#' Exploratory analysis of DESeq2 data
#'
#' @param dds DESeqDataSet object created by \code{DESeq2::DESeq}
#' @inheritParams deseq2_analysis
#'
#' @importFrom grDevices png dev.off
#' @importFrom DESeq2 plotDispEsts vst
#' @importFrom SummarizedExperiment assay
#' @importFrom utils write.table
exploratory_analysis <- function(dds, species, metadata) {
grDevices::png(
filename = "DESeq2_dispersionplot.png",
width = 8,
height = 8,
units = "in",
res = 500)
DESeq2::plotDispEsts(dds, genecol = "grey",
fitcol = "purple",
finalcol = "orange")
grDevices::dev.off()
vst <- DESeq2::vst(dds)
normcounts <- SummarizedExperiment::assay(vst)
rlddf <- data.frame(normcounts)
rownames(rlddf) <- names(dds)
colnames(rlddf) <- dds$sample
make_PCA(normcounts, metadata$sampleinfo)
utils::write.table(
x = rlddf,
file = "DESeq2_vst_normalisedcounts.txt",
sep = "\t", row.names = FALSE, quote = FALSE
)
}
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