R/overallGSEA.R

In Feng-Zhang/RNAseqFlow:

#  @title plot_overallGSEA
#  @description This function would generate bar plot for GSEA results
#  @param data Default dataset to use for plot.
#  @param x Default x of aesthetic mappings to use for plot. Generally, it is Description for enrichment pathway.
#  @param y Default y of aesthetic mappings to use for plot. Generally, it is NES.
#  @return a ggplot2 object
#  @examples
#  \dontrun{
#   data(geneList, package="DOSE")
#   geneChangeList <- sort(geneList, decreasing = TRUE)
#   ego <- gseGO(geneChangeList, ont="BP",OrgDb=org.Hs.eg.db,eps=0)
#   ego <- setReadable(ego, OrgDb =org.Hs.eg.db)
#   data <- ego[127:147,1:9]
#   print(overallGSEA(data,Description,NES))
#   }
#  @import ggplot2
#  @export
#
# plot_overallGSEA = function(data,x,y){
#   xExpr <- substitute(x)
#   yExpr <- substitute(y)
#   data <- data[order(eval(yExpr,data)),]
#   data[,"regulate"] <- ifelse(eval(yExpr,data)>0,"Up","Down")
#   #  data[,"regulate"] <- as.factor(data[,"regulate"])
#   data[,deparse(xExpr)] <- factor(eval(xExpr,data),levels = eval(xExpr,data))
#   p <- ggplot(data,aes_(xExpr,yExpr,fill=substitute(regulate)))+
#     geom_bar(stat = "identity")+
#     coord_flip()+scale_fill_manual(values =c("blue","red"))+
#     xlab("") + ylab("Normalized Enrichment Score (NES)")+labs(title = "Overall GSEA")+
#     theme_classic()+
#     theme(legend.position="none",
#           plot.title = element_text(colour = "black", face = "bold", size = 15, hjust = 0))
#   return(p)
# }


##' @title plot_overallGSEA
##' @description This function would generate bar plot for GSEA results
##' @param gsea_res Default dataset to use for plot.
##' @param x Default x of aesthetic mappings to use for plot. Generally, it is Description for enrichment pathway.
##' @param y Default y of aesthetic mappings to use for plot. Generally, it is NES.
##' @return a ggplot2 object
##' @examples
##' \dontrun{
##'  data(geneList, package="DOSE")
##'  geneChangeList <- sort(geneList, decreasing = TRUE)
##'  ego <- gseGO(geneChangeList, ont="BP",OrgDb=org.Hs.eg.db,eps=0)
##'  ego <- setReadable(ego, OrgDb =org.Hs.eg.db)
##'  data <- ego[127:147,1:9]
##'  print(overallGSEA(data,"Description","NES"))
##'  }
##' @import ggplot2
##' @export

plot_overallGSEA = function(gsea_res,x="Description",y="NES"){
  regulate <- NULL
  stopifnot(all(c(x,y)%in% colnames(gsea_res)))
  gsea_res <- gsea_res[order(gsea_res[,y]),]
  gsea_res[,"regulate"] <- ifelse(gsea_res[,y]>0,"Up","Down")
  gsea_res[,x] <- factor(gsea_res[,x],levels = gsea_res[,x])
  p <- ggplot(gsea_res,aes(.data[[x]],.data[[y]],fill=regulate))+
    geom_bar(stat = "identity")+
    coord_flip()+scale_fill_manual(values =c("blue","red"))+
    xlab("") + ylab("Normalized Enrichment Score (NES)")+labs(title = "Overall GSEA")+
    theme_classic()+
    theme(legend.position="none",
          plot.title = element_text(colour = "black", face = "bold", size = 15, hjust = 0))
  return(p)
}