Nothing
inst/application/body.R
In pguIMP: 'pguIMP'
#' Shiny app server object
#'
#' @importFrom shiny actionButton br checkboxInput column fileInput fluidPage fluidRow h1 h3 h5 hr htmlOutput numericInput plotOutput selectInput
#' @importFrom shinydashboard dashboardBody tabItem tabItems
#'
#' @author Sebastian Malkusch, \email{malkusch@@med.uni-frankfurt.de}
#'
#' @export
#'
# create the shiny application user interface body.
menueColumnWidth <- 3
dataColumnWidth <- 12 - menueColumnWidth
halfDataColumnWidth <- as.integer(dataColumnWidth/2)
body <- shinydashboard::dashboardBody(shinydashboard::tabItems(
shinydashboard::tabItem(
tabName = "tab_import",
shiny::fluidPage(
width = 12,
title = "Import",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Upload"),
shiny::fileInput(
inputId = "fi.import",
label = h5(" Select file "),
accept = c(".csv", ".txt", ".xls", ".xlsx"),
width = "100%"
),
shiny::numericInput(
inputId = "ni.importSheetIndex",
label = shiny::h5("Select sheet"),
value = 1,
min = 1,
step = 1,
width = "100%"
),
shiny::selectInput(
inputId = "si.importSeparator",
label = shiny::h5("Separator"),
choices = c(",", ";", "tab"),
selected = ",",
width = "100%"
),
shiny::numericInput(
inputId = "ni.importSkip",
label = shiny::h5("Skip rows"),
value = 0,
min = 0,
step = 1,
width = "100%"
),
shiny::selectInput(
inputId = "si.importColnames",
label = shiny::h5("Column names"),
choices = c("FALSE", "TRUE"),
selected = "TRUE",
width = "100%"
),
shiny::selectInput(
inputId = "si.importNaChar",
label = shiny::h5("Na character"),
choices = c("na", "nan", "Na"),
selected = "na",
width = "100%"
),
shiny::actionButton("ab.importReset",
label = h5("Reset"),
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.uploadHelp"),
shiny::h3("Data types"),
DT::dataTableOutput(
outputId = "tbl.importDataTypes",
width = "100%"),
shiny::hr(),
shiny::h3("Data summary"),
DT::dataTableOutput(
outputId = "tbl.importDataStatistics",
width = "100%"
),
shiny::br(),
shiny::h3("Missings summary"),
DT::dataTableOutput(
outputId = "tbl.importMissingsStatistics",
width = "100%"
)
)
)
)),
shinydashboard::tabItem(
tabName = "tab_filter",
shiny::fluidPage(
width = 12,
title = "Filter",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Filter"),
shiny::actionButton(
inputId = "ab.filterSet",
label = "Filter",
width = "100%"
),
shiny::actionButton(
inputId = "ab.filterInvSet",
label = "Filter inverse",
width = "100%"
),
shiny::actionButton(
inputId = "ab.filterReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.filterHelp"),
shiny::h3("Select Filter"),
DT::dataTableOutput("tbl.filterSelect", width = "100%"),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Statistics"),
DT::dataTableOutput("tbl.filterStatistics", width = "100%")
),
shiny::column(
width = 6,
shiny::h3("Missings"),
DT::dataTableOutput("tbl.filterMissings", width = "100%")
)
)
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_explore",
fluidPage(
width = 12,
title = "Explore",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Explore"),
selectInput(
"si.exploreAbs",
label = h5("Abscissa"),
choices = list(),
selected = 1,
width = "100%"
),
selectInput(
"si.exploreOrd",
label = h5("Ordinate"),
choices = list(),
selected = 1,
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.exploreHelp"),
shiny::h3("Feature Scatter Plot"),
shiny::plotOutput("plt.exploreGraphic"),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Abscissa Statistics"),
shiny::plotOutput("plt.exploreAbscissaGraphic"),
shiny::br(),
DT::dataTableOutput("tbl.exploreAbscissaStatistics")
),
shiny::column(
width = 6,
shiny::h3("Ordinate Statistics"),
shiny::plotOutput("plt.exploreOrdinateGraphic"),
shiny::br(),
DT::dataTableOutput("tbl.exploreOrdinateStatistics")
)
)
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_upload_loq",
shiny::fluidPage(
width = 12,
title = "Upload LOQs",
shiny::column(
width = menueColumnWidth,
shiny::h1("Import LOQs"),
shiny::fileInput(
inputId = "fi.LoqImport",
label = h5("Select file"),
accept = c(".csv", ".txt", ".xls", ".xlsx"),
width = "100%"
),
shiny::numericInput(
inputId = "ni.LoqSheetIndex",
label = shiny::h5("Select sheet"),
value = 1,
min = 1,
step = 1,
width = "100%"
),
shiny::selectInput(
inputId = "si.LoqSeparator",
label = shiny::h5("Separator"),
choices = c(",", ";", "tab"),
selected = ",",
width = "100%"
),
shiny::numericInput(
inputId = "ni.LoqSkip",
label = shiny::h5("Skip rows"),
value = 0,
min = 0,
step = 1,
width = "100%"
),
shiny::selectInput(
inputId = "si.LoqColnames",
label = shiny::h5("Column names"),
choices = c("FALSE", "TRUE"),
selected = "TRUE",
width = "100%"
),
shiny::selectInput(
inputId = "si.LoqNaChar",
label = shiny::h5("Na character"),
choices = c("na", "nan", "Na"),
selected = "na",
width = "100%"
),
shiny::actionButton(
inputId = "ab.LoqUploadReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.uploadLOQHelp"),
shiny::h3("LOQ values"),
DT::dataTableOutput("tbl.loqUploadValues")
)
)
),
shinydashboard::tabItem(
tabName = "tab_define_loq",
shiny::fluidPage(
width = 12,
title = "Define LOQs",
shiny::column(
width = menueColumnWidth,
shiny::h1("Define LOQs"),
shiny::selectInput(
inputId = "si.LoqDefineFeature",
label = shiny::h5("Feature"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::numericInput(
inputId = "ni.LoqDefineLLOQ",
label = h5("LLOQ"),
value = NA,
width = "100%"
),
shiny::numericInput(
inputId = "ni.LoqDefineULOQ",
