inst/shiny/ui.R

In zji90/GEOsearch: GEOsearch

######################################################
##                    GEOsearch                     ##
##             Interactive User Interface           ##
##                     UI File                      ##
##           Author:Zhicheng Ji, Hongkai Ji         ##
##       Maintainer:Zhicheng Ji (zji4@jhu.edu)      ##
######################################################

shinyUI(      
      navbarPage("",
                 tabPanel("GEOsearch",
                          
                          sidebarPanel(
                                p(),
                                width=2
                          ),
                          mainPanel(br(),
                                    br(),
                                    hr(),
                                    h2("GEOsearch: Extendable Search Engine for Gene Expression Omnibus"),
                                    h3("Overview"),
                                    p("GEOsearch provides comprehensive search results by automatically searching all alias of the gene names in the search term. The search results are then integrated and displayed in a compact table. After an initial search, GEOsearch summarize the biological contexts of the search results and allows users to perform second-round search to further narrow down the search results. Other functions are also provided in GEOsearch.
GEOsearch can be accessed by visiting the online user interface https://zhiji.shinyapps.io/GEOsearch. GEOsearch is also an R package that can be downloaded at https://github.com/zji90/GEOsearch.",style="font-size:20px"),
                                    h3("Manual"),
                                    p("The User Manual of GEOsearch provides the details about the various functions in GEOsearch:",style="font-size:20px"),
                                    tags$iframe(style="height:600px; width:100%", src="manual.pdf"),
                                    h3("Contact"),
                                    h5("Author: Zhicheng Ji, Hongkai Ji",style="font-size:20px"),
                                    h5("Maintainer: Zhicheng Ji (zji4@jhu.edu)",style="font-size:20px"),
                                    h5("Version: 1.0.0",style="font-size:20px")
                                    )  
                          
                 ),
                 tabPanel("Perform Search",
                          hr(),
                          hr(),
                          sidebarPanel(
                                h4("Search GEO"),                                         
                                radioButtons("searchoption",NULL,list("Traditional Search"="Traditional","Extended Search"="Expand")),
                                checkboxInput("searchGSMTF","Search GSM samples in addition to GSE series (may take a long time)",value=FALSE),
                                conditionalPanel(condition="input.searchoption=='Expand'",                                         
                                                 selectizeInput("searchexpandselectspecies","Select species in which gene alias will be searched",choices=c("Anopheles","Arabidopsis","Bovine","Worm","Canine","Fly","Zebrafish","E coli strain K12","E coli strain Sakai","Chicken","Human","Mouse","Rhesus","Malaria","Chimp","Rat","Yeast","Pig","Xenopus"),selected=c("Human","Mouse"),multiple=T),
                                                 helpText("Expand search will search all possible gene alias in the database. Search speed is slower for more species chosen.")
                                ),
                                textInput("searchterm","Enter Search Term"),
                                actionButton("searchbutton","Start Search"),
                                hr(),
                                h4("Download Full Results"),
                                checkboxInput("searchdownloadselectedparttf","Download Selected Part",value=FALSE),
                                downloadButton("searchdownloadbutton","Download GSE Search Results"),
                                conditionalPanel(condition="input.searchGSMTF=='1'",
                                                 checkboxInput("searchdownloadGSMselectedparttf","Download Selected Part",value=FALSE),
                                                 downloadButton("searchdownloadGSMbutton","Download GSM Search Results")
                                )
                                ,width=3),
                          mainPanel(uiOutput("searchshowtableui")
                          )
                 ),
                 tabPanel("Key Word Enrichment",
                          hr(),
                          hr(),
                          sidebarPanel(
                                h4("Key Word Enrichment Analysis"),
                                checkboxGroupInput("keywordselectterm","Include Following Information",choices = list("Disease"="disease","Cell Type"="celltype","Tissue"="tissue"),selected = c("disease","celltype","tissue")),
                                hr(),
                                h4("Download Full Results"),
                                downloadButton("keyworddownloadbuttonkeyword","Download Keyword Table"),
                                hr(),
                                checkboxInput("keyworddownloadselectedparttf","Download Selected Part",value=FALSE),
                                downloadButton("keyworddownloadbuttontable","Download GSE for Selected Terms")
                                ,width=3),
                          mainPanel(tabsetPanel(
                                tabPanel("Key Word",br(),DT::dataTableOutput("keywordshowkeyword")),
                                tabPanel("GSE for Selected Terms",br(),DT::dataTableOutput("keywordshowselectsample"))
                          )  
                          )
                          
                 ),
                 tabPanel("Sample Details",
                          hr(),
                          hr(),
                          sidebarPanel(
                                h4("Sample Details"),
                                radioButtons("sampleselectmethod",NULL,list("Choose from selected GSE in step 1"="select1","Choose from selected GSE in step 2"="select2","Enter new GSE"="new")),
                                uiOutput("sampleselectui"),                                       
                                actionButton("samplesearchbutton","Search Samples"),
                                hr(),
                                h4("Download Full Results"),
                                checkboxInput("sampledownloadselectedparttf","Download Selected Part",value=FALSE),
                                downloadButton("sampledownloadbutton","Download Search Results")
                                ,width=3),
                          mainPanel(DT::dataTableOutput("sampleshowtable")
                          )
                 ),
                 tabPanel("Batch Download",
                          hr(),
                          hr(),
                          sidebarPanel(
                                helpText("Before running this function, read instructions on the right."),
                                helpText("Multiple GSE or GSM name should be separated by ;"),
                                textInput("Batchinputtext","Enter GSE or GSM name"),
                                textInput("Batchinputpath","Specify the download path of the shell file","./"),
                                actionButton("Batchrunbutton","Make Shell File"),
                                br(),
                                br(),
                                downloadButton("Batchdownloadbutton","Download Shell File")
                                ,width=3),
                          mainPanel(
                                wellPanel(
                                      p("This function will return a shell file that will automatically download all the SRA files of the GSE or GSM if run."),
                                      p("The shell file must be run on user's own Linux/Unix computer with wget installed."),
                                      p("Note that GSE series with lots of samples will take the function a long time to finish. Use with care.")                                   
                                ),
                                h4("Shell File:"),
                                verbatimTextOutput("showbatchdownloadres")
                          )
                 ),id="MainMenu",position = "fixed-top",inverse=T
                 
      )
)