R/MetascapeUtils.R

In RyanYip-Kat/yipCat: Some function like ArchR style in Seurat Object

#' metascape GO result left and right plot
#' @param leftDF DataFrame show in left
#' @param rightDF DataFrame show in right
#' @param pal which color pal use
#' @example save whether save
#' @export
metascapeBarPlot<-function(leftDF=NULL,
                           rightDF=NULL,
                           pal="Set1",
                           save=TRUE,
                           outdir="metascape"){
  require(ggplot2)
  colNames<-colnames(rightDF)
  stopifnot(ncol(leftDF)==ncol(rightDF))
  stopifnot("Description"%in%colNames)
  stopifnot("Enrichment"%in%colNames)


  leftDF$Enrichment= -leftDF$Enrichment
  mydata<-rbind(leftDF,rightDF)

  mydata$Description<-as.character(mydata$Description)
  mydata<-transform(mydata, label1=ifelse(Enrichment>=0,Description, NA),

                    label2=ifelse(Enrichment>0, NA,Description))
  mydata$Description <- factor(mydata$Description, levels = mydata$Description[order(mydata$Enrichment)])
  p<-ggplot(data = mydata, aes(x =Description, y =Enrichment ,fill = Enrichment)) +
    geom_bar(stat = "identity", width = 0.8,colour="black",size=0.25)+
    scale_fill_gradient2(low=brewer.pal(7,pal)[2],mid="grey90",high=brewer.pal(7,pal)[1],midpoint=0)+
    geom_text(aes(y = 0,     label=label2),size=3,hjust=-0.1)+ #添加负值部分的数据标签
    geom_text(aes(y = -0.001,label=label1),size=3,hjust= 1.1)+ #添加正值部分的数据标签
    coord_flip() +   #坐标轴翻转
    ylim(-5,5)+
    theme_minimal() + #图表主题设定
    theme(
      panel.grid.major=element_blank(),
      panel.grid.minor=element_blank(),
      panel.grid.major.x = element_line(colour = "grey80",size=.25),
      panel.grid.minor.x = element_line(colour = "grey80",size=.25),
      plot.title=element_text(size=15,hjust=.5),
      axis.text.x = element_text(face="plain", color="black",
                                 size=11, angle=0),
      axis.text.y = element_blank(),
      legend.position="right",
      legend.text=element_text(size=10),
      legend.title=element_text(size=10))
  if(save){
    if(is.null(outdir)){
      outdir="plot"
    }
    if(!dir.exists(outdir)){
      dir.create(outdir,recursive = TRUE)
    }
    filename<-file.path(outdir,"metascapeGO.pdf")
    ggsave(filename = filename,plot = p,width = 8,height = 12)
  }
  return(p)
}