label = h5("ULOQ"),
value = NA,
width = "100%"
),
shiny::actionButton(
inputId = "ab.LoqDefineSet",
label = "set",
width = "100%"
),
shiny::actionButton(
inputId = "ab.LoqDefineSetGlobally",
label = "set globally",
width = "100%"
),
shiny::actionButton(
inputId = "ab.LoqDefineReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.defineLOQHelp"),
shiny::h3("LOQ values"),
DT::dataTableOutput("tbl.loqDefineValues")
)
)
),
shinydashboard::tabItem(
tabName = "tab_detect_loq",
shiny::fluidPage(
width = 12,
title = "Detect LOQ",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Detect LOQ Outliers"),
shiny::selectInput(
"si.loqDetectFeature",
width = '100%',
label = h5("Feature"),
choices = list(),
selected = 1
),
shiny::selectInput(
"si.loqNaHandling",
width = '100%',
label = h5("NA Handling"),
choices = list(),
selected = 1
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.detectLoq",
label = "Detect Outliers",
width = "100%"
),
shiny::actionButton(
inputId = "ab.resetDetectLoq",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.detectLOQHelp"),
shiny::h3("Define LOQ"),
DT::dataTableOutput("tbl.loqDefine", width = "100%"),
shiny::br(),
shiny::h3("LOQ Outliers Distribution"),
shiny::plotOutput("plt.loqDetectStatistics"),
shiny::br(),
shiny::fluidRow(
shiny::column(
width = 6,
h3("Feature Plot"),
shiny::plotOutput("plt.loqDetectFeature")
),
shiny::column(
width = 6,
h3("Feature Data"),
DT::dataTableOutput("tbl.loqDetectFeature")
)
),
shiny::br(),
shiny::br(),
shiny::h3("LOQ Outliers Statistics"),
DT::dataTableOutput("tbl.loqDetectStatistics"),
shiny::br(),
shiny::h3("LOQ Outliers"),
DT::dataTableOutput("tbl.loqDetectOutlier")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_mutate_loq",
shiny::fluidPage(
width = 12,
title = "Substitute LOQ Outliers",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Substitute LOQ Outliers"),
shiny::selectInput(
"si.loqMutateFeature",
width = '100%',
label = h5("Feature"),
choices = list(),
selected = 1
),
shiny::selectInput(
"si.lloqSubstitute",
width = '100%',
label = h5("LLOQ Substitute"),
choices = list(),
selected = 1
),
shiny::selectInput(
"si.uloqSubstitute",
width = '100%',
label = h5("ULOQ Substitute"),
choices = list(),
selected = 1
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.mutateLoq",
label = "Substitute Outliers",
width = "100%"
),
shiny::actionButton(
inputId = "ab.resetMutateLoq",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.substituteLOQHelp"),
shiny::h3("LOQ Outliers Distribution"),
shiny::plotOutput("plt.loqMutateStatistics"),
shiny::br(),
shiny::fluidRow(
shiny::column(
width = 6,
h3("Feature Plot"),
shiny::plotOutput("plt.loqMutateFeature")
),
shiny::column(
width = 6,
h3("Feature Data"),
DT::dataTableOutput("tbl.loqMutateFeature")
)
),
shiny::br(),
shiny::br(),
shiny::h3("Substituted LOQ Outliers Data"),
DT::dataTableOutput("tbl.loqMutateData")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_mutate_trafo",
fluidPage(
width = 12,
title = "Transformation",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Transform"),
selectInput(
"si.trafoMutateFeature",
label = h5("Feature"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::selectInput(
"si.trafoMutateType",
label = h5("Transformation Type"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::numericInput(
"ni.trafoMutateLambdaLOP",
label = h5("lambda LOP"),
value = 1,
min = -2,
max = 2,
step = 0.01,
width = "100%"
),
shiny::checkboxInput(
"cb.trafoMutateMirror",
label = h5("Mirror"),
value = FALSE
),
shiny::actionButton(
inputId = "ab.trafoMutateSetGlobal",
label = "Initialize Analysis",
width = "100%"
),
shiny::actionButton(
inputId = "ab.trafoMutateFeature",
label = "Transform Feature",
width = "100%"
),
shiny::actionButton(
inputId = "ab.trafoMutateReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.transformHelp"),
shiny::h3("Feature Transformation"),
shiny::plotOutput("plt.trafoMutateFeature", height = "600"),
shiny::br(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Model Parameter"),
DT::dataTableOutput("tbl.trafoMutateFeatureParameter")
),
shiny::column(
width = 6,
shiny::h3("Model Quality"),
DT::dataTableOutput("tbl.trafoMutateFeatureQuality")
)
),
shiny::br(),
shiny::br(),
shiny::h3("Global Transformation"),
shiny::h3("Transformation Parameter"),
DT::dataTableOutput("tbl.trafoMutateGlobalParameter"),
shiny::br(),
shiny::br(),
shiny::h3("Model Parameter"),
DT::dataTableOutput("tbl.trafoMutateGlobalModel"),
shiny::br(),
shiny::br(),
shiny::h3("Model Quality"),
DT::dataTableOutput("tbl.trafoMutateGlobalQuality"),
shiny::br(),
shiny::br(),
shiny::h3("Test Results"),
DT::dataTableOutput("tbl.trafoMutateGlobalTests"),
shiny::br(),
shiny::br(),
shiny::h3("Transformed Data"),
DT::dataTableOutput("tbl.trafoMutateGlobalData")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_normalize_trafo",
shiny::fluidPage(
width = 12,
title = "Normalization",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Normalize"),
selectInput(
"si.trafoNormFeature",
label = h5("Feature"),
choices = list(),
selected = 1,
width = "100%"
),
selectInput(
"si.trafoNormMethod",
label = h5("Normalization Type"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.trafoNormMutate",
label = "Normalize",
width = "100%"
),
shiny::actionButton(
inputId = "ab.trafoNormReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.normalizeHelp"),
shiny::fluidRow(
shiny::column(
