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ui.R
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library(shinyBS)
shinyUI(
fluidPage(
tags$head(includeHTML(("google-analytics.html"))),
titlePanel(title=div(
img(src="headerN.png", height = 100, width = 100),
span("SoybeanGDB:", style = "font-size:40px;color:white;"),
span("a comprehensive genome database of soybean", style = "font-size:30px;color:white;"),
style = "background-color:#0073B7;margin-left: -15px;margin-right: -15px;margin-top: -20px;margin-bottom: -10px;"
), windowTitle = "Welcome to SoybeanGDB!"),
includeCSS("www/footer.css"),
#includeScript("./www/script.js"),
shinydisconnect::disconnectMessage(
text = "Your session timed out, reload the application!",
refresh = "Reload now",
background = "#f89f43",
colour = "white",
overlayColour = "grey",
overlayOpacity = 0.75,
top = 250,
refreshColour = "brown"
),
#修改全局字体
#tags$style('* {font-size:15px;font-family:sans-serif;}'),
#tags$head(tags$style("#regB {font-size:20px;font-family:sans-serif;}")),
tags$style(type='text/css', ".selectize-input { font-size: 15px;line-height: 15px;font-family:sans-serif; } .selectize-dropdown { font-size: 15px; line-height: 15px; }"),
#tags$style(type='text/css', ".irs-grid-text { font-size: 18pt; }"),
navbarPage(
title = "",
windowTitle = "A comprehensive genome database of soybean",
id = "The_page",
#home
tabPanel(
title = HTML("<strong style='font-size:20px'>Home</strong>"), icon = icon("home"),
Homepage
),
#Search sequence, cds, pro and gff information
navbarMenu(
title = HTML("<strong style='font-size:20px'>Genomes</strong>"),
tabPanel(
title = HTML("<strong style='font-size:20px'>Search by gene IDs</strong>"), icon = icon("id-card"),
sidebarPanel(
width = 3,
tags$style("#BDG_Paste {font-size:15px;font-family:sans-serif;}"),
fixedRow(
column(12,
h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Search by gene IDs</b></font>'),
bsButton("qsgsid", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qsgsid", "Search any one of the 39 soybean genomes by gene IDs", trigger = "focus")
)
),
tags$style(type='text/css', ".selectize-dropdown-content {max-height: 600px; }"),
selectInput("variety_BDG", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Select a genome</b></font>')),
list(`Wild soybean (Glycine soja)` = list("PI 483463", "PI 562565", "PI 549046", "PI 578357", "W05"),
`Improved cultivar (Glycine max)` = list("Zhonghuang 13", "Williams 82", "Lee", "Xu Dou No.1", "Tie Feng No.18", "Ju Xuan No.23", "Wan Dou No.28", "Amsoy",
"Yu Dou No.22", "Jin Dou No.23", "Qi Huang No.34", "Han Dou No.5", "PI 548362",
"Ji Dou No.17", "Dong Nong No.50", "Hei He No.43", "Ke Shan No.1", "Tianlong1", "Hwangkeum"),
`Landrace (Glycine max)` = list("Zhutwinning2", "Zi Hua No.4", "Tong Shan Tian E Dan", "58-161", "PI 398296",
"Zhang Chun Man Cang Jin", "Feng Di Huang", "Tie Jia Si Li Huang", "Shi Sheng Chang Ye"),
`Perennial Glycine` = list("Glycine cyrtoloba", "Glycine dolichocarpa", "Glycine falcata", "Glycine stenophita", "Glycine syndetika", "Glycine tomentella D3"),
`All genomes` = list("All genomes")
) ,
selected = "Zhonghuang 13"
),
conditionalPanel(condition="input.variety_BDG == 'All genomes'",
textInput("BDG_Paste1", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Input a single gene ID</b></font>')), value = "SoyZH13_01G071100"),
),
conditionalPanel(condition="input.variety_BDG != 'All genomes'",
textAreaInput("BDG_Paste", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Input a list of gene model names</b></font>')),
value = "SoyZH13_03G069003\nSoyZH13_03G069001\nSoyZH13_03G069100\nSoyZH13_01G071100", resize = "vertical", height='200px', width = '200%',
placeholder = "The Gene ID must in the database"),
),
shinysky::actionButton("submit_GSID", strong("Submit!",
bsButton("qsgsid1", label="", icon=icon("question"), style="info", size="small")
), styleclass = "success"),
bsPopover("qsgsid1", "Whenever the Gene ID is updated, please click Submit!",
trigger = "focus"),
shinysky::actionButton("clearSERID", strong("Reset"), styleclass = "warning"),
shinysky::actionButton("SERExamID", strong("Load example"), styleclass = "info"),
conditionalPanel(condition="input.submit_GSID != '0'", shinysky::busyIndicator(HTML("<div style='color:red;font-size:30px'>Calculation In progress...</div>"), wait = 0))
