R/plotVolcanoApp.R

In bigPint: Big multivariate data plotted interactively

PKGENVIR <- new.env(parent=emptyenv()) # package level envir

#' @title Plot interactive volcano plots
#' 
#' @description Plot interactive volcano plots.
#' 
#' @param data DATA FRAME | Read counts
#' @param dataMetrics LIST | Differential expression metrics. This object must 
#' contain one column named "logFC" and one column named "PValue".
#' @param dataSE SUMMARIZEDEXPERIMENT | Summarized experiment format that
#' can be used in lieu of data; default NULL
#' @param option CHARACTER STRING ["hexagon" | "allPoints"] | The background of 
#' plot; default "hexagon"
#' @param pointColor CHARACTER STRING | Color of overlaid points on scatterplot 
#' matrix; default "orange"
#' @importFrom plotly plotlyOutput ggplotly renderPlotly config
#' @importFrom ggplot2 ggplot aes_string aes xlim ylim geom_boxplot theme
#' @importFrom shiny verbatimTextOutput fluidPage reactive renderPrint shinyUI 
#' sliderInput shinyServer shinyApp HTML br reactiveValues strong em div p img 
#' observeEvent selectInput selectizeInput numericInput actionButton 
#' @importFrom htmlwidgets onRender
#' @importFrom utils str
#' @importFrom tidyr gather
#' @importFrom stats qt lm coef
#' @importFrom hexbin hexbin hcell2xy
#' @importFrom stringr str_replace str_trim
#' @importFrom dplyr %>% select
#' @importFrom shinycssloaders withSpinner
#' @importFrom shinydashboard menuItem tabItem dashboardPage dashboardHeader 
#' dashboardSidebar sidebarMenu tabItems box
#' @importFrom Hmisc cut2
#' @importFrom RColorBrewer brewer.pal
#' @importFrom stats setNames
#' @return A Shiny application that shows a volcano plot and allows users to 
#' overlay genes depending on two values, usually a statistical value (such as
#' P-value) and a magnitude change value (such as log fold change). The user
#' can download a file that contains the gene IDs that pass these thresholds.
#' @export
#' @examples
#' # The first pair of examples use data and dataMetrics objects as input.
#' # The last pair of examples create the same plots now using the 
#' # SummarizedExperiment (i.e. dataSE) object input.
#' 
#' # Example 1: Create interactive volcano plot of logged data using hexagon
#' # bins for the background.
#' 
#' data(soybean_cn_sub)
#' data(soybean_cn_sub_metrics)
#' app <- plotVolcanoApp(data = soybean_cn_sub,
#'     dataMetrics = soybean_cn_sub_metrics)
#' if (interactive()) {
#'     shiny::runApp(app)
#' }
#' 
#' # Example 2: Create interactive volcano plot of logged data using points for 
#' # the background.
#' 
#' app <- plotVolcanoApp(data = soybean_cn_sub,
#'     dataMetrics = soybean_cn_sub_metrics, option = "allPoints",
#'     pointColor = "magenta")
#' if (interactive()) {
#'     shiny::runApp(app)
#' }
#' 
#' # Below is the same pair of examples, only now using the
#' # SummarizedExperiment (i.e. dataSE) object as input.
#' 
#' # Example 1: Create interactive volcano plot of logged data using hexagon
#' # bins for the background.
#' 
#' \dontrun{
#' data(se_soybean_cn_sub)
#' app <- plotVolcanoApp(dataSE = se_soybean_cn_sub)
#' if (interactive()) {
#'     shiny::runApp(app)
#' }
#' }
#' 
#' # Example 2: Create interactive volcano plot of logged data using points for 
#' # the background.
#' 
#' \dontrun{
#' app <- plotVolcanoApp(dataSE = se_soybean_cn_sub, option = "allPoints",
#'     pointColor = "magenta")
#' if (interactive()) {
#'     shiny::runApp(app)
#' }
#' }
#' 

plotVolcanoApp = function(data=data, dataMetrics=dataMetrics, dataSE = NULL,
    option=c("hexagon", "allPoints"), pointColor = "orange"){

option <- match.arg(option)

if (is.null(dataSE) && is.null(data)){
    helperTestHaveData()
}

if (!is.null(dataSE)){
    #Reverse engineer data
    data <- helperGetData(dataSE)
    
    if (ncol(rowData(dataSE))>0){
        #Reverse engineer dataMetrics
        reDataMetrics <- as.data.frame(rowData(dataSE))
        dataMetrics <- lapply(split.default(reDataMetrics[-1], 
        sub("\\..*", "",names(reDataMetrics[-1]))), function(x)
        cbind(reDataMetrics[1], setNames(x, sub(".*\\.", "", names(x)))))
        for (k in seq_len(length(dataMetrics))){
            colnames(dataMetrics[[k]])[1] = "ID"   
        }
    }
}

helperTestData(data)
if (!is.null(dataMetrics)){
    helperTestDataMetricsVolcanoApp(data, dataMetrics, "PValue", "logFC")
}

appDir <- system.file("shiny-examples", "plotVolcanoApp", package = "bigPint")
if (appDir == "") {
    stop("Could not find example directory. Try re-installing `bigPint`.",
    call. = FALSE)
}
PKGENVIR$DATA <- data # put the data into envir
PKGENVIR$DATAMETRICS <- dataMetrics # put the data into envir
PKGENVIR$OPTION <- option # put the option into envir
PKGENVIR$POINTCOLOR <- pointColor # put the pointColor into envir  
return(appDir)
}