R/Script_PLATE_08_DE_2_1_PlotDEValues_PSI_Distance.R

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

#' @title Plot differential splicing analysis results based on distance statistics.
#'
#' @description Ranked plot for differential splicing analysis results based on distance statistics. Only statistical test that assess the overall PSI distribution between two cell groups will be eligible for plotting here, e.g., Anderson-Darling and DTS. x-axis represents the distance statistics. y-axis represents the adjusted p-values.
#'
#' @param MarvelObject Marvel object. S3 object generated from \code{CompareValues} function.
#' @param method Character string. The statistical method used for differential splicing analysis.
#' @param pval Numeric value. Adjusted p-value below which the splcing events are considered as statistically significant and will consequently be color-annotated on the plot.
#' @param point.size Numeric value. The point size for the data points. Default value is \code{1}.
#' @param anno Logical value. If set to \code{TRUE}, the specific gene names will be annotated on the plot. Speficified together with \code{anno.tran_id}.
#' @param anno.tran_id Vector of character strings. When \code{anno} set to \code{TRUE}, the coordinates of the splicing events to be annotated on the plot.
#' @param label.size Numeric value. Only applicable if \code{anno} set to TRUE. Size of the gene name labels.
#' @param y.upper.offset Numeric value. The value in -log10(p-value) to increase the upper limit of the y-axis. To be used when \code{anno} set to TRUE so that gene labels will not be truncated at the upper limit of the y-axis.
#' @param xlabel.size Numeric value. Font size of the xtick labels. Default is \code{8}.
#'
#' @return An object of class S3 containing with new slot \code{MarvelObject$DE$PSI$Plot[["method"]]}.
#'
#' @importFrom plyr join
#' @import ggplot2
#' @import scales
#'
#' @export
#'
#' @examples
#' marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))
#'
#' marvel.demo <- PlotDEValues.PSI.Distance(MarvelObject=marvel.demo,
#'                                          method="ad",
#'                                          pval=0.10
#'                                          )
#'
#' # Check output
#' marvel.demo$DE$PSI$Plot[["ad"]]

PlotDEValues.PSI.Distance <- function(MarvelObject, method, pval, point.size=1, xlabel.size=8, anno=FALSE, anno.tran_id=NULL, label.size=2.5, y.upper.offset=5) {

    # Define arguments
    method <- method
    df <- MarvelObject$DE$PSI$Table[[method]]
    pval <- pval
    point.size <- point.size
    anno <- anno
    anno.tran_id <- anno.tran_id
    label.size <- label.size
    y.upper.offset <- y.upper.offset
    xlabel.size <- xlabel.size
    
    # Example arguments
    #method <- "ad"
    #df <- marvel$DE$PSI$Table[[method]]
    #pval <- 0.10
    #point.size <- 1
    #anno <- FALSE
    #anno.tran_id <- tran_ids
    #label.size <- 2.5
    
    # Remove outliers
    df <- df[which(df$outlier==FALSE), ]
    
    # Indicate sig events and direction
    df$sig <- ifelse(df$p.val.adj < pval, "sig", "n.s.")
    df$sig <- factor(df$sig, levels=c("sig", "n.s."))

    # Indicate direction on D statistic
    # df$statistic <- ifelse(df$mean.diff < 0, df$statistic * -1, df$statistic)
    
    # Create labels
    if(anno==TRUE) {
                           
       df$label <- paste(df$gene_short_name, " (", df$event_type, ")", sep="")
       df$label <- ifelse(df$tran_id %in% anno.tran_id, df$label, "")
                           
       # Definition
       data <- df
       x <- c(1:nrow(df))
       y <- -log10(data$p.val.adj)
       z <- data$sig
       label <- data$label
       maintitle <- ""
       xtitle <- "Rank"
       ytitle <- "-log10(p-value)"

       ymin <- 0 ; ymax <- max(y) + y.upper.offset ; yinterval <- 5
           
       sig <- sum(data$sig=="sig")
       n.s. <- sum(data$sig=="n.s.")

