R/gseSummary.R

In xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data

#' Summary GSE results
#'
#' @param obj a DEGContainer
#' @param dir a directory to store results
#' @param prefix a prefix of file names in this step
#' @param top top rows of up and down
#'
#' @return files
#' @export
#'
#' @examples
#' gseSummary(DEGContainer)
gseSummary <- function(obj, dir = ".", prefix = "4-runGSEA",top =10) {

  if (!fs::dir_exists(dir)) {
    fs::dir_create(dir)
  }

  ## get data
  # ui_info("Start summary ")
  res_list <- gseRes(obj = obj)$gseKEGG_res

  if(!is.null(res_list)){
    # ## KEGG data
    ## 条形图
    plot_list <- lapply(seq_along(res_list), function(i){
      x = res_list[[i]]
      GSEAbar(x,top = top) +
        theme(legend.position="none") +
        ggtitle(names(res_list)[i])

    })

    legend <- cowplot::get_legend(
      # create some space to the left of the legend
      plot_list[[1]] + ggplot2::theme(legend.position="right",legend.box.margin = ggplot2::margin(0, 0, 0, 12))
    )

    p <- cowplot::plot_grid(plotlist = plot_list,legend,ncol = 5, rel_widths = c(.4,3,3,3,3))

    ggplot2::ggsave(p,filename = glue::glue("{dir}/{prefix}_KEGG_bar.pdf"), width = 6400,height = 1200*(top*2/10),units = "px",limitsize = FALSE,device = cairo_pdf)

    ## 趋势图
    tmp <- lapply(seq_along(res_list), function(i){

      x = res_list[[i]]

      gseaplots_l <- GSEAplot(x,top =top)

      ## 保存gse富集趋势图到多页pdf
      mod <- names(res_list)[i]
      down_plots_pdf <- glue("{dir}/{prefix}_KEGG_{mod}_Down_gseplot.pdf")
      pdf(down_plots_pdf,height = 3,width = 4)
      invisible(lapply(gseaplots_l[["down_plots"]], print))
      dev.off()
      ui_done(glue("Enrichplot of KEGG head {top} {mod} in Down ploted in {ui_path({down_plots_pdf})}"))

      up_plots_pdf <- glue("{dir}/{prefix}_KEGG_{mod}_Up_gseplot.pdf")
      pdf(up_plots_pdf,height = 3,width = 4)
      invisible(lapply(gseaplots_l[["up_plots"]], print))
      dev.off()
      ui_done(glue("Enrichplot of KEGG head {top} {mod} in Up ploted in {ui_path({up_plots_pdf})}"))

    })

    ## csv
    tmp <- lapply(seq_along(res_list), function(i){

      res <- res_list[[i]]
      dat <- res@result

      res_name <- glue("{dir}/{prefix}_KEGG_{names(res_list)[i]}.csv")
      write.csv(dat,file = res_name)
      ui_done(glue("{names(res_list)[i]} GSE KEGG result in csv format is stored in {usethis::ui_path(res_name)}"))

    })
  }

  res_list <- gseRes(obj = obj)$gseGO_res

  if(!is.null(res_list)){

    # ## GO data
    ## 条形图
    plot_list <- lapply(seq_along(res_list), function(i){
      x = res_list[[i]]
      GSEAbar(x,top = top) +
        theme(legend.position="none") +
        ggtitle(names(res_list)[i])

    })

    legend <- cowplot::get_legend(
      # create some space to the left of the legend
      plot_list[[1]] + ggplot2::theme(legend.position="right",legend.box.margin = ggplot2::margin(0, 0, 0, 12))
    )

    p <- cowplot::plot_grid(plotlist = plot_list,legend,ncol = 5, rel_widths = c(.4,3,3,3,3))

    ggplot2::ggsave(p,filename = glue::glue("{dir}/{prefix}_GO_bar.pdf"), width = 6400,height = 1200*(top*2/10),units = "px",limitsize = FALSE,device = cairo_pdf)


    ## 趋势图
    tmp <- lapply(seq_along(res_list), function(i){

      x = res_list[[i]]

      gseaplots_l <- GSEAplot(x,top =top)

      ## 保存gse富集趋势图到多页pdf
      mod <- names(res_list)[i]
      down_plots_pdf <- glue("{dir}/{prefix}_GO_{mod}_Down_gseplot.pdf")
      pdf(down_plots_pdf,height = 3,width = 4)
      invisible(lapply(gseaplots_l[["down_plots"]], print))
      dev.off()
      ui_done(glue("Enrichplot of GO head {top} {mod} in Down ploted in {ui_path({down_plots_pdf})}"))

      up_plots_pdf <- glue("{dir}/{prefix}_GO_{mod}_Up_gseplot.pdf")
      pdf(up_plots_pdf,height = 3,width = 4)
      invisible(lapply(gseaplots_l[["up_plots"]], print))
      dev.off()
      ui_done(glue("Enrichplot of GO head {top} {mod} in Up ploted in {ui_path({up_plots_pdf})}"))

    })

    ## csv
    tmp <- lapply(seq_along(res_list), function(i){

      res <- res_list[[i]]
      if (!is.null(res)) {dat <- res@result}

      res_name <- glue("{dir}/{prefix}_GO_{names(res_list)[i]}.csv")
      write.csv(dat,file = res_name)
      ui_done(glue("{names(res_list)[i]} GSE GO result in csv format is stored in {usethis::ui_path(res_name)}"))

    })

  }


}