R/vsScatterMatrix.R

In btmonier/ggviseq: Create rapid visualizations of RNAseq data in R

#' @title
#' Scatter plot matrix of \eqn{log_{10}}(FPKM or CPM) values
#'
#' @author
#' Brandon Monier, \email{brandon.monier@sdstate.edu}
#'
#' @description
#' This function will generate a matrix of scatterplots for all possible
#' treatment combinations with additional distribution info.
#'
#' @param data output generated from calling the main routines of either
#'  \code{cuffdiff}, \code{DESeq2}, or \code{edgeR} analyses. For
#'  \code{cuffdiff}, this will be a \code{*_exp.diff} file. For \code{DESeq2},
#'  this will be a generated object of class \code{DESeqDataSet}. For
#'  \code{edgeR}, this will be a generated object of class \code{DGEList}.
#' @param d.factor a specified factor; for use with \code{DESeq2} objects only.
#'  This input equates to the first parameter for the contrast argument when
#'  invoking the \code{results()} function in \code{DESeq2}. Defaults to
#'  \code{NULL}.
#' @param type an analysis classifier to tell the function how to process the
#'  data. Must be either \code{cuffdiff}, \code{deseq}, or \code{edger}.
#'  \code{cuffdiff} must be used with \code{cuffdiff} data; \code{deseq} must
#'  be used for \code{DESeq2} output; \code{edgeR} must be used with
#'  \code{edgeR} data. See the \code{data} parameter for further details.
#' @param comp treatments you would like to compare in the form of a vector.
#'  If no parameter is specified, all possible treatment comparisons will be
#'  made. Defaults to \code{NULL}.
#' @param title display the main title of plot. Logical; defaults to
#'  \code{TRUE}. If set to \code{FALSE}, no title will display in plot.
#' @param grid display major and minor axis lines. Logical; defaults to
#'  \code{TRUE}. If set to \code{FALSE}, no axis lines will display in plot.
#' @param man.title a manually specified title at the authors discretion.
#'  Defaults to \code{NULL}.
#' @param data.return returns data output of plot. Logical; defaults to
#'  \code{FALSE}. If set to \code{TRUE}, a data frame will also be called.
#'  Assign to object for reproduction and saving of data frame. See final
#'  example for further details.
#' @param xaxis.title.size change the font size of the \code{x}-axis title
#'  text. Defaults to \code{10}.
#' @param xaxis.text.size change the font size of the \code{x}-axis text.
#'  Defaults to \code{9}.
#' @param yaxis.title.size change the font size of the \code{y}-axis title
#'  text. Defaults to \code{10}.
#' @param yaxis.text.size change the font size of the \code{y}-axis text.
#'  Defaults to \code{9}.
#' @param main.title.size change the font size of the plot title text.
#'  Defaults to \code{15}.
#' @param facet.title.size change the font size of the facet wrap title text.
#'  Defaults to \code{10}.
#'
#' @return An object created by \code{ggplot}
#'
#' @export
#'
#' @examples
#' # Cuffdiff example
#' data("df.cuff")
#' vsScatterMatrix(
#'      data = df.cuff, d.factor = NULL, type = "cuffdiff",
#'      comp = NULL, title = TRUE, grid = TRUE,
#'      man.title = "Example title"
#' )
#'
#' # DESeq2 example
#' data("df.deseq")
#' require(DESeq2)
#' vsScatterMatrix(
#'      data = df.deseq, d.factor = "condition", type = "deseq",
#'      comp = NULL, title = TRUE, grid = FALSE, man.title = NULL
#' )
#'
#' # edgeR example
#' data("df.edger")
#' require(edgeR)
#' vsScatterMatrix(
#'      data = df.edger, d.factor = NULL, type = "edger",
#'      comp = c("WM", "MM"), title = TRUE, grid = TRUE,
#'      man.title = NULL
#' )
#'
#' # Extract data frame from visualization
#' data("df.edger")
#' tmp <- vsScatterMatrix(
#'      data = df.edger, d.factor = NULL, type = "edger",
#'      comp = c("WM", "MM"), title = TRUE, grid = TRUE,
#'      man.title = NULL, data.return = TRUE
#' )
#' df_scatmat <- tmp[[1]] ## or use tmp$data
#' head(df_scatmat)
#'
#' # Show plot from object (see prior example for more details)
#' tmp[[2]] ## or use tmp$plot

vsScatterMatrix <- function(
    data, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"),
    comp = NULL, title = TRUE, grid = TRUE, man.title = NULL,
    data.return = FALSE, xaxis.text.size = 9, yaxis.text.size = 9,
    xaxis.title.size = 10, yaxis.title.size = 10, main.title.size = 15,
    facet.title.size = 10
) {
    if (missing(type) || !type %in% c("cuffdiff", "deseq", "edger")) {
        stop(
            paste(
                "Please specify analysis type",
                "(\"cuffdiff\", \"deseq\", or \"edger\")"
            )
        )
    }

    type <- match.arg(type)
    if (type == "cuffdiff") {
        dat <- .getCuffScatterMatrix(data)
    } else if (type == "deseq") {
        dat <- .getDeseqScatterMatrix(data, d.factor)
    } else if (type == "edger") {
        dat <- .getEdgeScatterMatrix(data)
    }

    if(!is.null(comp)) {
        comp <- comp
    } else {
        comp <- seq_len(ncol(dat))
    }

    if (!isTRUE(title)) {
        m.title <- NULL
    } else if (isTRUE(title) & !is.null(man.title)) {
        m.title <- ggtitle(man.title)
    } else if (isTRUE(title) & type == "edger") {
        m.title <- "CPM Comparisons"
    } else {
        m.title <- "FPKM Comparisons"
    }

    if (!isTRUE(grid)) {
        grid <- theme_classic()
    } else {
        grid <- theme_bw()
    }

    if (type == "edger") {
        aes.xlab <- bquote("log"["10"] ~ "(CPM)")
        aes.ylab <- bquote("log"["10"] ~ "(CPM)")
    } else {
        aes.xlab <- bquote("log"["10"] ~ "(FPM)")
        aes.ylab <- bquote("log"["10"] ~ "(FPM)")
    }

    text.size <- theme(
        axis.text.x = element_text(size = xaxis.text.size),
        axis.text.y = element_text(size = yaxis.text.size),
        axis.title.x = element_text(size = xaxis.title.size),
        axis.title.y = element_text(size = yaxis.title.size),
        plot.title = element_text(size = main.title.size),
        strip.text = element_text(size = facet.title.size)
    )

    tmp.plot <- GGally::ggpairs(
        log10(dat + 1),
        title = m.title,
        xlab = aes.xlab,
        ylab = aes.ylab,
        columns = comp,
        lower = list(continuous = wrap("points", size = 0.5))
    ) + grid + text.size

    if (isTRUE(data.return)) {
        plot.l <- list(data = dat, plot = tmp.plot)
    } else {
        print(tmp.plot)
    }
}