inst/shiny/ui_03_2_cluster.R

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

shinyPanelCluster <- fluidPage(
  tags$div(
    class = "container",
    h3("Clustering"),
    h5(tags$a(href = "https://compbiomed.github.io/sctk_docs/articles/clustering.html",
              "(help)", target = "_blank")),
    wellPanel(
      # CLUSTERING --> VISUALIZATION
      fluidRow(
        column(
          6,
          selectInput("clustAlgo", "Select Algorithm",
                      list("Scran SNN" = c("walktrap" = 1, "louvain" = 2,
                                           "infomap" = 3, "fastGreedy" = 4,
                                           "labelProp" = 5, "leadingEigen" = 6),
                           "K-Means" = c("Hartigan-Wong" = 7, "Lloyd" = 8,
                                         "MacQueen" = 9),
                           "Seurat" = c("louvain" = 10, "multilevel" = 11,
                                        "SLM" = 12)),
                      )
        )
      ),
      h4("Input Parameters:"),
      fluidRow(
        # Scran SNN ####
        conditionalPanel(
          "input.clustAlgo >=1 && input.clustAlgo <= 6",
          column(
            6,
            uiOutput("clustScranSNNMatUI"),
            uiOutput("clustScranSNNAltExpAssayUI")
          ),
          column(
            4,
            numericInput("clustScranSNNK", "K value:", 10, min = 1, step = 1),
          ),
          conditionalPanel(
            "input.clustScranSNNInType != 'ReducedDim'",
            column(
              4,
              numericInput("clustScranSNNd", "Number of Components:",
                           50, min = 2, step = 5)
            )
          ),
          column(
            4,
            selectInput("clustScranSNNType", "Edge Weight Type:",
                        c("rank", "number", "jaccard"), selected = "rank")
          )
        ),

        # K-Means ####
        conditionalPanel(
          "input.clustAlgo >= 7 && input.clustAlgo <= 9",
          column(
            6,
            selectInput("clustKMeansReddim", "Select A ReducedDim:", currreddim)
          ),
          column(6),
          column(
            12,
            helpText("A 'reducedDim' contains low-dimension representation of an assay.\n Dimension reduction has to be run in advance.")
          ),
          column(
            4,
            numericInput("clustKMeansN", "Number of Centers (Clusters):",
                         value = NULL),
          ),
          column(
            4,
            numericInput("clustKMeansNIter", "Max Number of Iterations:",
                         10, min = 2, step = 1)
          ),
          column(
            4,
            numericInput("clustKMeansNStart", "Number of Random Sets:",
                         1, min = 1, step = 1)
          )
        ),

        # Seurat ####
        conditionalPanel(
          "input.clustAlgo >= 10 && input.clustAlgo <= 12",
          column(
            6,
            selectInput("clustSeuratReddim", "Select A ReducedDim:", currreddim)
          ),
          column(6),
          column(
            12,
            helpText("A 'reducedDim' contains low-dimension representation of an assay.\n Dimension reduction has to be run in advance.")
          ),
          column(
            4,
            numericInput("clustSeuratDims", "How Many Dimensions to Use:", 10,
                         min = 2, step = 1),
          ),
          column(
            4,
            checkboxInput("clustSeuratGrpSgltn", "Group Singletons",
                          value = TRUE)
          ),
          column(
            4,
            numericInput("clustSeuratRes", "Resolution", 0.8, step = 0.05)
          )
        )
      ), # fuildRow ends here
      useShinyjs(),
      uiOutput("clustNameUI"),
      withBusyIndicatorUI(actionButton("clustRun", "Run"))
    ),
    h3("Visualization"),
    p("A cluster annotation needs to be specified, and a dimension reduction has to be provided.",
      style = "color:grey;"),
    panel(
      radioButtons("clustVisChoicesType", NULL,
                   c("Select from Current Results:" = 1,
                     "Select from All Present Annotation:" = 2),
                   selected = 1, inline = TRUE, ),
      conditionalPanel(
        "input.clustVisChoicesType == 1",
        selectInput("clustVisRes", NULL, "")
      ),
      conditionalPanel(
        "input.clustVisChoicesType == 2",
        selectInput("clustVisCol", NULL, clusterChoice)
      ),
      selectInput("clustVisReddim", "Use Reduction:", currreddim),
      withBusyIndicatorUI(actionButton("clustPlot", "Plot")),
      plotOutput("clustVisPlot")
    )
  )
)