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ui.R
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# ###########################################################
# # This file contain UI widgets. ##
# ###########################################################
####################
#pain
###################
pain_panel <- tabPanel(
titlePanel(h4("BPS")),
div(id="sidePanelGroupCmprsn_pain",sidebarPanel(
width = 2,
actionButton(inputId = "completeDATA_pain", label = "Complete Data",icon = icon("play-circle")),
h6("OR", align = "center"),
div(id = "geneNames_pain_form",selectizeInput(
'geneNames_pain',
label = 'Subset',
choices = "",
selected = NULL , multiple = TRUE,
options = list(maxItems = 10,'plugins' = list('remove_button'),
'create' = TRUE,
'persist' = FALSE)
)),
hr(style = "border-color: grey"),
fluidRow(column(12,numericInput("width_Pain", "Plot Width", min = 8, max = 80, value = 8))),
fluidRow(column(12,numericInput("height_Pain", "Plot Height", min = 8, max = 80, value = 8))),
)
),
mainPanel(
tabsetPanel(type = "tabs",
####################
#Tables
###################
tabPanel("Tables",
tabsetPanel(type = "tabs",
######Raw Read counts######
tabPanel("Read Counts",
fluidRow(
#column(1,offset = 0),
column(12,align="center",DT::dataTableOutput("painTable")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; padding: 10px;')
)),
######edgeR results######
tabPanel("edgeR result (all genes)",
fluidRow(
column(1,offset = 0),
column(11,align="center",DT::dataTableOutput("painTable_edger")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; padding: 10px;')
)),
######edgeR results(DEGs genes onyl)######
tabPanel("edgeR result (DEGs only)",
fluidRow(style = "font-size: 80%",
column(1,offset = 0),
column(11,align="center",DT::dataTableOutput("painTable_edger_degs")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; ,padding: 10px;')
))
)
),
####################
#Plots
###################
tabPanel("Plots",
tabsetPanel(type = "tabs",
######Volcano Plots######
tabPanel("Volcano Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_volcanoPain", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("volcanoPain")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;padding: 10px;'),
),
),
# ######Box Plots######
tabPanel("Box Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_boxplot_pain", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("boxplot_pain")%>% withSpinner(color="#0dc5c1")),
),
),
#######Line Plots######
tabPanel("Line Plot",
fluidRow(
column(1,offset = 0),
column(11,plotlyOutput("lineplot_pain")%>% withSpinner(color="#0dc5c1")),
)
)
)
),
####################
#Enrichment results
###################
tabPanel("GO Enrichment Plots",
tabsetPanel(type = "tabs",
# ######GSEA######
tabPanel("GSEA Ridge Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_gsea_ridgePlot_pain", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("gsea_ridgePlot_pain")%>% withSpinner(color="#0dc5c1")),
)
),
######GO ORA Treemap Plot######
tabPanel("ORA Treemap",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_goORATreemap_pain", label = " .pdf"))
),
br(),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("goORATreemap_pain")%>% withSpinner(color="#0dc5c1")),
)),
######GO ORA Interactive Plot######
tabPanel("ORA COW Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_goORA_Cowplot_pain", label = " .pdf")),
column(4,offset = 0),
column(2,disabled(actionButton(inputId = "makeMeInteractivebtn_pain", label = "Interactive Plot", icon = icon("play-circle"))),),
column(1,offset = 0),
column(2,actionButton(inputId = "showSideBarPanel_pain", label = "Show Sidebar Panel", icon = icon("play-circle")),)
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("goORA_Cowplot_pain")%>% withSpinner(color="#0dc5c1")),
),
br(), br(),br(),br(),br(),
br(), br(),br(),br(),br(),
br(), br(),br(),br(),br(),
fluidRow(
plotOutput("interactiveGoPlot_pain")
),
)
)
)
)
)
)
####################
#oab
###################
oab_panel <- tabPanel(
titlePanel(h4("DO")),
