inst/app/ui.R

In ELELAB/lipidQ: Lipidomics Analysis Tool

#' @author André Vidas Olsen
#' @import shiny
ui <- fluidPage(
  titlePanel("LipidQ"),

    navbarPage("CHOOSE OPERATION: ",
      tabPanel("Quantification",
        sidebarLayout(
          sidebarPanel(
            # input data
            fileInput(
              inputId = "dataList", multiple = TRUE, label =
              "Choose the input data sets (.csv-files):" , accept =
              c("text/csv", "text/comma-separated-values,text/plain", ".csv")
            ),

            # endogene database
            fileInput(
              inputId = "endogene_lipid_db", label =
              "Choose the endogene lipid database (.csv-file):",accept =
              c("text/csv", "text/comma-separated-values,text/plain", ".csv")
            ),

            # ISTD database
            fileInput(
              inputId = "ISTD_lipid_db", label =
              "Choose the ISTD lipid database (.csv-file):",
              accept = c("text/csv", "text/comma-separated-values,text/plain",
              ".csv")
            ),

            # userspecified colnames
            fileInput(
              inputId = "userSpecifiedColnames", label =
              "Choose user specified column names (.csv-file):",
              accept = c("text/csv", "text/comma-separated-values,text/plain",
              ".csv")
            ),
            br(),
            br(),

            # replicate filtering
            numericInput(
              "numberOfReps",
              "Number of replicates per sample (1 = no replicates):",1, min = 1,
              max = 100
            ),

            checkboxInput(
              "blnkReplicates", "Blank contains replicates", FALSE),
              numericInput("numberOfInstancesT",
              "Number of instances threshold:", 1, min = 1, max = 100
            ),

            numericInput(
              "thresholdValue","Threshold of instance:", 500, min = 0, max = 100
            ),

            br(),
            br(),
            br(),

            # LOQ
            checkboxInput(
              "LOQ", "LOQ activated", FALSE
            ),

            numericInput(
              "fixedDeviation", "Fixed deviation (%):", 0, min = 0, max = 100
            ),

            br(),
            br(),
            br(),

            # multiply parameter
            checkboxInput(
              "multiplyMS1",
              "Multiply MS1 columns by a factor (for LipidX users)", FALSE),

            fileInput(inputId = "list",
              label ="Choose the list of classes to be multiplied (.csv-file):",
              accept = c("text/csv", "text/comma-separated-values,text/plain",
              ".csv")
            ),

            numericInput(
              "multiplyPREC_value", "Set multiplication factor:", 2, min = 1,
              max = 100),

            br(),
            br(),
            br(),

            # spikeISTD
            numericInput(
              "spikeISTD", "Spike ISTD (uL):", NA, min = 1, max = 100
            ),

            # Threshold for rounding down to zero for mol% species
            numericInput(
              "zeroThresh",
              "Threshold for rounding down to zero for mol% species:", 0.001,
              min = 0, max = 10
            ),

            br(),
            checkboxInput(
              "QC_plots_MS1", "Create QC plots of MS1 intensity data", FALSE),
              checkboxInput("QC_plots_pmol",
              "Create QC plots of class pmol data", FALSE
            ),

            br(),
            br(),
            # output folder
            textInput(
              "dir", "Paste the filepath for the output files to be saved.",
              "/data/user/andre/lipidomics/results/"
            ),


            br(),
            br(),
            br(),

            actionButton("runAnalysis", "Run Analysis"),


            br(),
            br(),
            textOutput(
              "validateFields_quant"
            ),
            textOutput(
              "analysisDone"
            )
          ),

        mainPanel()
      )
             ),
             tabPanel("Merging of Final Output Data Sets",
                      sidebarLayout(
                        sidebarPanel(

                          fileInput(
                            inputId = "finalOutputList", multiple = TRUE,
                            label =
                            "Choose the final output data sets (.csv-files):",
                            accept = c("text/csv",
                            "text/comma-separated-values,text/plain", ".csv")
                          ),

                          textInput(
                            "dirFinalOutputs",
                            paste0("Paste the filepath for the output files to",
                            " be saved.",
                            "/data/user/andre/lipidomics/results/")
                          ),

                          br(),

                          actionButton(
                            "runFinalOutputMerging",
                            "Merge Final Output Data Sets"),

                          br(),
                          br(),

                          textOutput("validateFields_merging"),
                          textOutput("finalOutputMergingDone")
                        ),
                        mainPanel()
                      )
             ),
             tabPanel("Visualization",
                      sidebarLayout(
                        sidebarPanel(
                          # input data
                          fileInput(
                            inputId = "molPctFile", multiple = FALSE, label =
                              "Choose a mol% final output file (.csv-file):",
                              accept = c("text/csv",
                              "text/comma-separated-values,text/plain", ".csv")
                          ),

                          fileInput(
                            inputId = "sampleTypes", multiple = FALSE, label =
                              paste0("Choose a file containing sample type ",
                              "information for the data:"),
                              accept = c("text/csv",
                              "text/comma-separated-values,text/plain", ".csv")
                          ),

                          checkboxInput("log2Trans",
                              "log2 transformation of the data", FALSE),
                          numericInput("pseudoCount", "Pseudo count", NULL,
                              min = 0, max = 1000),


                          checkboxInput(
                            "PCA_plot",
                            "Create PCA biplots of mol% classes and species",
                            FALSE
                          ),

                          checkboxInput(
                            "heatmap_plot",
                            "Create heatmap plots of mol% classes and species",
                            FALSE
                          ),

                          numericInput(
                            "k",
                            "Optional selection of k clusters for the heatmap",
                            NULL, min = 0, max = 10
                          ),

                          textInput(
                            "dirPlots",
                            paste0("Paste the filepath for the output files to "
                            , "be saved."),
                            "/data/user/andre/lipidomics/results/plots"
                          ),

                          actionButton("createPlots", "Create Plots"),
                          textOutput("validateFields_visualization"),
                          textOutput("plotsDone")
                        ),
                        mainPanel()
                      )
            ),
            tabPanel("Global Options",
              sidebarLayout(
              sidebarPanel(

              h4("Create new user specified column names template"),
              numericInput(
                "numberOfMS2ix", "Number of MS2 columns in the input data", "7"
              ),

              br(),
              textInput(
                "dirColnamesTemplate",
                "Paste the filepath for the column template file to be saved.",
                "/data/user/andre/lipidomics/lipidQ/"),


              actionButton(
                "createColnamesTemplate",
                "Create Column Template File"
              ),
              textOutput(
                "validateFields_globalOptions_userSpec"
              ),
              textOutput(
                "createColTemplateDone"
              ),




              br(),
              br(),
              br(),
              h4("Create new database file"),
              checkboxInput("DB_type_endo", "endogene database", FALSE),
              checkboxInput("DB_type_ISTD", "ISTD database", FALSE),

              fileInput(
                inputId = "userSpecifiedColnamesCreateDatabase", label =
                "Choose list of colnames (.csv-file):", accept = c("text/csv",
                "text/comma-separated-values,text/plain", ".csv")
              ),

              textInput(
                "dirDatabase",
                "Paste the filepath for the database file to be saved.",
                "/data/user/andre/lipidomics/lipidQ/"
              ),



              actionButton(
                "createDatabase", "Create Database"
              ),
              textOutput(
                "validateFields_globalOptions_db"
              ),
              textOutput(
                "createDatabaseDone")
              ),
              mainPanel()
              )
          )
  )
)