R/plotVolcano.R

In bigPint: Big multivariate data plotted interactively

#' @title Plot static volcano plot
#' 
#' @description Plot static volcano plot.
#' 
#' @param data DATA FRAME | Read counts
#' @param dataMetrics LIST | Differential expression metrics. This object
#' must contain one column with magnitude changes (for the logFC parameter)
#' and one column with statistical values (for the PValue parameter),
#' unless geneList is not NULL
#' @param dataSE SUMMARIZEDEXPERIMENT | Summarized experiment format that
#' can be used in lieu of data and dataMetrics; default NULL
#' @param geneList CHARACTER ARRAY | List of gene IDs to be drawn onto the 
#' scatterplot matrix of all data. Use this parameter if you have
#' predetermined subset of genes to be superimposed. Otherwise, dataMetrics,
#' threshVar, and threshVal will be used to create genes to be superimposed
#' onto the volcano plot; default NULL
#' @param threshVar CHARACTER STRING | Name of column in dataMetrics object
#' that is used to determine genes to be overlaid; default "FDR"
#' @param threshVal INTEGER | Maximum value to threshold significance from 
#' threshVar object; default 0.05
#' @param option CHARACTER STRING ["hexagon" | "allPoints"] | The background
#' of plot; default "hexagon"
#' @param logFC CHARACTER STRING | Name of column in dataMetrics object that 
#' contains log fold change values; default "logFC"
#' @param PValue CHARACTER STRING | Name of column in dataMetrics object that 
#' contains p-values; default "PValue"
#' @param xbins INTEGER | Number of bins partitioning the range of the plot; 
#' default 10
#' @param pointSize INTEGER | Size of plotted points; default 0.5
#' @param pointColor CHARACTER STRING | Color of overlaid points on
#' scatterplot matrix; default "orange"
#' @param outDir CHARACTER STRING | Output directory to save all plots;
#' default tempdir()
#' @param saveFile BOOLEAN [TRUE | FALSE] | Save file to outDir; default TRUE
#' @param hover BOOLEAN [TRUE | FALSE] | Allow to hover over points to
#' identify IDs; default FALSE
#' @importFrom dplyr filter select %>%
#' @importFrom GGally ggpairs wrap
#' @importFrom ggplot2 ggplot aes_string aes geom_point xlim ylim geom_hex 
#' coord_cartesian xlab ylab geom_ribbon geom_boxplot geom_line geom_abline 
#' theme_gray ggtitle labs element_text scale_fill_gradientn
#' @importFrom grDevices jpeg dev.off
#' @importFrom hexbin hexbin hcell2xy
#' @importFrom htmlwidgets onRender
#' @importFrom plotly plotlyOutput ggplotly renderPlotly layout
#' @importFrom shiny verbatimTextOutput fluidPage reactive renderPrint
#' shinyApp
#' @importFrom stats lm predict
#' @importFrom tidyr gather
#' @importFrom utils str
#' @importFrom plyr mapvalues
#' @importFrom utils combn
#' @importFrom stats setNames
#' @return List of n elements of volcano plots, where n is the number of 
#' treatment pair combinations in the data object. The subset of genes that
#' are superimposed are determined through the dataMetrics or geneList
#' parameter. If the saveFile parameter has a value of TRUE, then each of
#' these volcano plots is saved to the location specified in the outDir
#' parameter as a JPG file.
#' @export
#' @examples
#' # The first set of four examples use data and dataMetrics objects as
#' # input. The last set of four examples create the same plots now
#' # using the SummarizedExperiment (i.e. dataSE) object input.
#' 
#' # Example 1: Plot volcano plot with default settings for overlaid points
#' # (FDR < 0.05).
#' 
#' data(soybean_ir_sub)
#' data(soybean_ir_sub_metrics)
#' ret <- plotVolcano(soybean_ir_sub, soybean_ir_sub_metrics, pointSize = 1,
#'     saveFile = FALSE)
#' ret[[1]]
#' 
#' # Example 2: Plot volcano plot and overlay points with PValue < 1e-15.
#' 
#' ret <- plotVolcano(soybean_ir_sub, soybean_ir_sub_metrics,
#'     pointColor = "red", pointSize = 1, threshVar = "PValue",
#'     threshVal = 1e-15, saveFile = FALSE)
#' ret[[1]]
#' 
#' # Example 3: Plot volcano plot and overlay points with PValue < 1e-15. This 
#' # time, plot all points (instead of hexagons) for the background.
#' 
#' ret <- plotVolcano(soybean_ir_sub, soybean_ir_sub_metrics,
#'     pointColor = "red", pointSize = 1, threshVar = "PValue",
#'     threshVal = 1e-15, option = "allPoints", saveFile = FALSE)
#' ret[[1]]
#' 
#' # Example 4: Plot volcano plot with points in background and overlay points 
#' # with PValue < 1e-15. This time, use a value of TRUE for the hover
#' # parameter so that you can hover over overlaid points and determine their
#' # IDs.
#' 
#' ret <- plotVolcano(soybean_ir_sub, soybean_ir_sub_metrics,
#'     pointColor = "red", pointSize = 1, threshVar = "PValue",
#'     threshVal = 1e-15, option = "allPoints", saveFile = FALSE,
#'     hover = TRUE)
#' ret[[1]]
#' 
#' # Below are the same four examples, only now using the
#' # SummarizedExperiment (i.e. dataSE) object as input.
#' 
#' # Example 1: Plot volcano plot with default settings for overlaid points
#' # (FDR < 0.05).
#' 
#' \dontrun{
#' data(se_soybean_ir_sub)
#' ret <- plotVolcano(dataSE = se_soybean_ir_sub, pointSize = 1,
#'     saveFile = FALSE)
#' ret[[1]]
#' }
#' 
#' # Example 2: Plot volcano plot and overlay points with PValue < 1e-15.
#' 
#' \dontrun{
#' ret <- plotVolcano(dataSE = se_soybean_ir_sub, pointColor = "red", 
#'     pointSize = 1, threshVar = "PValue", threshVal = 1e-15, 
#'     saveFile = FALSE)
#' ret[[1]]
#' }
#' 
#' # Example 3: Plot volcano plot and overlay points with PValue < 1e-15. This 
#' # time, plot all points (instead of hexagons) for the background.
#' 
#' \dontrun{
#' ret <- plotVolcano(dataSE = se_soybean_ir_sub, pointColor = "red", 
#'     pointSize = 1, threshVar = "PValue", threshVal = 1e-15, 
#'     option = "allPoints", saveFile = FALSE)
#' ret[[1]]
#' }
#' 
#' # Example 4: Plot volcano plot with points in background and overlay points 
#' # with PValue < 1e-15. This time, use a value of TRUE for the hover
#' # parameter so that you can hover over overlaid points and determine their
#' # IDs.
#' 
#' \dontrun{
#' ret <- plotVolcano(dataSE = se_soybean_ir_sub, pointColor = "red",
#'     pointSize = 1, threshVar = "PValue", threshVal = 1e-15, 
#'     option = "allPoints", saveFile = FALSE, hover = TRUE)
#' ret[[1]]
#' }
#' 

