R/density.R

In UMMS-Biocore/debrowser: Interactive Differential Expresion Analysis Browser

#' getDensityPlotUI
#'
#' Density plot UI.  
#'
#' @param id, namespace id
#' @note \code{getDensityPlotUI}
#' @return the panel for Density plots;
#'
#' @examples
#'     x <- getDensityPlotUI("density")
#'
#' @export
#'
getDensityPlotUI <- function(id) {
  ns <- NS(id)
  uiOutput(ns("DensityUI"))
}

#' debrowserdensityplot
#'
#' Module for a density plot that can be used in data prep and 
#' low count removal modules
#' 
#' @param input, input variables
#' @param output, output objects
#' @param session, session 
#' @param data, a matrix that includes expression values
#' @return density plot 
#' @export
#'
#' @examples
#'     x <- debrowserdensityplot()
#'
debrowserdensityplot <- function(input = NULL, output = NULL, session = NULL, data = NULL) {
    if(is.null(data)) return(NULL)
    output$Density <- renderPlotly({
        getDensityPlot(data, input)
    })
    output$DensityUI <- renderUI({
    shinydashboard::box(
        collapsible = TRUE, title = session$ns("plot"), status = "primary", 
        solidHeader = TRUE, width = NULL,
        draggable = TRUE,  plotlyOutput(session$ns("Density"),
             width = input$width, height=input$height))
    })
}

#' densityPlotControlsUI
#'
#' Generates the controls in the left menu for a densityPlot
#'
#' @note \code{densityPlotControlsUI}
#' @param id, namespace id
#' @return returns the left menu
#' @examples
#'     x <- densityPlotControlsUI("density")
#' @export
#'
densityPlotControlsUI <- function(id) {
  ns <- NS(id)
  shinydashboard::menuItem(paste0(id, " - Options"),
      textInput(ns("breaks"), "Breaks", value = "100" )
  )
}

#' getDensityPlot
#'
#' Makes Density plots
#'
#' @param data, count or normalized data
#' @param input, input
#' @param title, title
#'
#' @export
#'
#' @examples
#'     getDensityPlot()
#'
getDensityPlot <- function(data=NULL, input = NULL, title = ""){
  if (is.null(data)) return(NULL)
  data <- as.data.frame(data)
  cols <- colnames(data)
  data[, cols] <- apply(data[, cols], 2,
                        function(x) log10(as.integer(x) + 1))
  
  data <- addID(data)
  mdata <- melt(as.data.frame(data[,c("ID", cols)]),"ID")
  colnames(mdata)<-c("ID", "samples", "density")
  
  p <- ggplot(data=mdata, aes(x=density)) +
    geom_density(aes(fill = samples), alpha = 0.5) +
    labs(x = "logcount", y = "Density") +
    theme_minimal()
  if (!is.null(input$top))
      p <- p + theme( plot.margin = margin(t = input$top, r =input$right, b =input$bottom, l = input$left, "pt"))
  p <- ggplotly(p, width = input$width, height = input$height)
  if (!is.null(input$svg) && input$svg == TRUE)
    p <- p %>% config(toImageButtonOptions = list(format = "svg"))
  p$elementId <- NULL
  p
}