R/volGeneTE.R

In ferygood/twice: A collections of useful functions to analyze transcription factors and transposable elements data

#' Gene and TEs volcano plot function
#'
#' @description visualize the gene and TEs expression using volcano plots
#' @param resGene res Gene expression data from TEKRABber
#' @param resTE res TE expression data from TEKRABber
#' @param fileName specify the file name if you want to save the figure
#'
#' @import EnhancedVolcano
#' @import ggpubr
#' @return ggplot object
#' @export
#'
#' @examples
#' data(resHmChimpGene)
#' data(resHmChimpTE)
#'
#' volGeneTE(resHmChimpGene, resHmChimpTE)
#'
volGeneTE <- function(resGene, resTE, fileName=NULL) {

    #convert ensembl ID to gene name
    resGene <- ensIDtoName(resGene)

    # custom volcano func.
    vol <- function(df){
        EnhancedVolcano(df,
                        lab = rownames(df),
                        x = 'log2FoldChange',
                        y = 'pvalue',
                        labSize = 3.0,
                        FCcutoff = 1.0,
                        pCutoff = 0.05,
                        legendPosition = 'none',
                        legendLabSize = 10,
                        title = "",
                        subtitle = "",
                        caption = "")
    }

    geneVol <- vol(resGene)
    teVol <- vol(resTE)

    g <- ggarrange(geneVol, teVol)

    if (!is.null(fileName)) {
        ggsave(fileName,g, dpi=500, width=8.4, height=5.99)
    }

    g
}