R/plotSM.R

In bigPint: Big multivariate data plotted interactively

#' @title Plot static scatterplot matrices
#' 
#' @description Plot static scatterplot matrix. Optionally, superimpose
#' differentially expressed genes (DEGs) onto scatterplot matrix.
#' 
##' @details There are seven options:
##' \itemize{
##' \item{"foldChange": }{Plots DEGs onto scatterplot matrix of fold changes}
##' \item{"orthogonal": }{Plots DEGs onto scatterplot matrix of orthogonal 
##' distance}
##' \item{"hexagon": }{Plot DEGs onto scatterplot matrix of hexagon binning}
##' \item{"allPoints": }{Plot DEGs onto scatterplot matrix of all data points}
##' } 
#' 
#' @param data DATA FRAME | Read counts
#' @param dataMetrics LIST | Differential expression metrics; default 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 
#' genes to be drawn. Otherwise, use dataMetrics, threshVar, and threshVal to 
#' create genes to be drawn onto the scatterplot matrix; default NULL; used in 
#' "hexagon" and "allPoints"
#' @param threshVar CHARACTER STRING | Name of column in dataMetrics object
#' that is used to threshold significance; default "FDR"; used in all options
#' @param threshVal INTEGER | Maximum value to threshold significance from 
#' threshVar object; default 0.05; used in all options
#' @param option CHARACTER STRING ["foldChange" | "orthogonal" | "hexagon" | 
#' "allPoints"] | The type of plot; default "allPoints"
#' @param xbins INTEGER | Number of bins partitioning the range of the plot; 
#' default 10; used in option "hexagon"
#' @param threshFC INTEGER | Threshold of fold change; default 3; used in
#' option "foldChange"
#' @param threshOrth INTEGER | Threshold of orthogonal distance; default 3;
#' used in option "orthogonal"
#' @param pointSize INTEGER | Size of plotted points; default 0.5; used for
#' DEGs in "hexagon" and "allPoints" and used for all points in "foldChange"
#' and "orthogonal"
#' @param pointColor CHARACTER STRING | Color of overlaid points on scatterplot 
#' matrix; default "orange"; used for DEGs in "hexagon" and "allPoints" and
#' used for all points in "foldChange" and "orthogonal"
#' @param outDir CHARACTER STRING | Output directory to save all plots; default 
#' tempdir(); used in all options
#' @param saveFile BOOLEAN [TRUE | FALSE] | Save file to outDir; default TRUE; 
#' used in all options
#' @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
#' @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 stats setNames
#' @return List of n elements of scatterplot matrices, 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
#' scatterplot matrices is saved to the location specified in the outDir
#' parameter as a JPG file.
#' @export
#' @examples
#' 
#' # The first set of six examples use data and dataMetrics
#' # objects as input. The last set of six examples create the same plots now
#' # using the SummarizedExperiment (i.e. dataSE) object input.
#' 
#' # Read in data and metrics (need for first set of six examples)
#' data(soybean_cn_sub)
#' data(soybean_cn_sub_metrics)
#' data(soybean_ir_sub)
#' data(soybean_ir_sub_metrics)
#' 
#' # Create standardized version of data (need for first set of six examples)
#' library(matrixStats)
#' library(ggplot2)
#' soybean_cn_sub_st <- as.data.frame(t(apply(as.matrix(soybean_cn_sub[,-1]),
#'     1, scale)))
#' soybean_cn_sub_st$ID <- as.character(soybean_cn_sub$ID)
#' soybean_cn_sub_st <- soybean_cn_sub_st[,c(length(soybean_cn_sub_st),
#'     1:length(soybean_cn_sub_st)-1)]
#' colnames(soybean_cn_sub_st) <- colnames(soybean_cn_sub)
#' nID <- which(is.nan(soybean_cn_sub_st[,2]))
#' soybean_cn_sub_st[nID,2:length(soybean_cn_sub_st)] <- 0
#' 
#' # Example 1: Plot scatterplot matrix of points. Saves three plots to outDir 
#' # because saveFile equals TRUE by default.
#' 
#' \dontrun{
#' plotSM(soybean_cn_sub, soybean_cn_sub_metrics)
#' }
#' 
#' # Example 2: Plot scatterplot matrix of points. Return list of plots so user 
#' # can tailor them (such as add title) and does not save to outDir because 
#' # saveFile equals FALSE.
