R/eset_distribution.R

In IOBR/IOBR: Immune Oncology Biological Research

#' Title eset_distribution
#'
#' @description eset_distribution generates boxplots and density plots to analyze the distribution of expression values in an expression set (eset).
#' @param eset Expression set (matrix or data frame) containing gene expression data.
#' @param quantile Number of quantiles used for sampling columns in the eset matrix.
#' @param log Logical value indicating whether to perform log2 transformation of the expression values.
#' @param project Optional string specifying the name of the project. If not provided, a default name ('ESET') is used.
#'
#' @return
#' @export
#'
#' @examples
#' data(eset_gse62254, package = "IOBR")
#' eset <- anno_eset(eset = eset_gse62254, annotation = anno_hug133plus2)
#' eset_distribution(eset)
eset_distribution <- function(eset, quantile = 3, log = TRUE, project = NULL){



  feas <- feature_manipulation(data = eset, feature = rownames(eset), is_matrix = TRUE)
  eset<- eset[rownames(eset)%in%feas, ]

  index <- colnames(eset)[sample(1:ncol(eset), round(dim(eset)[2]/quantile,0))]
  eset1<-eset[, index]
  eset1 <- log2eset(eset1)

  eset1 <- eset1 %>% t %>% data.frame(Sample.Name = colnames(eset1))
  eset.melt <- reshape2:: melt(eset1, id = c("Sample.Name"))
  head(eset.melt)
  colnames(eset.melt)[2:3] <- c("Symbol", "Intensity")
  ######################################
  if(is.null(project)){
    path <- creat_folder("result")
    project <- "ESET"
  }else{
    path <- creat_folder(project)
  }

  p <- ggplot(eset.melt, aes(x = Sample.Name, y = Intensity)) +
    geom_boxplot() + theme_bw()+ theme(plot.title = element_text(size=23))
  p <- p + theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1.0))
  p <- p + ggtitle("Normalized signal intensity",
                   paste0("Patient No. is:  ", dim(eset)[2],"; ",
                          "Number of features is: ", dim(eset)[1], ";  ",
                          "Maximum is: ",round(max(eset),2)))+
    ylab("Intensity") + xlab("Sample")
  p <- p + theme(legend.position = "none", panel.grid.major = element_blank(),
                 panel.grid.minor = element_blank())+
    theme(plot.subtitle=element_text(size=18, hjust=0.1, face="italic", color="black"))
  ###################################
  ggsave(filename = paste0("1-",project,"-boxplot.png"), plot = p,
         width = 15 , height = 8,path = path$folder_name)
  ####################################

  p <- ggplot(eset.melt, aes(Intensity, group = Sample.Name)) + geom_density() + theme_bw()
  p <- p + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
  p <- p + ggtitle("Histogram of Log2 Expression") + ylab("Density") + xlab("Log2 Expression")
  ggsave(filename = paste0("2-", project,"-Densityplot.png"), plot = p,
          width = 9 , height = 6,path = path$folder_name)

}