),
mainPanel(
width = 9,
fluidRow(
column(3, uiOutput("downloadBDG01")),
column(3, uiOutput("downloadBDG02")),
column(3, uiOutput("downloadBDG03")),
column(3, uiOutput("downloadBDG04"))
),
htmlOutput("geneinfoid_title"),
column(12, DT::dataTableOutput("geneinfoid")),
tags$head(tags$style("#geneinfoid_title{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#geneinfoid{
width = 100%;
max-height: 300px;
}")
),
htmlOutput("geneticIDstructure_title"),
uiOutput("geneticIDstructureif"),
#plotOutput("geneticIDstructure", width = "100%", height = "100px"),
tags$head(tags$style("#geneticIDstructure_title{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
)),
htmlOutput("gene_title_id"),
verbatimTextOutput("gene_id"),
tags$head(tags$style("#gene_title_id{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#gene_id{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("cds_title_id"),
verbatimTextOutput("cds_id"),
tags$head(tags$style("#cds_title_id{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#cds_id{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("cdna_title_id"),
verbatimTextOutput("cdna_id"),
tags$head(tags$style("#cdna_title_id{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#cdna_id{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("pro_title_id"),
shiny::verbatimTextOutput("pro_id"),
tags$head(tags$style("#pro_title_id{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#pro_id{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("Functionaltitle_id"),
column(12,
DT::dataTableOutput("Functional_id")),
tags$head(tags$style("#Functionaltitle_id{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#Functional_id{
width = 100%;
max-height: 300px;
}")
),
htmlOutput("gffinfotitle_id"),
column(12,
DT::dataTableOutput("gffinfo_id")),
tags$head(tags$style("#gffinfotitle_id{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#gffinfo_id{
width = 100%;
max-height: 300px;
}")
),
column(12, br() ),
uiOutput("zhanwei3")
)
),
tabPanel(
title = HTML("<strong style='font-size:20px'>Search by genome location</strong>"), icon = icon("search-location"),
sidebarPanel(
width = 3,
tags$style("#geneinterval {font-size:15px;font-family:sans-serif;}"),
fixedRow(
column(12,
h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Search by genome location</b></font>'),
bsButton("qsgsit", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qsgsit", "Search any one of the 39 soybean genomes by genome location", trigger = "focus")
)
),
tags$style(type='text/css', ".selectize-dropdown-content {max-height: 600px; }"),
selectInput("variety_IT", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Select a genome</b></font>')),
list(`Wild soybean (Glycine soja)` = list("PI 483463", "PI 562565", "PI 549046", "PI 578357", "W05"),
`Improved cultivar (Glycine max)` = list("Zhonghuang 13", "Williams 82", "Lee", "Xu Dou No.1", "Tie Feng No.18", "Ju Xuan No.23", "Wan Dou No.28", "Amsoy",
"Yu Dou No.22", "Jin Dou No.23", "Qi Huang No.34", "Han Dou No.5", "PI 548362",
"Ji Dou No.17", "Dong Nong No.50", "Hei He No.43", "Ke Shan No.1", "Tianlong1", "Hwangkeum"),
`Landrace (Glycine max)` = list("Zhutwinning2", "Zi Hua No.4", "Tong Shan Tian E Dan", "58-161", "PI 398296",
"Zhang Chun Man Cang Jin", "Feng Di Huang", "Tie Jia Si Li Huang", "Shi Sheng Chang Ye"),
`Perennial Glycine` = list("Glycine cyrtoloba", "Glycine dolichocarpa", "Glycine falcata", "Glycine stenophita", "Glycine syndetika", "Glycine tomentella D3") ) ,
selected = "Zhonghuang 13"
),
textInput("geneinterval", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Input a genomic region</b></font>')),
value = "chr1:20260371-20686979"),
shinysky::actionButton("submit_GSIT", strong("Submit!",
bsButton("qsgsit1", label="", icon=icon("question"), style="info", size="small")
), styleclass = "success"),
bsPopover("qsgsit1", "Whenever the genome location is updated, please click Submit!",
trigger = "focus"),
shinysky::actionButton("clearSERIT", strong("Reset"), styleclass = "warning"),
shinysky::actionButton("SERExamIT", strong("Load example"), styleclass = "info"),
conditionalPanel(condition="input.submit_GSIT != '0'", shinysky::busyIndicator(HTML("<div style='color:red;font-size:30px'>Calculation In progress...</div>"), wait = 0))