#' 
#' ret <- plotSM(soybean_cn_sub, soybean_cn_sub_metrics, pointColor = "pink",
#'     saveFile = FALSE)
#' # Determine names of plots in returned list
#' names(ret)
#' ret[["S1_S2"]] + ggtitle("S1 versus S2")
#' ret[["S1_S3"]] + ggtitle("S1 versus S3")
#' ret[["S2_S3"]] + ggtitle("S2 versus S3")
#' 
#' # Example 3: Plot standardized data as scatterplot matrix of points.
#' 
#' ret <- plotSM(soybean_cn_sub_st, soybean_cn_sub_metrics,
#'     pointColor = "#00C379", saveFile = FALSE)
#' ret[[1]] + xlab("Standardized read counts") +
#' ylab("Standardized read counts")
#' 
#' # Example 4: Plot scatterplot matrix of hexagons.
#' 
#' ret <- plotSM(soybean_cn_sub, soybean_cn_sub_metrics, option = "hexagon", 
#'     xbins = 5, pointSize = 0.1, saveFile = FALSE)
#' ret[[2]]
#' 
#' # Example 5: Plot scatterplot matrix of orthogonal distance on the logged
#' # data, first without considering the metrics dataset and then considering
#' # it.
#' 
#' soybean_ir_sub[,-1] <- log(soybean_ir_sub[,-1] + 1) 
#' ret <- plotSM(soybean_ir_sub, option = "orthogonal", threshOrth = 2.5,
#'     pointSize = 0.2, saveFile = FALSE)
#' ret[[1]]
#' ret <- plotSM(soybean_ir_sub, soybean_ir_sub_metrics, option = "orthogonal", 
#'     threshOrth = 2.5, pointSize = 0.2, saveFile = FALSE)
#' ret[[1]]
#' 
#' # Example 6: Plot scatterplot matrix of fold change.
#' 
#' ret <- plotSM(soybean_cn_sub, soybean_cn_sub_metrics, option = "foldChange", 
#'     threshFC = 0.5, pointSize = 0.2, saveFile = FALSE)
#' ret[[1]]
#' 
#' # Below are the same six examples, only now using the
#' # SummarizedExperiment (i.e. dataSE) object as input.
#' 
#' # Read in data and metrics (need for first set of six examples)
#' data(se_soybean_cn_sub)
#' data(se_soybean_ir_sub)
#' 
#' # Create standardized version of data (need for first set of six examples)
#' library(matrixStats)
#' library(ggplot2)
#' library(SummarizedExperiment)
#' se_soybean_cn_sub_st = se_soybean_cn_sub
#' assay(se_soybean_cn_sub_st, withDimnames=FALSE) <-as.data.frame(t(
#'     apply(as.matrix(as.data.frame(assay(se_soybean_cn_sub))), 1, scale)))
#' nID <- which(is.nan(as.data.frame(assay(se_soybean_cn_sub_st))[,1]))
#' assay(se_soybean_cn_sub_st, withDimnames=FALSE)[nID,] <- 0
#' 
#' # Example 1: Plot scatterplot matrix of points. Saves three plots to outDir 
#' # because saveFile equals TRUE by default.
#' 
#' \dontrun{
#' plotSM(dataSE = se_soybean_cn_sub)
#' }
#' 
#' # Example 2: Plot scatterplot matrix of points. Return list of plots so user 
#' # can tailor them (such as add title) and does not save to outDir because 
#' # saveFile equals FALSE.
#' 
#' \dontrun{
#' ret <- plotSM(dataSE = se_soybean_cn_sub, pointColor = "pink",
#'     saveFile = FALSE)
#' # Determine names of plots in returned list
#' names(ret)
#' ret[["S1_S2"]] + ggtitle("S1 versus S2")
#' ret[["S1_S3"]] + ggtitle("S1 versus S3")
#' ret[["S2_S3"]] + ggtitle("S2 versus S3")
#' }
#' 
#' # Example 3: Plot standardized data as scatterplot matrix of points.
#' 
#' \dontrun{
#' ret <- plotSM(dataSE = se_soybean_cn_sub_st, pointColor = "#00C379",
#'     saveFile = FALSE)
#' ret[[1]] + xlab("Standardized read counts") +
#' ylab("Standardized read counts")
#' }
#' 
#' # Example 4: Plot scatterplot matrix of hexagons.
#' 
#' \dontrun{
#' ret <- plotSM(dataSE = se_soybean_cn_sub, option = "hexagon", xbins = 5, 
#'     pointSize = 0.1, saveFile = FALSE)
#' ret[[2]]
#' }
#' 
#' # Example 5: Plot scatterplot matrix of orthogonal distance on the logged
#' # data, first without considering the metrics dataset and then considering
#' # it.
#' 
#' \dontrun{
#' assay(se_soybean_ir_sub) <- log(as.data.frame(assay(se_soybean_ir_sub))+1)
#' ret <- plotSM(dataSE = se_soybean_ir_sub, option = "orthogonal",
#'     threshOrth = 2.5, pointSize = 0.2, saveFile = FALSE)
#' ret[[1]]
#' }
#' 
#' # Example 6: Plot scatterplot matrix of fold change.
#' 
#' \dontrun{
#' ret <- plotSM(dataSE = se_soybean_cn_sub, option = "foldChange", 
#'     threshFC = 0.5, pointSize = 0.2, saveFile = FALSE)
#' ret[[1]]
#' }
#' 

