#' @importFrom ggplot2 ggplot
globalVariables(".")
#'
#'
NULL
#' Produces CA plot
#' @param feat_count Count table from featurecounts
#' @param DESeq2_object A DESeq2 object
#' @param feature_name name of the feature from gff table that is being counted
#' @param outdir A folder to write all the files
#'
#'
#' @return creates PCA plot of PDF and PNG figures
#'
#' @export
#'
#'
DESeq2_CAplot <- function(feat_count, DESeq2_object, outdir, feature_name){
base::ifelse(!base::dir.exists(outdir),
base::dir.create(outdir),
print("already exist"))
dds <- DESeq2::DESeq(DESeq2_object)
pca_pdf <- file.path(outdir,
paste(strsplit(basename(feat_count), ".tsv")[[1]],
"_PCA.pdf", sep = ""))
pca_png <- file.path(outdir,
paste(strsplit(basename(feat_count), ".tsv")[[1]],
"_PCA.png", sep = ""))
dds_vts <- DESeq2::varianceStabilizingTransformation(dds)
pca <- DESeq2::plotPCA(dds_vts, intgroup = c("Group"))
ggplot2::ggsave(pca_pdf, pca, device = "pdf")
ggplot2::ggsave(pca_png, pca, device = "png")
}
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