div(id="sidePanelGroupCmprsn_OAB",sidebarPanel(
width = 2,
actionButton(inputId = "completeDATA_OAB", label = "Complete Data",icon = icon("play-circle")),
h6("OR", align = "center"),
div(id = "geneNames_OAB_form",selectizeInput(
'geneNames_OAB',
label = 'Subset',
choices = "",
selected = NULL , multiple = TRUE,
options = list(maxItems = 10,'plugins' = list('remove_button'),
'create' = TRUE,
'persist' = FALSE)
)),
hr(style = "border-color: grey"),
fluidRow(column(12,numericInput("width_OAB", "Plot Width", min = 8, max = 80, value = 8))),
fluidRow(column(12,numericInput("height_OAB", "Plot Height", min = 8, max = 80, value = 8))),
)
),
mainPanel(
tabsetPanel(type = "tabs",
####################
#Tables
###################
tabPanel("Tables",
tabsetPanel(type = "tabs",
######Raw Read counts######
tabPanel("Read Counts",
fluidRow(style = "font-size: 85%",
column(12,align="center",DT::dataTableOutput("oabTable")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; padding: 10px;')
)),
######edgeR results######
tabPanel("edgeR result (all genes)",
fluidRow(
column(1,offset = 0),
column(11,align="center",DT::dataTableOutput("oabTable_edger")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; padding: 10px;')
)),
######edgeR results(DEGs genes onyl)######
tabPanel("edgeR result (DEGs only)",
fluidRow(style = "font-size: 80%",
column(1,offset = 0),
column(11,align="center",DT::dataTableOutput("oabTable_edger_degs")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; ,padding: 10px;')
))
)
),
####################
#Plots
###################
tabPanel("Plots",
tabsetPanel(type = "tabs",
######Volcano Plots######
tabPanel("Volcano Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_volcano_oab", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("volcano_oab")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;padding: 10px;'),
),
),
# ######Box Plots######
tabPanel("Box Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_boxplot_OAB", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("boxplot_OAB")%>% withSpinner(color="#0dc5c1")),
),
),
#######Line Plots######
tabPanel("Line Plot",
fluidRow(
column(1,offset = 0),
column(11,plotlyOutput("lineplot_OAB")%>% withSpinner(color="#0dc5c1")),
)
)
)
),
####################
#Enrichment results
###################
tabPanel("GO Enrichment Plots",
tabsetPanel(type = "tabs",
# ######GSEA######
tabPanel("GSEA Ridge Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_gsea_ridgePlot_OAB", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("gsea_ridgePlot_OAB")%>% withSpinner(color="#0dc5c1")),
)
),
######GO ORA Treemap Plot######
tabPanel("ORA Treemap",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_goORATreemap_OAB", label = " .pdf"))
),
br(),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("goORATreemap_OAB")%>% withSpinner(color="#0dc5c1")),
)
)
,
######GO ORA Interactive Plot######
tabPanel("ORA COW Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_goORA_Cowplot_OAB", label = " .pdf")),
column(4,offset = 0),
column(2,disabled(actionButton(inputId = "makeMeInteractivebtn_OAB", label = "Interactive Plot", icon = icon("play-circle"))),),
column(1,offset = 0),
column(2,actionButton(inputId = "showSideBarPanel_OAB", label = "Show Sidebar Panel", icon = icon("play-circle")),)
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("goORA_Cowplot_OAB")%>% withSpinner(color="#0dc5c1")),
),
br(), br(),br(),br(),br(),
br(), br(),br(),br(),br(),
br(), br(),br(),br(),br(),
fluidRow(
plotOutput("interactiveGoPlot_OAB")
),
)
)
)
)
)
)
####################
#AC
###################
AC_panel <- tabPanel(
titlePanel(h4("UA")),
div(id="sidePanelGroupCmprsn_AC",sidebarPanel(
width = 2,
actionButton(inputId = "completeDATA_AC", label = "Complete Data",icon = icon("play-circle")),
h6("OR", align = "center"),
div(id = "geneNames_AC_form",selectizeInput(
'geneNames_AC',
label = 'Subset',
choices = "",
selected = NULL , multiple = TRUE,
options = list(maxItems = 10,'plugins' = list('remove_button'),
'create' = TRUE,
'persist' = FALSE)
)),