width = 6,
h3("Feature Plot"),
shiny::plotOutput("plt.trafoNormFeature")
),
shiny::column(
width = 6,
h3("Feature Statistics"),
DT::dataTableOutput("tbl.trafoNormFeatureStatistics")
)
),
shiny::br(),
shiny::br(),
shiny::h3("Model parameters"),
DT::dataTableOutput("tbl.trafoNormParameter"),
shiny::br(),
shiny::h3("Normalized data statistics"),
DT::dataTableOutput("tbl.trafoNormStatistics"),
shiny::br(),
shiny::h3("Normalized data"),
DT::dataTableOutput("tbl.trafoNormData")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_missings_impute",
shiny::fluidPage(
width = 12,
title = "Detect Missings",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Detect Missings"),
shiny::hr(),
shiny::actionButton(
inputId = "ab.imputeMissingsDetect",
label = "Detect Missings",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.missingsHelp"),
shiny::h3("Missings Statistics"),
shiny::plotOutput("plt.imputeMissingsSummary"),
shiny::br(),
shiny::br(),
shiny::h3("Missings Statistics"),
DT::dataTableOutput("tbl.imputeMissingsStatistics"),
shiny::br(),
shiny::br(),
shiny::h3("Missings Distribution"),
DT::dataTableOutput("tbl.imputeMissingsDistribution"),
shiny::br(),
shiny::br(),
shiny::hr(),
shiny::h3("Missings Vs. Exsitings"),
shiny::plotOutput("plt.imputeMissingsPairs"),
shiny::br(),
shiny::br(),
shiny::h3("Missings Statistics Mean (SD)"),
DT::dataTableOutput("tbl.imputeMissingsCharacteristics"),
shiny::br(),
shiny::br(),
shiny::hr(),
shiny::h3("Missings Details"),
DT::dataTableOutput("tbl.imputeMissingsDetail")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_outliers_impute",
shiny::fluidPage(
width = 12,
title = "Detect Anomalies",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Detect Anomalies"),
shiny::selectInput(
"si.imputeOutliersFeature",
label = h5("Feature"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::selectInput(
"si.imputeOutliersMethod",
label = h5("Detection Method"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::hr(),
shiny::h3("Grubbs parameters"),
shiny::numericInput(
"ni.imputeOutliersAlpha",
label = h5("alpha"),
value = 0.05,
min = 0.01,
max = 0.99,
step = 0.01,
width = "100%"
),
shiny::hr(),
shiny::h3("DBSCAN parameters"),
shiny::numericInput(
"ni.imputeOutliersEpsilon",
label = h5("espilon"),
value = 0.1,
min = 0.01,
step = 0.01,
width = "100%"
),
shiny::numericInput(
"ni.imputeOutliersMinSamples",
label = h5("minSamples"),
value = 5,
min = 1,
max = 10,
step = 1,
width = "100%"
),
shiny::hr(),
shiny::h3("SVM parameters"),
shiny::numericInput(
"ni.imputeOutliersGamma",
label = h5("gamma"),
value = 0.05,
min = 0.01,
step = 0.01,
width = "100%"
),
shiny::numericInput(
"ni.imputeOutliersNu",
label = h5("nu"),
value = 0.95,
min = 0.01,
max = 0.99,
step = 0.01,
width = "100%"
),
shiny::hr(),
shiny::h3("KNN parameters"),
shiny::numericInput(
"ni.imputeOutliersCutoff",
label = h5("cutoff"),
value = 0.99,
min = 0.01,
max = 0.99,
step = 0.01,
width = "100%"
),
shiny::numericInput(
"ni.imputeOutliersK",
label = h5("k"),
value = 5,
min = 1,
max = 10,
step = 1,
width = "100%"
),
shiny::numericInput(
"ni.imputeOutliersSeed",
label = h5("anomalies seed"),
value = 42,
width = "100%"
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.imputeOutliersDetect",
label = "Detect Anomalies",
width = "100%"
),
shiny::actionButton(
inputId = "ab.imputeOutliersReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.anomaliesHelp"),
shiny::h3("Outlier Distribution"),
shiny::plotOutput("plt.outliersImputeSummary"),
shiny::hr(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Feature Plot"),
shiny::plotOutput("plt.outliersImputeFeature")
),
shiny::column(
width = 6,
shiny::h3("Feature Data"),
DT::dataTableOutput("tbl.outliersImputeFeature")
)
),
shiny::hr(),
shiny::h3("Outlier Statistics"),
DT::dataTableOutput("tbl.outliersImputeStatistics"),
shiny::hr(),
shiny::h3("Outlier Details"),
DT::dataTableOutput("tbl.outliersImputeDetail")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_mutate_impute",
shiny::fluidPage(
width = 12,
title = "Substitute Imputation Sites",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Substitute Imputation Sites"),
shiny::selectInput(
"si.imputeMutateFeature",
label = h5("Feature"),
width = "100%",
choices = list(),
selected = 1
),
shiny::selectInput(
"si.imputeMutateMethod",
label = h5("Substitution Method"),
width = "100%",
choices = list(),
selected = 1
),
shiny::numericInput(
"ni.imputeMutateNumberOfNeighbors",
label = h5("number of neighbors"),
width = "100%",
min = 2,
max = 10,
step =1,
value = 3
),
shiny::numericInput(
"ni.imputeMutatePredFrac",
label = h5("fraction of predictors"),
width = "100%",
min = 0,
max = 1,
step =0.1,
value = 1.0
),
shiny::numericInput(
"ni.imputeMutateOutfluxThr",
label = h5("outflux threshold"),
width = "100%",
min = 0.1,
max = 1.0,
step = 0.01,
value = 0.5
),
shiny::numericInput(
"ni.imputeMutateSeed",
label = h5("imputation seed"),
width = "100%",
min = 1,
max = 1000,
step = 1,
value = 42
),
shiny::numericInput(
"ni.imputeMutateIterations",
label = h5("Iterations"),
width = "100%",
min = 1,
max = 10,
step = 1,
value = 4
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.imputeMutateMutate",
label = "Substitute imputation sites",
width = "100%"
),
shiny::actionButton(
inputId = "ab.imputeMutateReset",
label = "reset imputation settings",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.substituteImpHelp"),
shiny::h3("Imputation Site Heatmap"),