),
mainPanel(
width = 9,
fluidRow(
column(3, uiOutput("downloadgenesit01")),
column(3, uiOutput("downloadgenesit02")),
column(3, uiOutput("downloadgenesit03")),
column(3, uiOutput("downloadgenesit04"))
#column(3, downloadButton("sequence_IT.txt", "Download Interval Sequence", style = "width:100%;", class = "buttDown")),
#column(3, downloadButton("cdssequence_IT.txt", "Download CDS Sequence", style = "width:100%;", class = "buttDown")),
#column(3, downloadButton("cdnasequence_IT.txt", "Download cDNA Sequence", style = "width:100%;", class = "buttDown")),
#column(3, downloadButton("prosequence_IT.txt", "Download Protein Sequence", style = "width:100%;", class = "buttDown"))
),
htmlOutput("geneinfo_title"),
column(12, DT::dataTableOutput("geneinfo")),
tags$head(tags$style("#geneinfo_title{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#geneinfo{
width = 100%;
max-height: 300px;
}")
),
htmlOutput("geneticITstructure_title"),
uiOutput("geneticITstructureif"),
#plotOutput("geneticITstructure", width = "100%", height = "100px"),
tags$head(tags$style("#geneticITstructure_title{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
)),
htmlOutput("gene_title_it"),
verbatimTextOutput("gene_it"),
tags$head(tags$style("#gene_title_it{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#gene_it{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("cds_title_it"),
verbatimTextOutput("cds_it"),
tags$head(tags$style("#cds_title_it{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#cds_it{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("cdna_title_it"),
verbatimTextOutput("cdna_it"),
tags$head(tags$style("#cdna_title_it{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#cdna_it{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("pro_title_it"),
shiny::verbatimTextOutput("pro_it"),
tags$head(tags$style("#pro_title_it{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#pro_it{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("gffinfotitle_it"),
column(12,
DT::dataTableOutput("gffinfo_it")),
tags$head(tags$style("#gffinfotitle_it{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#gffinfo_it{
width = 100%;
max-height: 300px;
}")
),
htmlOutput("Functional_it_title"),
column(12,
DT::dataTableOutput("Functional_it_id")),
tags$head(tags$style("#Functional_it_title{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#Functional_it_id{
width = 100%;
max-height: 300px;
}")
),
htmlOutput("repeatmasker_title_it"),
column(12, DT::dataTableOutput("repeatmasker")),
column(12, br()),
tags$head(tags$style("#repeatmasker_title_it{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#repeatmasker{
width = 100%;
max-height: 300px;
}")
),
uiOutput("zhanwei2")
)
),
tabPanel(
title = HTML("<strong style='font-size:20px'>Genomic distribution of genes</strong>"),icon = icon("location-arrow"),
sidebarPanel(
width = 3,
tags$style("#GL_Paste {font-size:15px;font-family:sans-serif;}"),
h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Genomic distribution of genes</b></font>'),
bsButton("qGL0", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qGL0", "Visualize genomic distribution of genes", trigger = "focus"),
tags$style(type='text/css', ".selectize-dropdown-content {max-height: 600px; }"),
selectInput("variety_GL", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Select a genome</b></font>')),
list(`Wild soybean (Glycine soja)` = list("PI 483463", "PI 562565", "PI 549046", "PI 578357", "W05"),
`Improved cultivar (Glycine max)` = list("Zhonghuang 13", "Williams 82", "Lee", "Xu Dou No.1", "Tie Feng No.18", "Ju Xuan No.23", "Wan Dou No.28", "Amsoy",
"Yu Dou No.22", "Jin Dou No.23", "Qi Huang No.34", "Han Dou No.5", "PI 548362",
"Ji Dou No.17", "Dong Nong No.50", "Hei He No.43", "Ke Shan No.1", "Tianlong1", "Hwangkeum"),
`Landrace (Glycine max)` = list("Zhutwinning2", "Zi Hua No.4", "Tong Shan Tian E Dan", "58-161", "PI 398296",
"Zhang Chun Man Cang Jin", "Feng Di Huang", "Tie Jia Si Li Huang", "Shi Sheng Chang Ye"),
`Perennial Glycine` = list("Glycine cyrtoloba", "Glycine dolichocarpa", "Glycine falcata", "Glycine stenophita", "Glycine syndetika", "Glycine tomentella D3")),
selected = "Zhonghuang 13"
),
textAreaInput("GL_Paste", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Input a list of gene model names</b></font>')),