plotSM = function(data=data, dataMetrics=NULL, dataSE=NULL, geneList = NULL,
    threshVar="FDR", threshVal=0.05, option=c("allPoints", "foldChange",
    "orthogonal", "hexagon"), xbins=10, threshFC=3, threshOrth=3,
    pointSize=0.5, pointColor = "orange", outDir=tempdir(), saveFile = TRUE){
    
    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"   
            }
        }
    }
    
    # Check that input parameters fit required formats
    helperTestData(data)
    if (is.null(geneList) && !is.null(dataMetrics)){
        helperTestDataMetrics(data, dataMetrics, threshVar)
    }
    
    if (option=="foldChange"){
        
        ret <- helperSMFC(data, dataMetrics, outDir, pointSize, threshFC, threshVar,
                          threshVal)
        
        if (saveFile == TRUE){
            fName = paste0("_degSM_", threshFC, "_FC.jpg")
            helperSMPrint(ret, outDir, fName)
        }
        invisible(ret)
    }
    
    else if (option=="hexagon"){
        
        ret <- helperSMHex(data, dataMetrics, outDir, pointSize, pointColor, xbins, 
                           threshVar, threshVal, geneList)
        
        if (saveFile == TRUE){
            fName = paste0("_degSM_Hex_", threshVal, ".jpg")
            helperSMPrint(ret, outDir, fName)
        }
        invisible(ret)
    }
    
    else if (option=="orthogonal"){
        
        ret <- helperSMOrth(data, dataMetrics, outDir, pointSize, threshOrth,
                            threshVar, threshVal)
        
        if (saveFile == TRUE){
            fName = paste0("_degSM_", threshOrth, "_Orth.jpg")
            helperSMPrint(ret, outDir, fName)
        }
        invisible(ret)
    }  
    
    else if (option=="allPoints"){
        
        ret <- helperSMPoints(data, dataMetrics, outDir, pointSize, pointColor,
                              threshVar, threshVal, geneList)
        
        if (saveFile == TRUE){
            fName = paste0("_degSM_allPoints_", threshVar, "_", threshVal, ".jpg")
            helperSMPrint(ret, outDir, fName)
        }
        invisible(ret)
    }
    
    else {
        stop("Check that you selected a valid option parameter")
    }
}