PlexedPiper_ShinyApp/ui.R at master · JMoon1/PlexedPiper_ShinyApp · GitHub

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library(shinydashboard)

ui <- dashboardPage(

  dashboardHeader(title = "PlexedPiper"),

  # Sidebar panel ----
  dashboardSidebar(

    textInput(inputId = "DataPkgNumber",
              label = "Data Package ID:",
              value = "3606"),
    fluidRow(
      column(2,
             downloadButton("downloadData", "Download"), style = "padding-left:30px;")),
    radioButtons("proteome", label = "Proteome:", choices = c("Global", "Phospho"),
                 selected = "Global"),
    tags$style(".skin-blue .sidebar a { color: #444; }")
  ),
  # Main panel for displaying outputs ----
  dashboardBody(
    tags$head(
      tags$style(HTML("hr {border-top: 1px solid #000000;}")) # make hr() visible
    ),
    tags$head(
      tags$style("label{font-size: 15px}")
    ),
    fluidRow(

      # tags$div(class = "row",
      #          tags$div(class = "span")),
      column(5, uiOutput("ibox")),
      column(2, textInput(inputId = "s2n",
                          "S/N Ratio:",
                          value = 0),
             textInput(inputId = "interference_score",
                       "Interference Score:",
                       value = 0.5), style = 'padding-left:0px; padding-right:50px; padding-top:0px; padding-bottom:0px'),
      column(2, actionButton("submit", "MASIC"))
    ),
    br(),
    hr(),
    br(),
    fluidRow(

      column(5, uiOutput("ibox2")),
      column(2,
             # selectInput("org_name", "Organism:", choices = list("Rattus norvegicus" = 1,
             #                                                     "Homo sapiens" = 2)),
             conditionalPanel(
               condition = "input.proteome == 'Global'",
             textInput(inputId = "pep_fdr",
                       label = "Peptide-level FDR:",
                       value = 0.01),
             textInput("prot_fdr",
                       label = "Accession-level FDR:",
                       value = 0.01),
             checkboxInput("remap_genes",
                           "Remap to Genes"),
             checkboxInput("protein_inference",
                           "Parsimonious Inference"),
             checkboxInput("unique_only", "Drop Shared Peptides")),
             conditionalPanel(
               condition = "input.proteome == 'Phospho'",
               textInput(inputId = "pep_fdr",
                         label = "Peptide-level FDR:",
                         value = 0.01),
               checkboxInput("add_ascore",
                             "Add A-score"),
               checkboxInput("remap_genes",
                             "Remap to Genes"),
               checkboxInput("protein_inference",
                             "Parsimonious Inference"),
               checkboxInput("unique_only", "Drop Shared Peptides")),

             style = 'padding-left:0px; padding-right:50px; padding-top:0px; padding-bottom:0px'
      ),
      column(2, actionButton("submit2", "MS-GF+"))

    ),
    br(),
    hr(),
    br(),
    fluidRow(
      column(5, uiOutput("ibox3")),
      column(2,
             conditionalPanel(
               condition = "input.proteome == 'Global'",
               selectInput(inputId = "gl_aggregate_to",
                           label = "Roll up to:",
                           choices = list("Accession" = 1,
                                          "Peptide" = 2),
                           selected = 1)),
             conditionalPanel(
               condition = "input.proteome == 'Phospho'",
               selectInput(inputId = "ph_aggregate_to",
                           label = "Roll up to:",
                           choices = list("Peptide" = 1,
                                          "SiteID" = 2),
                           selected = 1)),
             style = 'padding-left:0px; padding-right:50px; padding-top:0px; padding-bottom:0px'),
      column(2, actionButton("submit3", "Quant"))
    ),
    fluidRow(
      textOutput('textout')
    )
  )
)