shiny::plotOutput("plt.imputeMutateSummary"),
shiny::hr(),
shiny::h3("Flux plot"),
shiny::plotOutput("plt.imputeMutateFlux"),
shiny::hr(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Feature Plot"),
shiny::plotOutput("plt.imputeMutateFeatureDetail")
),
shiny::column(
width = 6,
shiny::h3("Feature Data"),
DT::dataTableOutput("tbl.imputeMutateFeatureDetail")
)
),
shiny::br(),
shiny::br(),
shiny::h3("Imputation Site Statistics"),
DT::dataTableOutput("tbl.imputeMutateStatistics"),
shiny::br(),
shiny::br(),
shiny::h3("Imputation Site Distribution"),
DT::dataTableOutput("tbl.imputeMutateDistribution"),
shiny::br(),
shiny::br(),
shiny::h3("Imputation Site Detail"),
DT::dataTableOutput("tbl.imputeMutateDetail"),
shiny::br(),
shiny::br(),
shiny::h3("Imputation Site Data"),
DT::dataTableOutput("tbl.imputeMutateData")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_analysis_validation",
shiny::fluidPage(
width = 12,
title = "Validate Preprocessing",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Validate Imputation Procedure"),
shiny::selectInput(
"si.analysisValidationFeature",
label = h5("Feature"),
width = "100%",
choices = list(),
selected = 1
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.validation",
label = "Validate",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.validateHelp"),
shiny::h3("Validation analysis results"),
shiny::plotOutput("plt.analysisValidationFeature"),
shiny::hr(),
shiny::br(),
shiny::br(),
shiny::h3("Test results"),
DT::dataTableOutput("tbl.analysisValidationTest"),
shiny::br(),
shiny::br(),
shiny::h3("Central moments"),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Raw data"),
DT::dataTableOutput("tbl.centralMomentsOrg")
),
shiny::column(
width = 6,
shiny::h3("Imputed data"),
DT::dataTableOutput("tbl.centralMomentsImp")
)
),
shiny::h3("Deviation"),
DT::dataTableOutput("tbl.centralMomentsDelta"),
shiny::br(),
shiny::br(),
shiny::h3("Correlation Validation Analysis"),
shiny::plotOutput("plt.correlationValidationScatter"),
shiny::br(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Box Plot"),
shiny::plotOutput("plt.correlationValidationBoxPlot"),
),
shiny::column(
width = 6,
shiny::h3("Correlation Deviation Distribution"),
DT::dataTableOutput("tbl.correlationValidationDeviation")
),
),
shiny::br(),
shiny::h3("Correlation Validation Data"),
DT::dataTableOutput("tbl.correlationValidationData")
)
)
)
)
# shinydashboard::tabItem(
# tabName = "tab_analysis_correlation",
# shiny::fluidPage(
# width = 12,
# title = "Correlation",
# shiny::fluidRow(
# shiny::column(
# width = menueColumnWidth,
# shiny::h1("Correlation"),
# shiny::br(),
# shiny::br(),
# shiny::actionButton(
# inputId = "ab.correlation",
# label = h5("calculate"),
# width = "100%"
# )
# ),
# shiny::column(
# width = dataColumnWidth,
# shiny::h3("Pearson"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("R"),
# DT::dataTableOutput("tbl.correlationMatrixR")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.correlationMatrixPPearson")
# )
# ),
# shiny::hr(),
# shiny::br(),
# shiny::h3("Kendall"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("Tau"),
# DT::dataTableOutput("tbl.correlationMatrixTau")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.correlationMatrixPKendall")
# )
# ),
# shiny::hr(),
# shiny::br(),
# shiny::h3("Spearman"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("Rho"),
# DT::dataTableOutput("tbl.correlationMatrixRho")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.correlationMatrixPSpearman")
# )
# )
# )
# )
# )
# ),
# shinydashboard::tabItem(
# tabName = "tab_analysis_regression",
# shiny::fluidPage(
# width = 12,
# title = "Regression",
# shiny::fluidRow(
# shiny::column(
# width = menueColumnWidth,
# shiny::h1("Linear Regression"),
# shiny::br(),
# shiny::hr(),
# shiny::br(),
# shiny::selectInput(
# "si.regressionAbs",
# label = h5("Abscissa"),
# width = "100%",
# choices = list(),
# selected = 1
# ),
# shiny::selectInput(
# "si.regressionOrd",
# label = h5("Ordinate"),
# width = "100%",
# choices = list(),
# selected = 1
# ),
# shiny::br(),
# shiny::hr(),
# shiny::br(),
# shiny::actionButton(
# inputId = "ab.regression",
# label = h5("calculate"),
# width = "100%"
# )
# ),
# shiny::column(
# width = dataColumnWidth,
# shiny::h3("Model"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("Analysis"),
# shiny::plotOutput("plt.regressionFeature")
# ),
# shiny::column(
# width = 6,
# shiny::h3("Parameter"),
# DT::dataTableOutput("tbl.regressionFeature")
# )
# ),
# shiny::br(),
# shiny::br(),
# shiny::h3("Intercept"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("value"),
# DT::dataTableOutput("tbl.regressionIntercept")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.regressionPIntercept")
# )
# ),
# shiny::hr(),
# shiny::br(),
# shiny::h3("Slope"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("value"),
# DT::dataTableOutput("tbl.regressionSlope")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.regressionPSlope")
# )
# )
# )
# )
# )
# )
))
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#' Shiny app server object
#'
#' @importFrom shiny actionButton br checkboxInput column fileInput fluidPage fluidRow h1 h3 h5 hr htmlOutput numericInput plotOutput selectInput
#' @importFrom shinydashboard dashboardBody tabItem tabItems
#'
#' @author Sebastian Malkusch, \email{malkusch@@med.uni-frankfurt.de}
#'
#' @export
#'
