#' @title
#' Differential gene expression matrix
#'
#' @author
#' Brandon Monier, \email{brandon.monier@sdstate.edu}
#'
#' @description
#' This function allows you to visualize the number of differentially
#' expressed genes
#' (DEG) at a given #' adjusted P-value for each experimental treatment level.
#' Higher color intensity correlates to a higher number of DEGs.
#'
#' @param data output generated from calling the main routines of either
#' `cuffdiff`, `DESeq2`, or `edgeR` analyses. For `cuffdiff`, this will be a
#' `*_exp.diff` file. For `DESeq2`, this will be a generated object of class
#' `DESeqDataSet`. For `edgeR`, this will be a generated object of class
#' `DGEList`.
#' @param padj a user defined adjusted p-value cutoff point. Defaults to
#' `0.05`.
#' @param d.factor a specified factor; for use with `DESeq2` objects only.
#' This input equates to the first parameter for the contrast argument when
#' invoking the `results()` function in `DESeq2`. Defaults to `NULL`
#' @param type an analysis classifier to tell the function how to process the
#' data. Must be either `cuffdiff`, `deseq`, or `edger`. `cuffdiff` must be
#' used with `cuffdiff` data; `deseq` must be used for `DESeq2` output;
#' `edgeR` must be used with `edgeR` data. See the `data` parameter for
#' further details.
#' @param title display the main title of plot. Logical; defaults to `TRUE`.
#' If set to `FALSE`, no title will display in plot.
#' @param legend display legend of plot. Logical; defaults to `TRUE`.
#' If set to `FALSE`, no legend will display in plot.
#' @param grid display major and minor axis lines. Logical; defaults to `TRUE`.
#' If set to `FALSE`, no axis lines will display in plot.
#'
#' @return An object created by \code{ggplot}
#'
#' @export
#'
#' @examples
#' # cuffdiff example
#' data("df.cuff")
#' vsDEGMatrix(
#' df.cuff, padj = 0.05, d.factor = NULL, type = 'cuffdiff',
#' title = TRUE, legend = TRUE, grid = TRUE
#' )
#'
#' # DESeq2 example
#' data("df.deseq")
#' require(DESeq2)
#' vsDEGMatrix(
#' df.deseq, padj = 0.05, d.factor = 'condition', type = 'deseq',
#' title = TRUE, legend = TRUE, grid = TRUE
#' )
#'
#' # edgeR example
#' data("df.edger")
#' require(edgeR)
#' vsDEGMatrix(
#' df.edger, padj = 0.05, d.factor = NULL, type = 'edger',
#' title = TRUE, legend = TRUE, grid = TRUE
#' )
vsDEGMatrix <- function(
data, padj = 0.05, d.factor = NULL,
type = c("cuffdiff", "deseq", "edger"), title = TRUE, legend = TRUE,
grid = TRUE
) {
if (missing(type) || !type %in% c("cuffdiff", "deseq", "edger")) {
stop('Please specify analysis type ("cuffdiff", "deseq", or "edger")')
}
type <- match.arg(type)
if(type == 'cuffdiff'){
dat <- .getCuffDEGMat(data, padj)
} else if (type == 'deseq') {
dat <- .getDeseqDEGMat(data, d.factor, padj)
} else if (type == 'edger') {
dat <- .getEdgeDEGMat(data, padj)
}
if (!isTRUE(legend)) {
leg <- guides(fill = FALSE)
} else {
leg <- NULL
}
if (!isTRUE(title)) {
m.lab <- NULL
} else {
m.lab <- ggtitle(
bquote('Significant transcripts at ' ~ alpha ~ ' = ' ~ .(padj))
)
}
if (!isTRUE(grid)) {
grid <- theme_classic()
} else {
grid <- theme_bw()
}
x <- y <- ..n.. <- NULL
tmp.plot <- ggplot(dat, aes(x = x, y = y)) +
stat_sum(
aes(fill = ..n..),
color = "black", size = 0.3, geom = "tile"
) +
scale_fill_continuous(
low = "white", high = "royalblue3",
name = 'Number of \ntranscripts'
) +
expand_limits(fill = 0) + leg +
stat_sum(
aes(label = ..n..), geom = "text", size = 5, show.legend = FALSE
) +
m.lab + grid + xlab('') + ylab('')
print(tmp.plot)
}
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