value = "SoyZH13_20G124201\nSoyZH13_14G131103\nSoyZH13_10G049500\nSoyZH13_01G054202\nSoyZH13_13G043301\nSoyZH13_10G214500\nSoyZH13_05G061800\nSoyZH13_11G118400\nSoyZH13_02G038800\nSoyZH13_16G155300\nSoyZH13_13G319400\nSoyZH13_19G153500\nSoyZH13_20G135100\nSoyZH13_18G142622\nSoyZH13_12G186900\nSoyZH13_11G123500\nSoyZH13_18G024500\nSoyZH13_20G078300\nSoyZH13_02G231900\nSoyZH13_03G179600",
resize = "vertical", height='200px', width = '200%',
placeholder = "The Gene ID must in the database"),
shinysky::actionButton("GL_sbumit", strong("Submit!",
bsButton("qGL3", label="", icon=icon("question"), style="info", size="small")
), styleclass = "success"),
shinysky::actionButton("cleargl", strong("Reset"), styleclass = "warning"),
shinysky::actionButton("glExam", strong("Load example"), styleclass = "info"),
conditionalPanel(condition="GL_sbumit != '0'", shinysky::busyIndicator(HTML("<div style='color:red;font-size:30px'>Calculation In progress...</div>"), wait = 0)),
bsPopover("qGL3", "Whenever the list of Gene IDs is updated, please click Submit!",
trigger = "focus"),
br(),
numericInput("genelocheight", h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Plot height</b></font>')), value = 1000),
numericInput("genelocwidth", h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Plot width</b></font>')), value = 1000)
),
mainPanel(
width = 9,
br(),
column(6, uiOutput("downloadgeneloc1")),
column(6, uiOutput("downloadgeneloc2")),
#downloadButton("downloadSL.pdf", "Download pdf-file"),
#downloadButton("downloadGL.svg", "Download svg-file"),
uiOutput("genelocplotif"),
#plotOutput("GLplot", height = "800px", width = "100%"),
br(),
br(),
br()
)
),
tabPanel(
title = HTML("<strong style='font-size:20px'>Transcription factors/regulators</strong>"),icon = icon("house-user"),
sidebarPanel(
tags$head(tags$script(HTML('Shiny.addCustomMessageHandler("jsCode",function(message) {eval(message.value);});')),
tags$style(
HTML(
"
.multicol{
-webkit-column-count: 5; /* Chrome, Safari, Opera */
-moz-column-count: 5; /* Firefox */
column-count: 5;
column-gap: 40px;
}
"
) #/ HTML
) #/ style
), #/ head
width = 3,
h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Transcription factors/regulators</b></font>'),
bsButton("qtrf0", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qtrf0", "Genome-wide Prediction and Classification of Soybean Transcription Factors (TF) and Transcriptional Regulators (TR)", trigger = "focus"),
tags$style(type='text/css', ".selectize-dropdown-content {max-height: 600px; }"),
selectInput("variety_trf", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Select a genome</b></font>')),
list(`Wild soybean (Glycine soja)` = list("PI 483463", "PI 562565", "PI 549046", "PI 578357", "W05"),
`Improved cultivar (Glycine max)` = list("Zhonghuang 13", "Williams 82", "Lee", "Xu Dou No.1", "Tie Feng No.18", "Ju Xuan No.23", "Wan Dou No.28", "Amsoy",
"Yu Dou No.22", "Jin Dou No.23", "Qi Huang No.34", "Han Dou No.5", "PI 548362",
"Ji Dou No.17", "Dong Nong No.50", "Hei He No.43", "Ke Shan No.1", "Tianlong1", "Hwangkeum"),
`Landrace (Glycine max)` = list("Zhutwinning2", "Zi Hua No.4", "Tong Shan Tian E Dan", "58-161", "PI 398296",
"Zhang Chun Man Cang Jin", "Feng Di Huang", "Tie Jia Si Li Huang", "Shi Sheng Chang Ye"),
`Perennial Glycine` = list("Glycine cyrtoloba", "Glycine dolichocarpa", "Glycine falcata", "Glycine stenophita", "Glycine syndetika", "Glycine tomentella D3") ),
selected = "Zhonghuang 13"
),
conditionalPanel(condition="ORT_sbumit != '0'", shinysky::busyIndicator(HTML("<div style='color:red;font-size:30px'>Calculation In progress...</div>"), wait = 0))
),
mainPanel(
width = 9,
column(12,htmlOutput("trfaccessions_title")),
column(12,uiOutput("trfaccessions")),
tags$head(tags$style("#trfaccessions_title{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
)),
column(12,br()),
column(12,htmlOutput("trftitle_BDG")),
column(12,DT::dataTableOutput("trf_BDG")),
tags$head(tags$style("#trftitle_BDG{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#trf_BDG{
width = 100%;
max-height: 300px;
}")
),
htmlOutput("description_title_trf"),
verbatimTextOutput("description_trf"),
tags$head(tags$style("#description_title_trf{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#description_trf{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("gene_title_trf"),