# create the shiny application user interface body.
menueColumnWidth <- 3
dataColumnWidth <- 12 - menueColumnWidth
halfDataColumnWidth <- as.integer(dataColumnWidth/2)
body <- shinydashboard::dashboardBody(shinydashboard::tabItems(
shinydashboard::tabItem(
tabName = "tab_import",
shiny::fluidPage(
width = 12,
title = "Import",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Upload"),
shiny::fileInput(
inputId = "fi.import",
label = h5(" Select file "),
accept = c(".csv", ".txt", ".xls", ".xlsx"),
width = "100%"
),
shiny::numericInput(
inputId = "ni.importSheetIndex",
label = shiny::h5("Select sheet"),
value = 1,
min = 1,
step = 1,
width = "100%"
),
shiny::selectInput(
inputId = "si.importSeparator",
label = shiny::h5("Separator"),
choices = c(",", ";", "tab"),
selected = ",",
width = "100%"
),
shiny::numericInput(
inputId = "ni.importSkip",
label = shiny::h5("Skip rows"),
value = 0,
min = 0,
step = 1,
width = "100%"
),
shiny::selectInput(
inputId = "si.importColnames",
label = shiny::h5("Column names"),
choices = c("FALSE", "TRUE"),
selected = "TRUE",
width = "100%"
),
shiny::selectInput(
inputId = "si.importNaChar",
label = shiny::h5("Na character"),
choices = c("na", "nan", "Na"),
selected = "na",
width = "100%"
),
shiny::actionButton("ab.importReset",
label = h5("Reset"),
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.uploadHelp"),
shiny::h3("Data types"),
DT::dataTableOutput(
outputId = "tbl.importDataTypes",
width = "100%"),
shiny::hr(),
shiny::h3("Data summary"),
DT::dataTableOutput(
outputId = "tbl.importDataStatistics",
width = "100%"
),
shiny::br(),
shiny::h3("Missings summary"),
DT::dataTableOutput(
outputId = "tbl.importMissingsStatistics",
width = "100%"
)
)
)
)),
shinydashboard::tabItem(
tabName = "tab_filter",
shiny::fluidPage(
width = 12,
title = "Filter",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Filter"),
shiny::actionButton(
inputId = "ab.filterSet",
label = "Filter",
width = "100%"
),
shiny::actionButton(
inputId = "ab.filterInvSet",
label = "Filter inverse",
width = "100%"
),
shiny::actionButton(
inputId = "ab.filterReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.filterHelp"),
shiny::h3("Select Filter"),
DT::dataTableOutput("tbl.filterSelect", width = "100%"),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Statistics"),
DT::dataTableOutput("tbl.filterStatistics", width = "100%")
),
shiny::column(
width = 6,
shiny::h3("Missings"),
DT::dataTableOutput("tbl.filterMissings", width = "100%")
)
)
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_explore",
fluidPage(
width = 12,
title = "Explore",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Explore"),
selectInput(
"si.exploreAbs",
label = h5("Abscissa"),
choices = list(),
selected = 1,
width = "100%"
),
selectInput(
"si.exploreOrd",
label = h5("Ordinate"),
choices = list(),
selected = 1,
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.exploreHelp"),
shiny::h3("Feature Scatter Plot"),
shiny::plotOutput("plt.exploreGraphic"),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Abscissa Statistics"),
shiny::plotOutput("plt.exploreAbscissaGraphic"),
shiny::br(),
DT::dataTableOutput("tbl.exploreAbscissaStatistics")
),
shiny::column(
width = 6,
shiny::h3("Ordinate Statistics"),
shiny::plotOutput("plt.exploreOrdinateGraphic"),
shiny::br(),
DT::dataTableOutput("tbl.exploreOrdinateStatistics")
)
)
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_upload_loq",
shiny::fluidPage(
width = 12,
title = "Upload LOQs",
shiny::column(
width = menueColumnWidth,
shiny::h1("Import LOQs"),
shiny::fileInput(
inputId = "fi.LoqImport",
label = h5("Select file"),
accept = c(".csv", ".txt", ".xls", ".xlsx"),
width = "100%"
),
shiny::numericInput(
inputId = "ni.LoqSheetIndex",
label = shiny::h5("Select sheet"),
value = 1,
min = 1,
step = 1,
width = "100%"
),
shiny::selectInput(
inputId = "si.LoqSeparator",
label = shiny::h5("Separator"),
choices = c(",", ";", "tab"),
selected = ",",
width = "100%"
),
shiny::numericInput(
inputId = "ni.LoqSkip",
label = shiny::h5("Skip rows"),
value = 0,
min = 0,
step = 1,
width = "100%"
),
shiny::selectInput(
inputId = "si.LoqColnames",
label = shiny::h5("Column names"),
choices = c("FALSE", "TRUE"),
selected = "TRUE",
width = "100%"
),
shiny::selectInput(
inputId = "si.LoqNaChar",
label = shiny::h5("Na character"),
choices = c("na", "nan", "Na"),
selected = "na",
width = "100%"
),
shiny::actionButton(
inputId = "ab.LoqUploadReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.uploadLOQHelp"),
shiny::h3("LOQ values"),
DT::dataTableOutput("tbl.loqUploadValues")
)
)
),
shinydashboard::tabItem(
tabName = "tab_define_loq",
shiny::fluidPage(
width = 12,
title = "Define LOQs",
shiny::column(
width = menueColumnWidth,
shiny::h1("Define LOQs"),
shiny::selectInput(
inputId = "si.LoqDefineFeature",
label = shiny::h5("Feature"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::numericInput(
inputId = "ni.LoqDefineLLOQ",
label = h5("LLOQ"),
value = NA,
width = "100%"
),
shiny::numericInput(
inputId = "ni.LoqDefineULOQ",
label = h5("ULOQ"),
value = NA,
width = "100%"
),
shiny::actionButton(
inputId = "ab.LoqDefineSet",
label = "set",
width = "100%"
),
shiny::actionButton(
inputId = "ab.LoqDefineSetGlobally",
label = "set globally",
width = "100%"