plotVolcano = function(data = data, dataMetrics = dataMetrics, dataSE=NULL,
    geneList = NULL, threshVar = "FDR", threshVal = 0.05,
    option = c("hexagon", "allPoints"), logFC = "logFC", PValue = "PValue",
    xbins = 10, pointSize = 0.5, pointColor = "orange", outDir = tempdir(), 
    saveFile=TRUE, hover = FALSE){

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)))))            
    }
}

# Check that input parameters fit required formats
helperTestData(data)
if (is.null(geneList) && !is.null(dataMetrics)){
    helperTestDataMetricsVolcano(data, dataMetrics, threshVar, PValue,
    logFC)
}

if (!is.null(dataMetrics)){
    helperTestDataMetricsVolcano(data, dataMetrics, threshVar, PValue,
    logFC)
}

countColor2 <- counts <- hexID <- ID <- NULL
myPairs <- helperMakePairs(data)[["myPairs"]]
colGroups <- helperMakePairs(data)[["colGroups"]]
cols.combn <- combn(myPairs, 2, simplify = FALSE) ### ADDED
ifelse(!dir.exists(outDir), dir.create(outDir), FALSE)

ret <- lapply(cols.combn, function(x){
    group1 = x[1]
    group2 = x[2]
    datSel = cbind(ID=data$ID, data[,which(colGroups %in%
    c(group1, group2))])
    curPairDF1 = dataMetrics[[paste0(group1, "_", group2)]]
    curPairDF2 = dataMetrics[[paste0(group2, "_", group1)]]
    
    if (!is.null(curPairDF1)){curPairDF = curPairDF1}
    if (!is.null(curPairDF2)){curPairDF = curPairDF2}
    
