R/ui_meta_analysis.R

In CompEpigen/FactorViz: Visualization app for methylome decomposition experiments

# This script contains the code related to K selection tab
meta_analysis <- function() {
  tabPanel(
    "Meta Analysis",
    id = "met_analysis",
    sidebarPanel(
      width = 3,
      uiOutput("groupSelector_5"),
      uiOutput("lambdaSelector_5"),
      uiOutput("Kselector_5"),
      uiOutput("analyType"),
      conditionalPanel('input.analysisType === "compare LMCs" ',
                       wellPanel(
                         h5("Select a reference run:"),
                         uiOutput("compareRunSelector"),
                         uiOutput("Kselector_ref"),
                         uiOutput("lambdaSelector_ref")
                       ),

                       selectizeInput('compareMatrices', 'Select matrices:',
                                      choices = list(
                                        "Current run" = c(`LMCs (\\hat{T})` = 'That', `Data` = 'D', `Reference (T^star)` = 'Tstar'),
                                        "Reference run" = c(`LMCs (\\hat{T})` = 'refThat', `Data` = 'refD', `Reference (T^star)` = 'refTstar')
                                      ), multiple = TRUE),

                       selectInput("PlotType", "Output type:", c("dendrogram","heatmap","correlation heatmap"), selected=1),
                       uiOutput("topSDcgsSelectorCompare"),
                       radioButtons("SDCompareMatrices", "Calculate SD on:",
                                    c(`All`= "All", `Estimates (\\hat{T})` = 'That', `Data` = 'D', `Reference (T^star)` = 'Tstar')),
                       uiOutput("analysisTokensInput")

      ),
      conditionalPanel(' input.analysisType === "differential methylation" ||
                        input.analysisType === "Enrichments"',
                        conditionalPanel(' input.analysisType === "Enrichments" ',
                        selectInput('diffOutputType', "Output type:", c("GO Enrichments", "LOLA Enrichments"), selected=1)),
                       uiOutput("diffTabT"),
                       sliderInput('dmr_threshold', 'Threshold', min=0.0, max=1.0, step=0.01, value=1.0)
      ),
      conditionalPanel(' input.analysisType === "differential methylation" ',
                        uiOutput("dmCGComponentSelector")
      ),
      conditionalPanel(' input.analysisType === "Enrichments" &&
                       (input.diffOutputType === "GO Enrichments" || input.diffOutputType === "LOLA Enrichments" )',
                       uiOutput("region_selector"),
                       uiOutput("assemblySelector"),
                       numericInput("pValcut", "p-value cutoff", min = 0, max = 1, value=0.01),
                       conditionalPanel('input.diffOutputType === "GO Enrichments" ',
                        selectInput('r_compute', "Reference Compution:", c("median","mean","lmcs"), selected=1),
                        conditionalPanel('input.r_compute === "lmcs" ',
                                         uiOutput('lmcs_selector_go')
                        ),
                        uiOutput("lmcgoSelector"),
                        actionButton('GOsubmitQuery', "Submit GO query")),
                       conditionalPanel('input.diffOutputType === "LOLA Enrichments" ',
                        selectInput('r_compute', "Reference Compution:", c("median","mean","lmcs"), selected=1),
                        conditionalPanel('input.r_compute === "lmcs" ',
                          uiOutput('lmcs_selector')
                        ),
                       uiOutput("lmclolaSelector"),
                         actionButton('LOLAsubmitQuery', "Submit LOLA query"))

      ),
      conditionalPanel(' input.analysisType === "compare LMCs" &&
                       input.PlotType !== "heatmap"  ',
                       checkboxInput("correlationCentered_5", "Center matrices", value=FALSE)
      ),
      conditionalPanel(' input.analysisType === "Trait Association" ',
                       selectInput("tatstat", "Type", choices=c("quantitative", "qualitative", "linear model"), selected=1)
      )
    ),
    mainPanel(uiOutput('metaAnalysisPanel'))
  )
}