hr(style = "border-color: grey"),
fluidRow(column(12,numericInput("width_AC", "Plot Width", min = 8, max = 80, value = 8))),
fluidRow(column(12,numericInput("height_AC", "Plot Height", min = 8, max = 80, value = 8))),
)
),
mainPanel(
tabsetPanel(type = "tabs",
####################
#Tables
###################
tabPanel("Tables",
tabsetPanel(type = "tabs",
######Raw Read counts######
tabPanel("Read Counts",
fluidRow(style = "font-size: 85%",
#column(1,offset = 0),
column(12,align="center",DT::dataTableOutput("ACTable")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; padding: 10px;')
)),
######edgeR results######
tabPanel("edgeR result (all genes)",
fluidRow(
column(1,offset = 0),
column(11,align="center",DT::dataTableOutput("ACTable_edger")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; padding: 10px;')
)),
######edgeR results(DEGs genes onyl)######
tabPanel("edgeR result (DEGs only)",
fluidRow(style = "font-size: 80%",
column(1,offset = 0),
column(11,align="center",DT::dataTableOutput("ACTable_edger_degs")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; ,padding: 10px;')
))
)
),
####################
#Plots
###################
tabPanel("Plots",
tabsetPanel(type = "tabs",
######Volcano Plots######
tabPanel("Volcano Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_volcano_AC", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("volcano_AC")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;padding: 10px;'),
),
),
# ######Box Plots######
tabPanel("Box Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_boxplot_AC", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("boxplot_AC")%>% withSpinner(color="#0dc5c1")),
),
),
#######Line Plots######
tabPanel("Line Plot",
fluidRow(
column(1,offset = 0),
column(11,plotlyOutput("lineplot_AC")%>% withSpinner(color="#0dc5c1")),
)
)
)
),
####################
#Enrichment results
###################
tabPanel("GO Enrichment Plots",
tabsetPanel(type = "tabs",
# ######GSEA######
tabPanel("GSEA Ridge Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_gsea_ridgePlot_AC", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("gsea_ridgePlot_AC")%>% withSpinner(color="#0dc5c1")),
)
),
######GO ORA Treemap Plot######
tabPanel("ORA Treemap",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_goORATreemap_AC", label = " .pdf"))
),
br(),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("goORATreemap_AC")%>% withSpinner(color="#0dc5c1")),
)
),
######GO ORA Interactive Plot######
tabPanel("ORA COW Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_goORA_Cowplot_AC", label = " .pdf")),
column(4,offset = 0),
column(2,disabled(actionButton(inputId = "makeMeInteractivebtn_AC", label = "Interactive Plot", icon = icon("play-circle"))),),
column(1,offset = 0),
column(2,actionButton(inputId = "showSideBarPanel_AC", label = "Show Sidebar Panel", icon = icon("play-circle")),)
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("goORA_Cowplot_AC")%>% withSpinner(color="#0dc5c1")),
),
br(), br(),br(),br(),br(),
br(), br(),br(),br(),br(),
br(), br(),br(),br(),br(),
fluidRow(
plotOutput("interactiveGoPlot_AC")
),
)
)
)
)
)
)
####################
#BOO
###################
BOO_panel <- tabPanel(
titlePanel(h4("BOO")),
div(id="sidePanelGroupCmprsn_BOO",sidebarPanel(
width = 2,
actionButton(inputId = "completeDATA_BOO", label = "Complete Data",icon = icon("play-circle")),
h6("OR", align = "center"),
div(id = "geneNames_BOO_form",selectizeInput(
'geneNames_BOO',
label = 'Subset',
choices = "",
selected = NULL , multiple = TRUE,
options = list(maxItems = 10,'plugins' = list('remove_button'),
'create' = TRUE,
'persist' = FALSE)
)),
hr(style = "border-color: grey"),
fluidRow(column(12,numericInput("width_BOO", "Plot Width", min = 8, max = 80, value = 8))),
fluidRow(column(12,numericInput("height_BOO", "Plot Height", min = 8, max = 80, value = 8))),
)
),
mainPanel(
tabsetPanel(type = "tabs",
####################
#Tables
###################
tabPanel("Tables",
tabsetPanel(type = "tabs",
######Raw Read counts######
tabPanel("Read Counts",