    cpd0 = which(curPairDF[[PValue]]==0)
    curPairDF[[PValue]][cpd0] = sort(unique(curPairDF[[PValue]]))[2]
    xMax = max(curPairDF[[logFC]])
    xMin = min(curPairDF[[logFC]])
    yMax = -log(min(curPairDF[[PValue]]))
    yMin = -log(max(curPairDF[[PValue]]))
    fcMax = ceiling(max(exp(xMax), 1/exp(xMin)))
    curPairSel = curPairDF[which(curPairDF[[threshVar]] < threshVal),]
    degData = filter(datSel, ID %in% curPairSel$ID)
    if (!is.null(geneList)){
        curPairSel = curPairDF[which(curPairDF$ID %in% geneList),]
        degData = filter(datSel, ID %in% geneList)
    }
    
    x = curPairDF[[logFC]]
    y = -log(curPairDF[[PValue]])
    x2 = curPairSel[[logFC]]
    y2 = -log(curPairSel[[PValue]])
    h = hexbin(x=x, y=y, xbins=xbins, shape=3, IDs=TRUE,
    xbnds=c(xMin, xMax), ybnds=c(yMin, yMax))
    hexdf = helperMakeHexDF(h)[["hexdf"]]
    clrs = helperMakeHexDF(h)[["clrs"]]
    my_breaks = helperMakeHexDF(h)[["my_breaks"]]
    
    seqVec = seq_along(strsplit(levels(hexdf$countColor2), "-"))
    datSp1 <- vapply(seqVec, function(x){strsplit(levels(hexdf$countColor2),
    "-")[[x]][1]}, character(1))
    
    seqVec = seq_along(strsplit(datSp1, "\\+"))
    datSp2 <- vapply(seqVec, function(x){strsplit(datSp1, "\\+")[[x]][1]},
    character(1))
    bin <- mapvalues(hexdf$countColor2, from = levels(hexdf$countColor2),
    to = datSp2)
    hexdf$bin <- as.integer(bin)
    
    if (option == "allPoints"){
        mainPoints = data.frame(x=x, y=y)
        overlayPoints = data.frame(x=x2, y=y2)
        p <- ggplot(mainPoints, aes(x=x, y=y)) + geom_point(size =
        pointSize) + geom_point(data = overlayPoints, aes_string(x=x2,
        y=y2), colour = pointColor, size = pointSize) +
        theme(axis.text=element_text(size=15),
        axis.title=element_text(size=15),
        legend.title=element_text(size=15),
        legend.text=element_text(size=15)) +
        coord_cartesian(xlim = c(xMin, xMax), ylim = c(yMin, yMax)) +
        xlab(logFC) + ylab(paste0("-log10(", PValue, ")"))
        
        if (hover == TRUE){
            IDs=curPairSel$ID
            gP <- ggplotly(p)
            gP[["x"]][["data"]][[1]][["hoverinfo"]] <- "none"
            newText = IDs
            gP[["x"]][["data"]][[2]][["text"]] <- newText
        }
    }
    else{
        overlayPoints = data.frame(x=x2, y=y2)
        p <- ggplot(hexdf, aes(x=x, y=y)) + geom_hex(stat="identity",
        aes(fill=bin)) + scale_fill_gradientn(colors=rev(clrs[-1]),
        guide="legend", labels=levels(hexdf$countColor2), name="Count") +
        theme(axis.text=element_text(size=15), axis.title=
        element_text(size=15), legend.title=element_text(size=15),
        legend.text=element_text(size=15)) + coord_cartesian(xlim =
        c(xMin,xMax), ylim=c(yMin,yMax)) + geom_point(data=overlayPoints,
        aes_string(x=x2, y=y2), color = pointColor, size = pointSize,
        inherit.aes=FALSE) + xlab(logFC) +
        ylab(paste0("-log10(", PValue, ")"))
        
        if (hover == TRUE){
            IDs = curPairSel$ID
            gP <- ggplotly(p)
            seqVec = seq(length(gP[["x"]][["data"]])-1)
            for (l in seq_along(seqVec)){
            gP[["x"]][["data"]][[l]][["hoverinfo"]] <- "none"}
            newText = IDs
            gP[["x"]][["data"]][[length(gP[["x"]][["data"]])]][["text"]] <-
            newText 
        }
    }
    if (saveFile == TRUE){
        jpeg(filename=paste0(outDir, "/", group1, "_", group2,
        "_degVolcano.jpg"), height=700, width=1100)
        print(p)
        dev.off()
    }
    if (hover == FALSE){
        return(list(plot = p, name = paste0(group1, "_", group2)))    
    }
    else{
        return(list(plot = gP, name = paste0(group1, "_", group2)))        
    }
})
retPlots <- lapply(ret, function(x) {x$plot})
retNames <- lapply(ret, function(x) {x$name})
names(retPlots) <- retNames
invisible(retPlots)
}