verbatimTextOutput("gene_trf"),
tags$head(tags$style("#gene_title_trf{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#gene_trf{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("cds_title_trf"),
verbatimTextOutput("cds_trf"),
tags$head(tags$style("#cds_title_trf{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#cds_trf{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("cdna_title_trf"),
verbatimTextOutput("cdna_trf"),
tags$head(tags$style("#cdna_title_trf{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#cdna_trf{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("pro_title_trf"),
shiny::verbatimTextOutput("pro_trf"),
tags$head(tags$style("#pro_title_trf{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#pro_trf{
width = 100%;
max-height: 300px;
white-space: pre-wrap;
}")
),
htmlOutput("gffinfotitle_trf"),
column(12,
DT::dataTableOutput("gffinfo_trf")),
tags$head(tags$style("#gffinfotitle_trf{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
),
tags$style("#gffinfo_trf{
width = 100%;
max-height: 300px;
}")
),
column(12,br()),
column(12,br())
)
),
#Genome synteny
tabPanel(
title = HTML("<strong style='font-size:20px'>Genome synteny</strong>"),icon = icon("bezier-curve"),
sidebarPanel(
width = 3,
h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Genome synteny</b></font>'),
bsButton("qgsy0", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qgsy0", "Browse syntenic chromosome regions between different soybean genomes.", trigger = "focus"),
tags$style(type='text/css', ".selectize-dropdown-content {max-height: 600px; }"),
selectInput("variety_gsy1", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Choose a reference genome</b></font>')),
c("Zhonghuang 13", "Williams 82"),
selected = "Zhonghuang 13"
),
conditionalPanel(condition="input.variety_gsy1 == 'Zhonghuang 13'",
selectInput("variety_gsy21", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Choose a genome to query</b></font>')),
list(`Wild soybean (Glycine soja)` = list("PI 483463", "PI 562565", "PI 549046", "PI 578357", "W05"),
`Improved cultivar (Glycine max)` = list("Williams 82", "Lee", "Xu Dou No.1", "Tie Feng No.18", "Ju Xuan No.23", "Wan Dou No.28", "Amsoy",
"Yu Dou No.22", "Jin Dou No.23", "Qi Huang No.34", "Han Dou No.5", "PI 548362",
"Ji Dou No.17", "Dong Nong No.50", "Hei He No.43", "Ke Shan No.1", "Tianlong1", "Hwangkeum"),
`Landrace (Glycine max)` = list("Zhutwinning2", "Zi Hua No.4", "Tong Shan Tian E Dan", "58-161", "PI 398296",
"Zhang Chun Man Cang Jin", "Feng Di Huang", "Tie Jia Si Li Huang", "Shi Sheng Chang Ye"),
`Perennial Glycine` = list("Glycine cyrtoloba", "Glycine falcata", "Glycine stenophita", "Glycine syndetika", "Glycine tomentella D3") ),
selected = "W05"
)
),
conditionalPanel(condition="input.variety_gsy1 == 'Williams 82'",
selectInput("variety_gsy22", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Choose a genome to query</b></font>')),
list(`Wild soybean (Glycine soja)` = list("PI 483463", "PI 562565", "PI 549046", "PI 578357", "W05"),
`Improved cultivar (Glycine max)` = list("Zhonghuang 13", "Lee", "Xu Dou No.1", "Tie Feng No.18", "Ju Xuan No.23", "Wan Dou No.28", "Amsoy",
"Yu Dou No.22", "Jin Dou No.23", "Qi Huang No.34", "Han Dou No.5", "PI 548362",
"Ji Dou No.17", "Dong Nong No.50", "Hei He No.43", "Ke Shan No.1", "Tianlong1", "Hwangkeum"),
`Landrace (Glycine max)` = list("Zhutwinning2", "Zi Hua No.4", "Tong Shan Tian E Dan", "58-161", "PI 398296",
"Zhang Chun Man Cang Jin", "Feng Di Huang", "Tie Jia Si Li Huang", "Shi Sheng Chang Ye"),
`Perennial Glycine` = list("Glycine cyrtoloba", "Glycine falcata", "Glycine stenophita", "Glycine syndetika", "Glycine tomentella D3") ),
selected = "W05"
)
),
selectInput("variety_gsy3", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Choose a chromosome</b></font>')),
c(paste0("chr", 1:20)),
selected = "chr1"
),
conditionalPanel(condition="submit_gsy != '0'", shinysky::busyIndicator(HTML("<div style='color:red;font-size:30px'>Calculation In progress...</div>"), wait = 0)),
shinysky::actionButton("submit_gsy", strong("Submit!"), styleclass = "success")
),
mainPanel(
width = 9,
uiOutput("zhanwei5"),
column(12,htmlOutput("gsy_BDG_title")),
