R/draw_boxplot_gene.R

In jmzeng1314/humanid: gene id annotation

#' draw boxplot for a specific gene's values between two groups
#'
#'
#' @param gene  specific a gene which should be the rownames of exprSet
#' @param exprSet An expression matrix which rownames are genes and columns are samples
#' @param group_list defined which sample belong to which group
#' @return create a boxplot
#' @export
#' @keywords batch_enrichment
#' @examples
#' #'  draw_boxplot_gene(x,exprSet,group_list)
#'
#'

draw_boxplot_gene <- function(gene = "VCX3A", exprSet, group_list) {
    if (length(unique(group_list)) != 2) 
        stop("we just accept 2 groups for the group_list!!!")
    if (gene %in% rownames(exprSet)) {
        png(paste0(gene, "_boxplot.png"))
        dat1 = data.frame(value = as.numeric(exprSet[gene, ]), type = group_list)
        boxplot(value ~ type, data = dat1, lwd = 2, ylab = "value")
        title(main = gene, sub = t.test(value ~ type, data = dat1)$p.value)
        stripchart(value ~ type, vertical = TRUE, data = dat1, method = "jitter", add = TRUE, pch = 20, col = "blue")
        dev.off()
    }
}
# CTlist=read.table('CTlist.txt',stringsAsFactors = F)[,1] lapply(CTlist, function(x)
# draw_boxplot_gene(x,exprSet,group_list) )