R/plot_gsea.R

In ylab-hi/lncGSEA: lncRNA Associated Gene Set Enrichement Analysis

#' plot enriched pathways
#' A function to plot enriched pathways, y axis is normalized enrichment
#' score, x axis is sign(NES)*(-log10(FDR))
#' @param gsea.df A data frame, output from sg_gsea function
#' @param pathway.list Pathways user provided to label, a character variable
#' @param direction A string, "pos" or "neg" or "both" to label positive or negative or both enriched pathways
#' @param n A number, defining how many pos or neg or both pathways to label
#'
#' @import ggplot2
#' @import RColorBrewer
#' @import ggrepel
#' @import dplyr
#'
#' @return A pdf plot with NES as y axis and sign(NES)*(-log10(FDR)) as x axis
#'
#' @example
#'
#' test <- plot_gsea("T025160_OV_cor.txt")
#' test <- plot_gsea("T025160_OV_cor.txt", direction = "user",
#' pathway.list = "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION")
#' test <- plot_gsea("ENST00000417354_OV_cor_hallmark.txt")
#'
#' @export


plot_gsea <- function(gsea.df,pathway.list=NULL,direction=c("both","pos","neg"),n=3){

    # process data for plot ---
    dat <- read.delim(gsea.df, header = TRUE, stringsAsFactors = FALSE, sep = "\t")
    dat <- dat[, c("pathway","NES","padj")]
    dat$RANK <- order(dat$NES)
    dat$logP <- -log10(dat$padj + 0.00001)
    dat$logP.sign <- sign(dat$NES)*dat$logP

    direction <- match.arg(direction)

    # pathway to label ---
    if (is.null(pathway.list)) {
        if (direction == "both"){
            label.max <- slice_max(dat, order_by = NES, n=n)
            label.min <- slice_min(dat, order_by = NES, n=n)
            label <- rbind(label.max, label.min)

        }
        if (direction == "pos"){
            label <- slice_max(dat, order_by = NES, n=n)
        }
        if (direction == "neg") {
            label <- slice_min(dat, order_by = NES, n=n)
        }
    } else {
        print("Label pathways user provided.")
        label <- data.frame(pathway=pathway.list)
    }
    # label top or bottom pathways ---
    for (i in 1:nrow(dat)){
        dat$name[i] <- ifelse(dat$pathway[i]%in%label$pathway, "Yes","No")
    }


    ptest<-ggplot(dat,aes(x=logP.sign,y=NES,label = ifelse(name == "Yes",as.character(pathway),"")))+
        geom_point(aes(color = logP))+
        scale_color_gradient(low = "blue", high = "red") +
        geom_vline(xintercept = 1.30103,linetype="dashed",size=0.5,alpha=0.2)+
        geom_vline(xintercept = -1.30103,linetype="dashed",size=0.5,alpha=0.2)+
        geom_hline(yintercept = 0,linetype="dashed",size=0.5,alpha=0.2)+
        labs(x="sign(NES)*(-log10(FDR))",y="Normal Enrichement Score",color='-log10(q)')+
        theme_bw()+
        theme(panel.grid.major=element_blank(),
              panel.grid.minor=element_blank())+
        theme(legend.position = c(0.89, 0.25),
              text = element_text(size=12))

    set.seed(00)
    ppd<-ptest+geom_text_repel(data=dat,nudge_x=-1,direction="y",force=2,max.iter=4000,hjust=1,segment.size=0.2,size = 2)

    ppd
}