       if(sig != 0 & n.s. != 0) {

           col.breaks <- c("red", "gray")
           
       } else if(sig != 0 & n.s. == 0) {

           col.breaks <- "red"
           
       } else if(sig == 0 & n.s. != 0) {

           col.breaks <- "gray"

       }

       # Plot
       plot <- ggplot() +
                  geom_point(data, mapping=aes(x=x, y=y, color=z), shape=20, alpha = 0.75, size=point.size) +
                  ggrepel::geom_text_repel(data, mapping=aes(x=x, y=y, label=label), max.overlaps = Inf, box.padding = 1.0, size=label.size, max.time = 1, max.iter = 1e5, segment.alpha=0.5, segment.size=0.1, min.segment.length = 0) +
                  scale_colour_manual(values=col.breaks) +
                  #scale_x_log10(breaks=c(1, 10, 25, 50, 100), limits=c(1, 200)) +
                  scale_y_continuous(breaks=seq(ymin, ymax, by=yinterval), limits=c(ymin, ymax)) +
                  labs(title=maintitle, x=xtitle, y=ytitle) +
                   theme(panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       panel.background = element_blank(),
                       panel.border=element_blank(),
                       plot.title=element_text(hjust = 0.5, size=15),
                       plot.subtitle=element_text(hjust = 0.5, size=15),
                       axis.line.y.left = element_line(color="black"),
                       axis.line.x = element_line(color="black"),
                       axis.title=element_text(size=12),
                       axis.text=element_text(size=12),
                       axis.text.x=element_text(size=xlabel.size, colour="black"),
                       axis.text.y=element_text(size=10, colour="black"),
                       legend.position="none",
                       legend.title=element_text(size=8),
                       legend.text=element_text(size=8)
                       )
    
    } else {
        
        # Definition
        data <- df
        x <- c(1:nrow(df))
        y <- -log10(data$p.val.adj)
        z <- data$sig
        maintitle <- ""
        xtitle <- "Rank"
        ytitle <- "-log10(p-value)"

        ymin <- 0 ; ymax <- max(y) ; yinterval <- 5
            
        sig <- sum(data$sig=="sig")
        n.s. <- sum(data$sig=="n.s.")

        if(sig != 0 & n.s. != 0) {

            col.breaks <- c("red", "gray")
            
        } else if(sig != 0 & n.s. == 0) {

            col.breaks <- "red"
            
        } else if(sig == 0 & n.s. != 0) {

            col.breaks <- "gray"

        }

        # Plot
        plot <- ggplot() +
                   geom_point(data, mapping=aes(x=x, y=y, color=z), shape=20, alpha = 0.75, size=point.size) +
                   scale_colour_manual(values=col.breaks) +
                   #scale_x_log10(breaks=c(1, 10, 25, 50, 100), limits=c(1, 200)) +
                   scale_y_continuous(breaks=seq(ymin, ymax, by=yinterval), limits=c(ymin, ymax)) +
                   labs(title=maintitle, x=xtitle, y=ytitle) +
                    theme(panel.grid.major = element_blank(),
                        panel.grid.minor = element_blank(),
                        panel.background = element_blank(),
                        panel.border=element_blank(),
                        plot.title=element_text(hjust = 0.5, size=15),
                        plot.subtitle=element_text(hjust = 0.5, size=15),
                        axis.line.y.left = element_line(color="black"),
                        axis.line.x = element_line(color="black"),
                        axis.title=element_text(size=12),
                        axis.text=element_text(size=12),
                        axis.text.x=element_text(size=xlabel.size, colour="black"),
                        axis.text.y=element_text(size=10, colour="black"),
                        legend.position="none",
                        legend.title=element_text(size=8),
                        legend.text=element_text(size=8)
                        )
    
    }
                          
    # Save to new slot
    MarvelObject$DE$PSI$Plot[[method]] <- plot
  
    return(MarvelObject)
        
}