column(12,DT::dataTableOutput("gsy_BDG")),
tags$head(tags$style("#trfaccessions_title{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
)),
column(12,htmlOutput("genomedata1_title")),
column(12,DT::dataTableOutput("genomedata1")),
tags$head(tags$style("#trfaccessions_title{color: red;
font-style: bold;
font-size: 18px;
font-family:Times New Roman;
}"
)),
column(12,htmlOutput("genomedata2_title")),
column(12,DT::dataTableOutput("genomedata2")),
column(12,br()),
column(12,br())
)
),
#Structural variations
tabPanel(
title = HTML("<strong style='font-size:20px'>Structural variations</strong>"), icon = icon("sliders-h"),
sidebarPanel(
width = 3,
h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Structural variations</b></font>'),
bsButton("qgsv0", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qgsv0", "Browse structural variations identified between different soybean genomes.", trigger = "focus"),
tags$style(type='text/css', ".selectize-dropdown-content {max-height: 600px; }"),
selectInput("variety_gsv1", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Choose a reference genome</b></font>')),
c("Zhonghuang 13", "Williams 82"),
selected = "Zhonghuang 13"
),
conditionalPanel(condition="input.variety_gsv1 == 'Zhonghuang 13'",
selectInput("variety_gsv21", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Choose a genome to query</b></font>')),
list(`Wild soybean (Glycine soja)` = list("PI 483463", "PI 562565", "PI 549046", "PI 578357", "W05"),
`Improved cultivar (Glycine max)` = list("Williams 82", "Lee", "Xu Dou No.1", "Tie Feng No.18", "Ju Xuan No.23", "Wan Dou No.28", "Amsoy",
"Yu Dou No.22", "Jin Dou No.23", "Qi Huang No.34", "Han Dou No.5", "PI 548362",
"Ji Dou No.17", "Dong Nong No.50", "Hei He No.43", "Ke Shan No.1", "Tianlong1", "Hwangkeum"),
`Landrace (Glycine max)` = list("Zhutwinning2", "Zi Hua No.4", "Tong Shan Tian E Dan", "58-161", "PI 398296",
"Zhang Chun Man Cang Jin", "Feng Di Huang", "Tie Jia Si Li Huang", "Shi Sheng Chang Ye"),
`Perennial Glycine` = list("Glycine cyrtoloba", "Glycine falcata", "Glycine stenophita", "Glycine syndetika", "Glycine tomentella D3") ),
selected = "W05"
),
),
conditionalPanel(condition="input.variety_gsv1 == 'Williams 82'",
selectInput("variety_gsv22", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Choose a genome to query</b></font>')),
list(`Wild soybean (Glycine soja)` = list("PI 483463", "PI 562565", "PI 549046", "PI 578357", "W05"),
`Improved cultivar (Glycine max)` = list("Zhonghuang 13", "Lee", "Xu Dou No.1", "Tie Feng No.18", "Ju Xuan No.23", "Wan Dou No.28", "Amsoy",
"Yu Dou No.22", "Jin Dou No.23", "Qi Huang No.34", "Han Dou No.5", "PI 548362",
"Ji Dou No.17", "Dong Nong No.50", "Hei He No.43", "Ke Shan No.1", "Tianlong1", "Hwangkeum"),
`Landrace (Glycine max)` = list("Zhutwinning2", "Zi Hua No.4", "Tong Shan Tian E Dan", "58-161", "PI 398296",
"Zhang Chun Man Cang Jin", "Feng Di Huang", "Tie Jia Si Li Huang", "Shi Sheng Chang Ye"),
`Perennial Glycine` = list("Glycine cyrtoloba", "Glycine falcata", "Glycine stenophita", "Glycine syndetika", "Glycine tomentella D3") ),
selected = "W05"
),
),
selectInput("variety_gsv3", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Choose a chromosome</b></font>')),
c(paste0("chr", 1:20)),
selected = "chr1"
),
conditionalPanel(condition="submit_gsv != '0'", shinysky::busyIndicator(HTML("<div style='color:red;font-size:30px'>Calculation In progress...</div>"), wait = 0)),
shinysky::actionButton("submit_gsv", strong("Submit!"), styleclass = "success")
),
mainPanel(
uiOutput("genestructure_tab_show")
# tabsetPanel(id = "genestructure_tab",
# tabPanel("Duplication",
# fixedRow(
# DT::dataTableOutput("dupresult"),
# column(12,htmlOutput("dupdata1_title")),
# column(12,DT::dataTableOutput("dupdata1")),
# tags$head(tags$style("#trfaccessions_title{color: red;
# font-style: bold;
# font-size: 18px;
# font-family:Times New Roman;
# }"
# )),
# column(12,htmlOutput("dupdata2_title")),
# column(12,DT::dataTableOutput("dupdata2")))
#
# ),
#
# tabPanel("Inversion",
# fixedRow(
# DT::dataTableOutput("invresult"),
# column(12,htmlOutput("invdata1_title")),
# column(12,DT::dataTableOutput("invdata1")),
# tags$head(tags$style("#trfaccessions_title{color: red;
# font-style: bold;
# font-size: 18px;