fluidRow(style = "font-size: 85%",
#column(1,offset = 0),
column(12,align="center",DT::dataTableOutput("BOOTable")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; padding: 10px;')
)),
######edgeR results######
tabPanel("edgeR result (all genes)",
fluidRow(
column(1,offset = 0),
column(11,align="center",DT::dataTableOutput("BOOTable_edger")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; padding: 10px;')
)),
######edgeR results(DEGs genes onyl)######
tabPanel("edgeR result (DEGs only)",
fluidRow(style = "font-size: 80%",
column(1,offset = 0),
column(11,align="center",DT::dataTableOutput("BOOTable_edger_degs")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;border:1px solid; ,padding: 10px;')
))
)
),
####################
#Plots
###################
tabPanel("Plots",
tabsetPanel(type = "tabs",
######Volcano Plots######
tabPanel("Volcano Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_volcano_BOO", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("volcano_BOO")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px;padding: 10px;'),
),
),
# ######Box Plots######
tabPanel("Box Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_boxplot_BOO", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("boxplot_BOO")%>% withSpinner(color="#0dc5c1")),
),
),
#######Line Plots######
tabPanel("Line Plot",
fluidRow(
column(1,offset = 0),
column(11,plotlyOutput("lineplot_BOO")%>% withSpinner(color="#0dc5c1")),
)
)
)
),
####################
#Enrichment results
###################
tabPanel("GO Enrichment Plots",
tabsetPanel(type = "tabs",
# ######GSEA######
tabPanel("GSEA Ridge Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_gsea_ridgePlot_BOO", label = " .pdf"))
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("gsea_ridgePlot_BOO")%>% withSpinner(color="#0dc5c1")),
)
),
######GO ORA Treemap Plot######
tabPanel("ORA Treemap",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_goORATreemap_BOO", label = " .pdf"))
),
br(),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("goORATreemap_BOO")%>% withSpinner(color="#0dc5c1")),
)
)
,
######GO ORA Interactive Plot######
tabPanel("ORA COW Plot",
br(),
fluidRow(
column(2,downloadButton(outputId = "down_goORA_Cowplot_BOO", label = " .pdf")),
column(4,offset = 0),
column(2,disabled(actionButton(inputId = "makeMeInteractivebtn_BOO", label = "Interactive Plot", icon = icon("play-circle"))),),
column(1,offset = 0),
column(2,actionButton(inputId = "showSideBarPanel_BOO", label = "Show Sidebar Panel", icon = icon("play-circle")),)
),
fluidRow(
column(1,offset = 0),
column(11,plotOutput("goORA_Cowplot_BOO")%>% withSpinner(color="#0dc5c1")),
),
br(), br(),br(),br(),br(),
br(), br(),br(),br(),br(),
br(), br(),br(),br(),br(),
fluidRow(
plotOutput("interactiveGoPlot_BOO")
),
)
)
)
)
)
)
####################
#goEnrichment_panel
###################
goEnrichment_panel <- tabPanel(
titlePanel(h4("Functional Enrichment Exploration")),
div(id="sidePanelGO_enrich",sidebarPanel(
width = 2,
selectizeInput(
'groupName',
label = 'Select Group',
choices = c("BPS vs Control","DO vs Control","UA vs Control","BOO vs Control"),
selected = "BPS vs Control"
),
selectizeInput(
'enrichmentType',
label = 'Enrichment Type',
choices = c("ORA","GSEA"),
selected = "ORA"
),
selectizeInput(
'goTermName',
label = 'Select GO Term',
choices = "",
selected = NULL
),
actionButton(inputId = "plotVolcanoFor_goTerm", label = "Plot",icon = icon("play-circle")),
hr(style = "border-color: grey"),
fluidRow(column(12,numericInput("width_goTerm", "Plot Width", min = 8, max = 80, value = 8))),
fluidRow(column(12,numericInput("height_goTerm", "Plot Height", min = 8, max = 80, value = 8))),
downloadButton(outputId = "down_volcanoGoTerm", label = " Download")
)
),
mainPanel(fluidRow(
column(1,offset = 0),
column(11,plotOutput("volcano_plot_ForGOTerm")%>% withSpinner(color="#0dc5c1")),
),
br(),br(),br(),
fluidRow(
column(12,align="center",DT::dataTableOutput("table_ForGOTerm")%>% withSpinner(color="#0dc5c1"), style='margin-bottom:30px; padding: 10px;')
)
)
)