),
shiny::actionButton(
inputId = "ab.LoqDefineReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.defineLOQHelp"),
shiny::h3("LOQ values"),
DT::dataTableOutput("tbl.loqDefineValues")
)
)
),
shinydashboard::tabItem(
tabName = "tab_detect_loq",
shiny::fluidPage(
width = 12,
title = "Detect LOQ",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Detect LOQ Outliers"),
shiny::selectInput(
"si.loqDetectFeature",
width = '100%',
label = h5("Feature"),
choices = list(),
selected = 1
),
shiny::selectInput(
"si.loqNaHandling",
width = '100%',
label = h5("NA Handling"),
choices = list(),
selected = 1
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.detectLoq",
label = "Detect Outliers",
width = "100%"
),
shiny::actionButton(
inputId = "ab.resetDetectLoq",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.detectLOQHelp"),
shiny::h3("Define LOQ"),
DT::dataTableOutput("tbl.loqDefine", width = "100%"),
shiny::br(),
shiny::h3("LOQ Outliers Distribution"),
shiny::plotOutput("plt.loqDetectStatistics"),
shiny::br(),
shiny::fluidRow(
shiny::column(
width = 6,
h3("Feature Plot"),
shiny::plotOutput("plt.loqDetectFeature")
),
shiny::column(
width = 6,
h3("Feature Data"),
DT::dataTableOutput("tbl.loqDetectFeature")
)
),
shiny::br(),
shiny::br(),
shiny::h3("LOQ Outliers Statistics"),
DT::dataTableOutput("tbl.loqDetectStatistics"),
shiny::br(),
shiny::h3("LOQ Outliers"),
DT::dataTableOutput("tbl.loqDetectOutlier")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_mutate_loq",
shiny::fluidPage(
width = 12,
title = "Substitute LOQ Outliers",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Substitute LOQ Outliers"),
shiny::selectInput(
"si.loqMutateFeature",
width = '100%',
label = h5("Feature"),
choices = list(),
selected = 1
),
shiny::selectInput(
"si.lloqSubstitute",
width = '100%',
label = h5("LLOQ Substitute"),
choices = list(),
selected = 1
),
shiny::selectInput(
"si.uloqSubstitute",
width = '100%',
label = h5("ULOQ Substitute"),
choices = list(),
selected = 1
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.mutateLoq",
label = "Substitute Outliers",
width = "100%"
),
shiny::actionButton(
inputId = "ab.resetMutateLoq",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.substituteLOQHelp"),
shiny::h3("LOQ Outliers Distribution"),
shiny::plotOutput("plt.loqMutateStatistics"),
shiny::br(),
shiny::fluidRow(
shiny::column(
width = 6,
h3("Feature Plot"),
shiny::plotOutput("plt.loqMutateFeature")
),
shiny::column(
width = 6,
h3("Feature Data"),
DT::dataTableOutput("tbl.loqMutateFeature")
)
),
shiny::br(),
shiny::br(),
shiny::h3("Substituted LOQ Outliers Data"),
DT::dataTableOutput("tbl.loqMutateData")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_mutate_trafo",
fluidPage(
width = 12,
title = "Transformation",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Transform"),
selectInput(
"si.trafoMutateFeature",
label = h5("Feature"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::selectInput(
"si.trafoMutateType",
label = h5("Transformation Type"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::numericInput(
"ni.trafoMutateLambdaLOP",
label = h5("lambda LOP"),
value = 1,
min = -2,
max = 2,
step = 0.01,
width = "100%"
),
shiny::checkboxInput(
"cb.trafoMutateMirror",
label = h5("Mirror"),
value = FALSE
),
shiny::actionButton(
inputId = "ab.trafoMutateSetGlobal",
label = "Initialize Analysis",
width = "100%"
),
shiny::actionButton(
inputId = "ab.trafoMutateFeature",
label = "Transform Feature",
width = "100%"
),
shiny::actionButton(
inputId = "ab.trafoMutateReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.transformHelp"),
shiny::h3("Feature Transformation"),
shiny::plotOutput("plt.trafoMutateFeature", height = "600"),
shiny::br(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Model Parameter"),
DT::dataTableOutput("tbl.trafoMutateFeatureParameter")
),
shiny::column(
width = 6,
shiny::h3("Model Quality"),
DT::dataTableOutput("tbl.trafoMutateFeatureQuality")
)
),
shiny::br(),
shiny::br(),
shiny::h3("Global Transformation"),
shiny::h3("Transformation Parameter"),
DT::dataTableOutput("tbl.trafoMutateGlobalParameter"),
shiny::br(),
shiny::br(),
shiny::h3("Model Parameter"),
DT::dataTableOutput("tbl.trafoMutateGlobalModel"),
shiny::br(),
shiny::br(),
shiny::h3("Model Quality"),
DT::dataTableOutput("tbl.trafoMutateGlobalQuality"),
shiny::br(),
shiny::br(),
shiny::h3("Test Results"),
DT::dataTableOutput("tbl.trafoMutateGlobalTests"),
shiny::br(),
shiny::br(),
shiny::h3("Transformed Data"),
DT::dataTableOutput("tbl.trafoMutateGlobalData")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_normalize_trafo",
shiny::fluidPage(
width = 12,
title = "Normalization",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Normalize"),
selectInput(
"si.trafoNormFeature",
label = h5("Feature"),
choices = list(),
selected = 1,
width = "100%"
),
selectInput(
"si.trafoNormMethod",
label = h5("Normalization Type"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.trafoNormMutate",
label = "Normalize",
width = "100%"
),
shiny::actionButton(
inputId = "ab.trafoNormReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.normalizeHelp"),
shiny::fluidRow(
shiny::column(
width = 6,
h3("Feature Plot"),
shiny::plotOutput("plt.trafoNormFeature")
),
shiny::column(
