inst/app/processUI.R

In jordirofes/OmniOmics: Analysis of metabolomics (LC-MS) and transcriptomics (Microarray) data

processUI <- function(id){
    ns <- NS(id)
    fluidPage(
        tabsetPanel(
            tabPanel(title = "Process",
                fluidRow(
                    column(width = 4,
                        selectInput(inputId = ns("object"), label = "Select an object to process:",
                            choices = "")
                    ),
                    column(width = 4,
                        selectInput(inputId = ns("omic"), label = "Select an omic:",
                            choices = c("Metabolomics", "Transcriptomics"))
                    ),
                    column(width = 4,
                        actionButton(inputId = ns("proc"), label = "Process data:")
                    )
                ),
                conditionalPanel("input.omic == 'Metabolomics'",
                    fluidRow(
                        column(width = 4,
                            switchInput(inputId = ns("rtcorrect"), label = "RTcorrection", value = TRUE),
                            switchInput(inputId = ns("peakmerge"), label = "Peak Merging", value = TRUE),
                            switchInput(inputId = ns("peakfill"), label = "Peak filling", value = TRUE)
                            ),
                        column(width = 4,
                            radioButtons(inputId = ns("annotation"),
                                        choiceNames = c("No annotation", "CAMERA", "cliqueMS"),
                                        choiceValues = c("none", "camera", "cliqueMS"),
                                        label = "Choose an annotation step:")
                        ),
                    ),
                    fluidRow(
                        column(width = 3,
                            numericInput(inputId = ns("ppm"), label = "Allowed ppm error:",
                                        value = 40, min = 1, max = 300, step = 1),
                            numericInput(inputId = ns("pwlb"), label = "Peak width lower bound:",
                                        value = 20, min = 1, max = 200, step = 1),
                            numericInput(inputId = ns("pwup"), label = "Peak width upper bound:",
                                        value = 100, min = 1, max = 200, step = 1),
                            numericInput(inputId = ns("noise"), label = "Noise param:",
                                        value = 0, min = 0, max = 10000, step = 1),
                            numericInput(inputId = ns("snr"), label = "Minimum signal to noise ratio (SNR):",
                                        value = 0, min = 0, max = 100000, step = 1)
                        ),
                        column(width = 3,
                            selectInput(inputId = ns("phenoVar"), label = "Grouping Variable:",
                                        choices = ""),
                            numericInput(inputId = ns("minfrac"), label = "Grouping minimun fraction of peaks:",
                                        value = 0.4, min = 0, max = 1),
                            numericInput(inputId = ns("binwidth"), label = "Grouping binwidth:",
                                        value = 30, min = 1, max = 100)
                        ),
                        column(width = 3,
                            conditionalPanel("input.peakmerge",
                                numericInput(inputId = ns("binsize"), label = "Peak merge bin size:",
                                            value = 4, min = 1, max = 100)
                            ,ns = ns),
                            conditionalPanel("input.rtcorrect",
                                numericInput(inputId = ns("expandrt"), label = "RTcorrection bindwith (Obiwarp):",
                                            value = 0.6, min = 0, max = 10, step = 1)
                            ,ns = ns),
                            conditionalPanel("input.annotation != 'none'",
                                radioButtons(inputId = ns("polarity"), label = "Polarity:",
                                            choices = c("positive", "negative"))
                            ,ns = ns),
                            conditionalPanel("input.annotation == 'cliqueMS'",
                                selectInput(inputId = ns("cliqueSample"),
                                            label = "Select which sample will be used for the cliqueMS annotation:",
                                            multiple = FALSE, choices = "")
                            ,ns = ns)
                        )
                    )
                , ns = ns),
                conditionalPanel("input.omic == 'Transcriptomics'",
                    fluidRow(
                        column(width = 4,
                            selectInput(inputId = ns("database"), label = "Select an annotation gene database: (requires installed package)",
                                        choices = "Default")
                        )
                    )
                , ns = ns)
                    ),
            tabPanel(title = "QC",
                fluidPage(
                    fluidRow(
                        column(width = 6,
                            selectInput(inputId = ns("objectDt"), label = "Select an object to process:",
                                choices = ""),
                           # selectizeInput(inputId = ns("files"), label = "", choices = "", multiple = TRUE),
                           switchInput(inputId = ns("order"), label = "File order"),
                           switchInput(inputId = ns("violin"), label = "Violin"),

                        ),
                        column(width = 6,
                            selectInput(inputId = ns("omic2"), label = "Select an omic:",
                                choices = c("Metabolomics", "Transcriptomics")),
                            selectInput(inputId = ns("groupVar"), label = "Select a grouping variable", choices = ""),
                            selectInput(inputId = ns("groupFilt"), label = "Select a group name to filter:", choices = "")
                        ),
                    ),
                    conditionalPanel("input.omic2 == 'Metabolomics'",
                        fluidRow(
                            column(width = 12,
                                plotlyOutput(ns("ggtic"))
                            )
                        )
                    , ns = ns),
                    conditionalPanel("input.omic2 == 'Transcriptomics'",
                        fluidRow(
                            column(width = 12,
                                plotlyOutput(ns("ggdistr"))
                            )
                        ),
                        fluidRow(
                            column(width = 12,
                                plotlyOutput(ns("ggdens"))
                            )
                        )
                    , ns = ns)
                )
            )
        )

    )
}