##########################################################
# about ##
###########################################################
about <- tabPanel(
titlePanel(h4("About")),
# General info.
tabPanel(
"Overview",
tags$h2("About LUTD-Base"),
tags$p(HTML("LUTD-Base is an easy, interactive, and user-friendly shiny
based web application that allows the other researcher to
deeply explore the bulk RNA-Seq data, differential expression,
functional enrichment analysis results, etc. from multiple
LUTD related studies carried out by our group.")),
tags$p(HTML("LUTD-Base web application is developed at
<a href=\"http://www.urofun.ch/\" target=\"_blank\"> Functional Urology</a>
lab at the
<a href=\"https://www.unibe.ch/index_eng.html/\" target=\"_blank\"> University of Bern</a>.
Source code is available at <a href=\"https://github.com/FunctionalUrology/LUTD-Base/\" target=\"_blank\"> https://github.com/FunctionalUrology/LUTD-Base</a>.")),
tags$h4("Application"),
tags$p(HTML("LUTD-Base contains 5 main tabs, one for each LUTD subtype
and a Functional Enrichment Exploration tab. Each tab consists
of 3 different panels named Tables, Plots, GO Enrichment plots.
Users can explore the raw read counts and edgeR results using
the table panel. It allows users to explore the read counts
and differential expression analysis results for the
subset of genes using the plot panel. GO Enrichment plots
provide static as well as interactive plots to explore
functional enrichment analysis results. All the plots and
tables are available with a download option.")),
tags$h4("Contact"),
tags$p(HTML("Bug reports and feature requests can be communicated via:")),
tags$ul(
tags$li(HTML("Github: <a href=\"https://github.com/FunctionalUrology/LUTD-Base/issues\" target=\"_blank\">https://github.com/FunctionalUrology/LUTD-Base/issues</a>")),
tags$li(HTML("Email: <a href=\"mailto:[email protected]\" target=\"_blank\">[email protected]</a> <br>
     
<a href=\"mailto:[email protected]\" target=\"_blank\">[email protected]</a>"))
),
tags$h4("Citation"),
tags$p(HTML("If LUTD-Base helps you in any way, please cite the following articles:")),
tags$ul(
tags$li(HTML("Gheinani, Ali Hashemi et al. “Characterization of
miRNA-regulated networks, hubs of signaling, and
biomarkers in obstruction-induced bladder dysfunction.”
JCI insight vol. 2,2 e89560. 26 Jan. 2017, doi:
<a href=\"https://doi.org/10.1172/jci.insight.89560\" target=\"_blank\">10.1172/jci.insight.89560</a>")),
tags$li(HTML("Gheinani, Ali Hashemi et al. “Integrated mRNA-miRNA
transcriptome analysis of bladder biopsies from patients
with bladder pain syndrome identifies signaling alterations
contributing to the disease pathogenesis.”
BMC urology vol. 21,1 172. 7 Dec. 2021, doi:
<a href=\"https://doi.org/10.1186/s12894-021-00934-0\" target=\"_blank\">10.1186/s12894-021-00934-0</a>"))
)
),
)
#combine everything
ui <- fluidPage(
theme = shinytheme("journal"),
navbarPage(
pain_panel,
oab_panel,
AC_panel,
BOO_panel,
goEnrichment_panel,
about,
useShinyjs(),
title= tags$h2(p(em("LUTD-Base")),style="color: #4d1a00;"),
# Create Right Side Logo/Image with Link
tags$script(HTML("var header = $('.navbar > .container-fluid');
header.append('<div style=\"float:right\"><a href=\"https://www.unibe.ch/index_ger.html\" target=\"_blank\" ><img src=\"https://www.unibe.ch/media/[email protected]\" alt=\"alt\" style=\"float:right;width:142px;height:108.86 px;padding-top:2px;padding-bottom:2px;\"> </a>`</div>');
console.log(header)")
)
))