width = 6,
h3("Feature Statistics"),
DT::dataTableOutput("tbl.trafoNormFeatureStatistics")
)
),
shiny::br(),
shiny::br(),
shiny::h3("Model parameters"),
DT::dataTableOutput("tbl.trafoNormParameter"),
shiny::br(),
shiny::h3("Normalized data statistics"),
DT::dataTableOutput("tbl.trafoNormStatistics"),
shiny::br(),
shiny::h3("Normalized data"),
DT::dataTableOutput("tbl.trafoNormData")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_missings_impute",
shiny::fluidPage(
width = 12,
title = "Detect Missings",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Detect Missings"),
shiny::hr(),
shiny::actionButton(
inputId = "ab.imputeMissingsDetect",
label = "Detect Missings",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.missingsHelp"),
shiny::h3("Missings Statistics"),
shiny::plotOutput("plt.imputeMissingsSummary"),
shiny::br(),
shiny::br(),
shiny::h3("Missings Statistics"),
DT::dataTableOutput("tbl.imputeMissingsStatistics"),
shiny::br(),
shiny::br(),
shiny::h3("Missings Distribution"),
DT::dataTableOutput("tbl.imputeMissingsDistribution"),
shiny::br(),
shiny::br(),
shiny::hr(),
shiny::h3("Missings Vs. Exsitings"),
shiny::plotOutput("plt.imputeMissingsPairs"),
shiny::br(),
shiny::br(),
shiny::h3("Missings Statistics Mean (SD)"),
DT::dataTableOutput("tbl.imputeMissingsCharacteristics"),
shiny::br(),
shiny::br(),
shiny::hr(),
shiny::h3("Missings Details"),
DT::dataTableOutput("tbl.imputeMissingsDetail")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_outliers_impute",
shiny::fluidPage(
width = 12,
title = "Detect Anomalies",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Detect Anomalies"),
shiny::selectInput(
"si.imputeOutliersFeature",
label = h5("Feature"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::selectInput(
"si.imputeOutliersMethod",
label = h5("Detection Method"),
choices = list(),
selected = 1,
width = "100%"
),
shiny::hr(),
shiny::h3("Grubbs parameters"),
shiny::numericInput(
"ni.imputeOutliersAlpha",
label = h5("alpha"),
value = 0.05,
min = 0.01,
max = 0.99,
step = 0.01,
width = "100%"
),
shiny::hr(),
shiny::h3("DBSCAN parameters"),
shiny::numericInput(
"ni.imputeOutliersEpsilon",
label = h5("espilon"),
value = 0.1,
min = 0.01,
step = 0.01,
width = "100%"
),
shiny::numericInput(
"ni.imputeOutliersMinSamples",
label = h5("minSamples"),
value = 5,
min = 1,
max = 10,
step = 1,
width = "100%"
),
shiny::hr(),
shiny::h3("SVM parameters"),
shiny::numericInput(
"ni.imputeOutliersGamma",
label = h5("gamma"),
value = 0.05,
min = 0.01,
step = 0.01,
width = "100%"
),
shiny::numericInput(
"ni.imputeOutliersNu",
label = h5("nu"),
value = 0.95,
min = 0.01,
max = 0.99,
step = 0.01,
width = "100%"
),
shiny::hr(),
shiny::h3("KNN parameters"),
shiny::numericInput(
"ni.imputeOutliersCutoff",
label = h5("cutoff"),
value = 0.99,
min = 0.01,
max = 0.99,
step = 0.01,
width = "100%"
),
shiny::numericInput(
"ni.imputeOutliersK",
label = h5("k"),
value = 5,
min = 1,
max = 10,
step = 1,
width = "100%"
),
shiny::numericInput(
"ni.imputeOutliersSeed",
label = h5("anomalies seed"),
value = 42,
width = "100%"
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.imputeOutliersDetect",
label = "Detect Anomalies",
width = "100%"
),
shiny::actionButton(
inputId = "ab.imputeOutliersReset",
label = "Reset",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.anomaliesHelp"),
shiny::h3("Outlier Distribution"),
shiny::plotOutput("plt.outliersImputeSummary"),
shiny::hr(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Feature Plot"),
shiny::plotOutput("plt.outliersImputeFeature")
),
shiny::column(
width = 6,
shiny::h3("Feature Data"),
DT::dataTableOutput("tbl.outliersImputeFeature")
)
),
shiny::hr(),
shiny::h3("Outlier Statistics"),
DT::dataTableOutput("tbl.outliersImputeStatistics"),
shiny::hr(),
shiny::h3("Outlier Details"),
DT::dataTableOutput("tbl.outliersImputeDetail")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_mutate_impute",
shiny::fluidPage(
width = 12,
title = "Substitute Imputation Sites",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Substitute Imputation Sites"),
shiny::selectInput(
"si.imputeMutateFeature",
label = h5("Feature"),
width = "100%",
choices = list(),
selected = 1
),
shiny::selectInput(
"si.imputeMutateMethod",
label = h5("Substitution Method"),
width = "100%",
choices = list(),
selected = 1
),
shiny::numericInput(
"ni.imputeMutateNumberOfNeighbors",
label = h5("number of neighbors"),
width = "100%",
min = 2,
max = 10,
step =1,
value = 3
),
shiny::numericInput(
"ni.imputeMutatePredFrac",
label = h5("fraction of predictors"),
width = "100%",
min = 0,
max = 1,
step =0.1,
value = 1.0
),
shiny::numericInput(
"ni.imputeMutateOutfluxThr",
label = h5("outflux threshold"),
width = "100%",
min = 0.1,
max = 1.0,
step = 0.01,
value = 0.5
),
shiny::numericInput(
"ni.imputeMutateSeed",
label = h5("imputation seed"),
width = "100%",
min = 1,
max = 1000,
step = 1,
value = 42
),
shiny::numericInput(
"ni.imputeMutateIterations",
label = h5("Iterations"),
width = "100%",
min = 1,
max = 10,
step = 1,
value = 4
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.imputeMutateMutate",
label = "Substitute imputation sites",
width = "100%"
),
shiny::actionButton(
inputId = "ab.imputeMutateReset",
