class = "fa-solid fa-magnifying-glass-chart", style = "font-size: 100%; color: darkred; margin-right: 10px;"), "表型汇总",
style = "font-size: 100%; color: black;"),
h1( tags$p(tags$i(class = "fa fa-kiwi-bird", style = "font-size: 60%; color: #1491a8; margin-right: 6px;"), "表型基本统计",
style = "font-size: 40%; color: black;")),
div(withSpinner(DT::dataTableOutput("pheno_table")), style = "font-size:80%"),
h1( tags$p(tags$i(class = "fa fa-kiwi-bird", style = "font-size: 60%; color: #1491a8; margin-right: 6px;"), "表型分布统计",
style = "font-size: 40%; color: black;")),
div( withSpinner(plotOutput("pheno_plot")), style = "font-size:80%"),width=4
),
tabPanel(
title = tags$p(tags$i(class = "fa-solid fa-square-poll-horizontal", style = "font-size: 100%; color: darkred; margin-right: 10px;"), "方差组分和遗传力",
style = "font-size: 100%; color: black;"),
solidHeader = TRUE,
h1( tags$p(tags$i(class = "fa fa-kiwi-bird", style = "font-size: 60%; color: #1491a8; margin-right: 6px;"), "方差组分计算",
style = "font-size: 40%; color: black;")),
div(withSpinner(DT::dataTableOutput("var_table")), style = "font-size:80%"),
h1( tags$p(tags$i(class = "fa fa-kiwi-bird", style = "font-size: 60%; color: #1491a8; margin-right: 6px;"), "遗传力",
style = "font-size: 40%; color: black;")),
div(withSpinner(DT::dataTableOutput("h2_table")), style = "font-size:80%"),width=4
),
tabPanel(
title = tags$p(tags$i(class = "fa-solid fa-square-poll-horizontal", style = "font-size: 100%; color: darkred; margin-right: 10px;"), "育种值",
style = "font-size: 100%; color: black;"),
solidHeader = TRUE,
h1( tags$p(tags$i(class = "fa fa-kiwi-bird", style = "font-size: 60%; color: #1491a8; margin-right: 6px;"), "固定效应",
style = "font-size: 40%; color: black;")),
div(withSpinner(DT::dataTableOutput("fix_table")), style = "font-size:80%"),
h1( tags$p(tags$i(class = "fa fa-kiwi-bird", style = "font-size: 60%; color: #1491a8; margin-right: 6px;"), "育种值",
style = "font-size: 40%; color: black;")),
div(withSpinner(DT::dataTableOutput("ebv")), style = "font-size:80%"),width=4,
downloadButton("download_ebv", "下载育种值",style="color: #fff; background-color: #337ab7; border-color: #2e6da4")
)
)
)
)
),
tabPanel("下载IASBLUP R包",
icon = icon("cloud-arrow-down"),
# title = HTML("下载IASBLUP R包"),icon = tags$i(class = "fa-solid fa-cloud-arrow-down", style="font-size: 20px;color:#302f4b"),
fluidRow(
column(width = 2,downloadButton("R_pack", "IASbreedingR包",style="color: #fff; background-color: #20894d; border-color: #20894d")),
column(width = 2,downloadButton("Manu", "IASbreeding用户手册",style="color: #fff; background-color: #20894d; border-color: #20894d"))
),
includeMarkdown("Download_README.md")),
tabPanel("下载C++软件",
icon = icon("cloud-arrow-down"),
#tabPanel(title = HTML("下载IASBLUP C++"),icon = tags$i(class = "fa-solid fa-cloud-arrow-down", style="font-size: 20px;color:#302f4b"),
fluidPage(
tags$head(
tags$style(HTML("
.custom-download-button {
color: #fff;
background-color: #20894d;
border: 1px solid #20894d;
font-size: 16px;
font-weight: bold;
}
.custom-download-button:hover {
background-color: #177a40; /* Darker shade for hover */
border-color: #177a40;
}
"))
),
fluidRow(
column(width = 3,
downloadButton("win",
label = tagList(icon("windows", style = "color: #ffffff;"), " Windows version"), class = "custom-download-button"
)
),
column(width = 3,
downloadButton("linux",
label = tagList(icon("linux", style = "color: #ffffff;"), " Linux version"), class = "custom-download-button"
)
#downloadButton('linux', 'Download', class = "butt"),
#tags$head(tags$style(".butt{background-color:#add8e6;} .butt{color: #337ab7;}"))
),
column(width = 3,
downloadButton("mac",
label = tagList(icon("apple", style = "color: #ffffff;"), " MacOS version"),
class = "custom-download-button"
)
)
)
),
includeMarkdown("Download_CPP_README_zh.md")),
tabPanel("关于",
icon = icon("circle-question"),
#title = HTML("关于"),icon = tags$i(class = "fa-solid fa-circle-exclamation", style="font-size: 20px;color:#8a988e"),
includeMarkdown("README.md"))
),
# tags$footer(id = "myFooter",
# shiny::includeHTML("www/footer.html"),
# ),
# 页脚
# 你的内容区
div(class = "container",
span("依托单位：", style = "font-size:30px; color:#6a994e; margin-top: -460px;font-weight: bold;"),
div(class = "row",
div(class = "col-sm-3",
p(style = "color: black;font-size: 18px;font-weight: bold;",
"国家水禽产业技术体系研发中心"),
h2(class = "logo",
img(src = "研发中心.jpg", height = "130", width = "220"))),
div(class = "col-sm-3",
p(style = "color: black;font-size: 18px;font-weight: bold;",
"国家水禽遗传评估中心"),
h2(class = "logo",
img(src = "NWGEC.png", height = "130", width = "220"))),
div(class = "col-sm-3",
p(style = "color: black;font-size: 18px;font-weight: bold;",
"中国农科院北京畜牧兽医研究所"),
h2(class = "logo", style = "margin-left: 90px;",
a(href = "https://ias.caas.cn/", target = "_blank",
img(src = "IAS.png", height = "130", width = "130")))),
div(class = "col-sm-3",
p(style = "color: black;font-size: 18px;font-weight: bold;",
"开发：水禽育种与营养创新团队"),
tags$ul( # 使用 tags$ul() 创建无序列表
tags$li(h4(a(href = "https://github.com/WentaoCai", target = "_blank", "GitHub"))),
tags$li(h4(a(href = "https://scholar.google.com/citations?user=mQCQs9kAAAAJ&hl=en", target = "_blank", "Google Scholar"))),
tags$li(h4(a(href = "https://www.researchgate.net/profile/Wentao-Cai-2", target = "_blank", "ResearchGate"))),
tags$li(h4(a(href = "https://orcid.org/0000-0002-5639-1755", target = "_blank", "ORCID"))),
tags$li(h4("联系方式：蔡文涛caiwentao@caas.cn"))
)
)
)
),
div(class = "footer text-center",
h4("Copyright © 2025 ",
a("大模型与计算育种实验室", href = "https://iasbreeding.cn/us/", target = "_blank"),
"| 水禽育种与营养创新团队 | ",
a("中国农业科学院北京畜牧兽医研究所", href = "https://ias.caas.cn/", target = "_blank"),
", ",
a("京ICP备2024071370号-2", href = "https://beian.miit.gov.cn/#/Integrated/recordQuery", target = "_blank")),
h4("地址：北京市海淀区圆明园西路2号 | 邮编：100193"),
h4("本网站使用R Shiny开发 | 最后更新：2025年6月"),
div(class = "visit-counter",
textOutput("visitorCount")
)
)
# downloadButton("downloadGB.pdf", "Download pdf-file"),
)
)