inst/app/sc_modules.R

In BioData-PT/D-cellerate: D-Cellerate

plot.pca.scree <- function(sobj) {
  ElbowPlot(sobj, ndims = length(sobj[["pca"]]@stdev))
}

plot.pca <- function(sobj, dim1=1, dim2=2, dim3=3) {
  p1 <- DimPlot(sobj, dims = c(dim1, dim2))
  p2 <- DimPlot(sobj, dims = c(dim3, dim2))
  CombinePlots(plots = list(p1, p2), legend="none")
}

sc_pcavizUI <- function(id, show.scree=TRUE) {
  ns <- NS(id)
  
  if (show.scree == TRUE) {
    scree.ui <- tagList(
      plotOutput(ns("plot_scree")),
      helpText('PCA "scree plot" (or "elbow plot") showing the proportion',
               'of variance explained by each proncipal component.'),
      hr())
  } else {
    scree.ui <- NULL
  }
  
  tagList(
    scree.ui,
    plotOutput(ns("plot_pca"), height="auto"),
    inputPanel(
      numericInput(ns("num_pc1"), "Dim1", value = 1),
      numericInput(ns("num_pc2"), "Dim2", value = 2),
      numericInput(ns("num_pc3"), "Dim3", value = 3)
    ),
    helpText('Scatterplots of the output of the principal component',
             'analysis. Three components may be displayed. The second seclected component',
             'will be reused in the Y-axis of the second plot.')
  )
}

sc_pcavizServer <- function(input, output, session, sobj, cluster.name=NA) {
  
  output$plot_pca <- renderPlot({
    req(sobj())
 
    # if (!is.na(cluster.name)) {
    #   .sobj <- SetAllIdent(.sobj, cluster.name)
    #   print("New ident")
    # }
    # 
    # table(.sobj@ident)
    
    dim1 <- input$num_pc1
    dim2 <- input$num_pc2
    dim3 <- input$num_pc3
    
    plot.pca(sobj(), dim1, dim2, dim3)
    
  }, height = function() {
    session$clientData[[ paste0("output_", session$ns("plot_pca"), "_width") ]] / 2
  })
  
  output$plot_scree <- renderPlot({
    req(sobj())
    
    # eigs <- sobj()@dr$pca@sdev**2
    # props <- eigs / sum(eigs)
    # plot(props, ylab="Proportion of variance", xlab="Principal Component", pch=20, cex=1.5)
    plot.pca.scree(sobj())
  })
  
  return(list(
    scree.plot = plot.pca.scree,
    pca.plot = plot.pca
  ))
  
}

#--------------------------------------------------------------------------------------------
#
## AGGS code:

plot.tsne <- function( sobj, choice ) { # WARNING: change choice to allow multiple inputs
  if ( ( choice %in% c( "nCount_RNA", "nFeature_RNA", "percent.mito" ) ) | grepl("^PC", choice) ) {
    FeaturePlot( sobj, features = choice, reduction = "tsne" )
  } else {
    .sobj <- sobj
    if ( choice == "Original Clusters" ) {
      Idents(.sobj) <- .sobj@meta.data$new.clusters # TAKE ATTENTION TO THE NAME OF A CLT
    } else if (choice == "Renamed Clusters") {
      Idents(.sobj) <- .sobj@meta.data$new.clusters
    }
    DimPlot( .sobj, reduction = "tsne", label = TRUE )
  }
} 

#-------------------------------------------------------------------------------------------


sc_tsnevizUI <- function(id) {
  ns <- NS(id)
  
  tagList(
    plotOutput(ns("plot_tsne"), width = "100%"),
    inputPanel(
      radioButtons(ns("radio_col_by"), label = "Color by", choices=c("Cluster", "Feature")),
      selectInput(ns("sel_col_by"), label = "", choices=NULL),
      checkboxInput(ns("check_legend"), label = "Show legend", value = TRUE)
    )
  )
}

sc_tsnevizServer <- function(input, output, session, status, sobj, cluster.name=NA) {
  
  observe({
    if (!status$tsne_ready)
      return()
    
    if (input$radio_col_by == "Cluster") {
      choices <- "Unclustered"
      selected <- "Unclustered"
      
      if (status$clustering_ready == TRUE) {
        choices <- c("Original Clusters", "Renamed Clusters")
        
        selected <- "Renamed Clusters"
      }
    } else {
        choices <- c("nCount_RNA", "nFeature_RNA", "percent.mito")
        selected <- "nCount_RNA"
        
        if (status$pca_ready == TRUE) {
          req(sobj())
          
          choices <- c(choices, colnames(sobj()@reductions$pca@cell.embeddings))
        }
    }
    
    updateSelectInput(session, "sel_col_by", choices = choices, selected = selected)
  })
  
  output$plot_tsne <- renderPlot({
    req(sobj())

    choice <- input$sel_col_by # aggs
    plot.tsne( sobj(), choice )
    
  })   
  return(list(
    plot.tsne = plot.tsne
  ))

}