label = "reset imputation settings",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.substituteImpHelp"),
shiny::h3("Imputation Site Heatmap"),
shiny::plotOutput("plt.imputeMutateSummary"),
shiny::hr(),
shiny::h3("Flux plot"),
shiny::plotOutput("plt.imputeMutateFlux"),
shiny::hr(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Feature Plot"),
shiny::plotOutput("plt.imputeMutateFeatureDetail")
),
shiny::column(
width = 6,
shiny::h3("Feature Data"),
DT::dataTableOutput("tbl.imputeMutateFeatureDetail")
)
),
shiny::br(),
shiny::br(),
shiny::h3("Imputation Site Statistics"),
DT::dataTableOutput("tbl.imputeMutateStatistics"),
shiny::br(),
shiny::br(),
shiny::h3("Imputation Site Distribution"),
DT::dataTableOutput("tbl.imputeMutateDistribution"),
shiny::br(),
shiny::br(),
shiny::h3("Imputation Site Detail"),
DT::dataTableOutput("tbl.imputeMutateDetail"),
shiny::br(),
shiny::br(),
shiny::h3("Imputation Site Data"),
DT::dataTableOutput("tbl.imputeMutateData")
)
)
)
),
shinydashboard::tabItem(
tabName = "tab_analysis_validation",
shiny::fluidPage(
width = 12,
title = "Validate Preprocessing",
shiny::fluidRow(
shiny::column(
width = menueColumnWidth,
shiny::h1("Validate Imputation Procedure"),
shiny::selectInput(
"si.analysisValidationFeature",
label = h5("Feature"),
width = "100%",
choices = list(),
selected = 1
),
shiny::hr(),
shiny::actionButton(
inputId = "ab.validation",
label = "Validate",
width = "100%"
)
),
shiny::column(
width = dataColumnWidth,
shiny::htmlOutput(outputId = "html.validateHelp"),
shiny::h3("Validation analysis results"),
shiny::plotOutput("plt.analysisValidationFeature"),
shiny::hr(),
shiny::br(),
shiny::br(),
shiny::h3("Test results"),
DT::dataTableOutput("tbl.analysisValidationTest"),
shiny::br(),
shiny::br(),
shiny::h3("Central moments"),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Raw data"),
DT::dataTableOutput("tbl.centralMomentsOrg")
),
shiny::column(
width = 6,
shiny::h3("Imputed data"),
DT::dataTableOutput("tbl.centralMomentsImp")
)
),
shiny::h3("Deviation"),
DT::dataTableOutput("tbl.centralMomentsDelta"),
shiny::br(),
shiny::br(),
shiny::h3("Correlation Validation Analysis"),
shiny::plotOutput("plt.correlationValidationScatter"),
shiny::br(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h3("Box Plot"),
shiny::plotOutput("plt.correlationValidationBoxPlot"),
),
shiny::column(
width = 6,
shiny::h3("Correlation Deviation Distribution"),
DT::dataTableOutput("tbl.correlationValidationDeviation")
),
),
shiny::br(),
shiny::h3("Correlation Validation Data"),
DT::dataTableOutput("tbl.correlationValidationData")
)
)
)
)
# shinydashboard::tabItem(
# tabName = "tab_analysis_correlation",
# shiny::fluidPage(
# width = 12,
# title = "Correlation",
# shiny::fluidRow(
# shiny::column(
# width = menueColumnWidth,
# shiny::h1("Correlation"),
# shiny::br(),
# shiny::br(),
# shiny::actionButton(
# inputId = "ab.correlation",
# label = h5("calculate"),
# width = "100%"
# )
# ),
# shiny::column(
# width = dataColumnWidth,
# shiny::h3("Pearson"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("R"),
# DT::dataTableOutput("tbl.correlationMatrixR")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.correlationMatrixPPearson")
# )
# ),
# shiny::hr(),
# shiny::br(),
# shiny::h3("Kendall"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("Tau"),
# DT::dataTableOutput("tbl.correlationMatrixTau")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.correlationMatrixPKendall")
# )
# ),
# shiny::hr(),
# shiny::br(),
# shiny::h3("Spearman"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("Rho"),
# DT::dataTableOutput("tbl.correlationMatrixRho")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.correlationMatrixPSpearman")
# )
# )
# )
# )
# )
# ),
# shinydashboard::tabItem(
# tabName = "tab_analysis_regression",
# shiny::fluidPage(
# width = 12,
# title = "Regression",
# shiny::fluidRow(
# shiny::column(
# width = menueColumnWidth,
# shiny::h1("Linear Regression"),
# shiny::br(),
# shiny::hr(),
# shiny::br(),
# shiny::selectInput(
# "si.regressionAbs",
# label = h5("Abscissa"),
# width = "100%",
# choices = list(),
# selected = 1
# ),
# shiny::selectInput(
# "si.regressionOrd",
# label = h5("Ordinate"),
# width = "100%",
# choices = list(),
# selected = 1
# ),
# shiny::br(),
# shiny::hr(),
# shiny::br(),
# shiny::actionButton(
# inputId = "ab.regression",
# label = h5("calculate"),
# width = "100%"
# )
# ),
# shiny::column(
# width = dataColumnWidth,
# shiny::h3("Model"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("Analysis"),
# shiny::plotOutput("plt.regressionFeature")
# ),
# shiny::column(
# width = 6,
# shiny::h3("Parameter"),
# DT::dataTableOutput("tbl.regressionFeature")
# )
# ),
# shiny::br(),
# shiny::br(),
# shiny::h3("Intercept"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("value"),
# DT::dataTableOutput("tbl.regressionIntercept")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.regressionPIntercept")
# )
# ),
# shiny::hr(),
# shiny::br(),
# shiny::h3("Slope"),
# shiny::fluidRow(
# shiny::column(
# width = 6,
# shiny::h3("value"),
# DT::dataTableOutput("tbl.regressionSlope")
# ),
# shiny::column(
# width = 6,
# shiny::h3("p value"),
# DT::dataTableOutput("tbl.regressionPSlope")
# )
# )
# )
# )
# )
# )
))
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