# font-family:Times New Roman;
# }"
# )),
# column(12,htmlOutput("invdata2_title")),
# column(12,DT::dataTableOutput("invdata2")))
# ),
#
# tabPanel("Tandem repeat",
# fixedRow(
# DT::dataTableOutput("tdmresult"),
# column(12,htmlOutput("tdmdata1_title")),
# column(12,DT::dataTableOutput("tdmdata1")),
# tags$head(tags$style("#trfaccessions_title{color: red;
# font-style: bold;
# font-size: 18px;
# font-family:Times New Roman;
# }"
# )),
# column(12,htmlOutput("tdmdata2_title")),
# column(12,DT::dataTableOutput("tdmdata2")))
# ),
#
# tabPanel("Translocation",
# fixedRow(
# DT::dataTableOutput("transresult"),
# column(12,htmlOutput("transdata1_title")),
# column(12,DT::dataTableOutput("transdata1")),
# tags$head(tags$style("#trfaccessions_title{color: red;
# font-style: bold;
# font-size: 18px;
# font-family:Times New Roman;
# }"
# )),
# column(12,htmlOutput("transdata2_title")),
# column(12,DT::dataTableOutput("transdata2")))
# ),
#
# tabPanel("Deletion",
# fixedRow(
# DT::dataTableOutput("delresult"),
# column(12,htmlOutput("deldata1_title")),
# column(12,DT::dataTableOutput("deldata1")),
# tags$head(tags$style("#trfaccessions_title{color: red;
# font-style: bold;
# font-size: 18px;
# font-family:Times New Roman;
# }"
# )),
# column(12,htmlOutput("deldata2_title")),
# column(12,DT::dataTableOutput("deldata2")))
# ),
#
# tabPanel("Insertion",
# fixedRow(
# DT::dataTableOutput("insresult"),
# column(12,htmlOutput("insdata1_title")),
# column(12,DT::dataTableOutput("insdata1")),
# tags$head(tags$style("#trfaccessions_title{color: red;
# font-style: bold;
# font-size: 18px;
# font-family:Times New Roman;
# }"
# )),
# column(12,htmlOutput("insdata2_title")),
# column(12,DT::dataTableOutput("insdata2")))
# ),
# br()
# )
)
)
),
# JBrowse
tabPanel(
title = HTML("<strong style='font-size:20px'>JBrowse</strong>"), icon = icon("list"),
h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>JBrowse of 39 soybean genomes</b></font>'),
bsButton("qjb1", label="", icon=icon("question"), style="info", size="small")),
bsPopover("qjb1", "Click the name of a soybean genome to view in JBrowse", trigger = "focus"),
DT::dataTableOutput('JBrowsetable'),
br()
),
navbarMenu(
title = HTML("<strong style='font-size:20px'>SNPs</strong>"),
# Genome browse
tabPanel(
title = HTML("<strong style='font-size:20px'>Browse</strong>"), icon = icon("folder-open"),
tabsetPanel(id = "Browse_key",
tabPanel(HTML("<strong style='font-size:18px'>Information of 2898 soybean accessions</strong>"),
sidebarPanel(
#text input
tags$style("#regB {font-size:15px;font-family:sans-serif;}"),
width = 3,
tags$div(h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Browse SNPs</b></font>'),
bsButton("qgbv", label="", icon=icon("question"), style="info", size="small"))),
bsPopover("qgbv", "For a specified genomic region or gene model, all the SNPs among user-selected soybean accessions were extracted and subjected to genome browser visualization", trigger = "focus"),
textInput("regB", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Genomic region</b></font>'),
bsButton("q6", label="", icon=icon("question"), style="info", size="small")),
value = "chr1:29765419-29793053"),
bsPopover("q6", "A genomic region can be determined by chromosome positions or gene locus. For example, chr1:29765419-29793053 or SoyZH13_01G225600.",
trigger = "focus"),
shinysky::actionButton("submit_browse", strong("Submit!",
bsButton("q7", label="", icon=icon("question"), style="info", size="small")
), width = "90%", styleclass = "success"),
bsPopover("q7", "Whenever the genomic region is updated, please click Submit!",
trigger = "focus"),
shinysky::actionButton("clearGB", strong("Reset"), styleclass = "warning"),
shinysky::actionButton("GBExam", strong("Load example"), styleclass = "info"),
conditionalPanel(condition="input.submit_browse != '0'", shinysky::busyIndicator(HTML("<div style='color:red;font-size:30px'>Calculation In progress...</div>"), wait = 0)),
sliderInput(inputId = "GBUP", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Upstream (bp)</b></font>'),
bsButton("qg2", label="", icon=icon("question"), style="info", size="small")
), min = 0, max = 50000, value = 0, ticks = FALSE),
bsPopover("qg2", "Extend the input genomic region to its upstream.",
trigger = "focus"),
sliderInput("GBDOWN", h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Downstream (bp)</b></font>'),
bsButton("qg4", label="", icon=icon("question"), style="info", size="small")
), min = 0, max = 50000, value = 0, ticks = FALSE),
bsPopover("qg4", "Extend the input genomic region to its downstream.", trigger = "focus"),
shinyWidgets::multiInput("mychooserB", h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Select soybean accessions</b></font>'),
bsButton("qg3", label="", icon=icon("question"), style="info", size="small")),
choices = all.soya.cho,
selected = all.soya.cho,
width = 800,
options = list(
enable_search = TRUE,
non_selected_header = "Choose from:",
selected_header = "You have selected:"
)
),
bsPopover("qg3", "Only the chosen soybean accessions will be used.", trigger = "focus"),
fluidRow(
column(6, actionButton("browsenone1", strong("Deselect all"), width = "100%", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")),
column(6, actionButton("browseall1", strong("Select all"), width = "100%", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
),
shinyWidgets::multiInput("GB_mut_group", h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Mutation effect</b></font>'),
bsButton("qg1", label="", icon=icon("question"), style="info", size="small")),
choices = mutationtypes,
selected = mutationtypes,
width = 800,
options = list(
enable_search = TRUE,
non_selected_header = "Choose from:",
selected_header = "You have selected:"
)
),
bsPopover("qg1", "Only SNPs with selected mutation effects will be used.", trigger = "focus"),
fluidRow(
column(6, actionButton("browsenone2", strong("Deselect all"), width = "100%", style="color: #fff; background-color: #337ab7; border-color: #2e6da4")),
column(6, actionButton("browseall2", strong("Select all"), width = "100%", style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
)
),
mainPanel(
width = 9,
fluidRow(
column(4, uiOutput("downloadBro01")),
column(4, uiOutput("downloadBro02")),
column(4, uiOutput("downloadBro03"))
#column(4, downloadButton("downloadsnp.txt", style = "width:100%;", "Download genotype data", class = "buttDown")),
#column(4, downloadButton("downloadsnpInfo.txt", style = "width:100%;", "Download SNPs information", class = "buttDown")),
#column(4, downloadButton("downloadGB.pdf", style = "width:100%;", "Download pdf-file", class = "buttDown")),
#tags$style(".buttDown{background-color:black; color: white; font-size: 16px;}")
),
plotly::plotlyOutput("gbrowser", height = '600px', width = '100%')
)
),
tabPanel(HTML("<strong style='font-size:18px'>Information of 481soybean accessions</strong>"),
sidebarPanel(
#text input
tags$style("#regB82 {font-size:15px;font-family:sans-serif;}"),
width = 3,
tags$div(h4(HTML('<i class="fa fa-circle" aria-hidden="true"></i> <font size="4" color="red"><b>Browse SNPs</b></font>'),
bsButton("qgbv82", label="", icon=icon("question"), style="info", size="small"))),
bsPopover("qgbv82", "For a specified genomic region or gene model, all the SNPs among user-selected soybean accessions were extracted and subjected to genome browser visualization", trigger = "focus"),
textInput("regB82", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Genomic region</b></font>'),
bsButton("q682", label="", icon=icon("question"), style="info", size="small")),
value = "chr15:1000000-1011111"),
bsPopover("q682", "A genomic region can be determined by chromosome positions or gene locus. For example, chr15:1000000-1011111 or Glyma.01G000050.",
trigger = "focus"),
shinysky::actionButton("submit_browse82", strong("Submit!",
bsButton("q782", label="", icon=icon("question"), style="info", size="small")
), width = "90%", styleclass = "success"),
bsPopover("q782", "Whenever the genomic region is updated, please click Submit!",
trigger = "focus"),
shinysky::actionButton("clearGB82", strong("Reset"), styleclass = "warning"),
shinysky::actionButton("GBExam82", strong("Load example"), styleclass = "info"),
conditionalPanel(condition="input.submit_browse82 != '0'", shinysky::busyIndicator(HTML("<div style='color:red;font-size:30px'>Calculation In progress...</div>"), wait = 0)),
sliderInput(inputId = "GBUP82", label = h4(HTML('<i class="fa fa-play" aria-hidden="true"></i> <font size="4" color="red"><b>Upstream (bp)</b></font>'),