R/plotLog2FC.R

In tschauer/HelpersforDESeq2: This is a collection of helper functions for DESeq2

#' plotLog2FC
#'
#' compare log2FC values from two DESeq2 results table
#' @export





plotLog2FC <- function(res1,
                       res2,
                       main_title = "",
                       x_label = "log2FC",
                       y_label = "log2FC",
                       lims = c(-5,5),
                       point_size = 0.25,
                       point_color = rgb(0.7,0.7,0.7,0.5),
                       selection_ids = NULL,
                       selection_id_type = "symbol",
                       selection_color = rgb(0.8,0,0,1),
                       selection_point_size = 0.5,
                       selection_legend = NULL,
                       selection_text_label = FALSE,
                       selection_text_size = 1.1,
                       selection_text_adj = -0.5,
                       add_lowess_line = F,
                       lowess_line_color = rgb(0.7,0,0.9,1),
                       lowess_line_width = 1.5,
                       legend_pos = "topleft"){


        res_merged <- merge(x = as.data.frame(res1),
                            y = as.data.frame(res2),
                            by = "row.names")

        plot(x = res_merged$log2FoldChange.x,
             y = res_merged$log2FoldChange.y,
             main = "",
             xlab = x_label,
             ylab = y_label,
             ylim = lims,
             xlim = lims,
             col = point_color,
             pch = 19, cex = point_size)

        if(add_lowess_line){
                lines(lowess(x = res_merged$log2FoldChange.x, y = res_merged$log2FoldChange.y),
                      col = lowess_line_color, lwd = lowess_line_width)
        }

        abline(h=0, v=0, col="grey32")
        abline(coef = c(0,1), col="grey32", lty=2)


        if(!(is.null(selection_ids))){

                selection_id_type <- paste0(selection_id_type, ".x")

                selection_vector <- res_merged[selection_id_type][,1] %in% selection_ids

                points(x = res_merged$log2FoldChange.x[selection_vector],
                       y = res_merged$log2FoldChange.y[selection_vector],
                       col = selection_color,
                       pch = 19, cex = selection_point_size)

                if(selection_text_label){
                        text(x = res_merged$log2FoldChange.x[selection_vector],
                             y = res_merged$log2FoldChange.y[selection_vector],
                             labels = res_merged[selection_id_type][,1][selection_vector],
                             adj = c(0, selection_text_adj),
                             col = selection_color, cex = selection_text_size)
                }
        } else {
                selection_vector <- FALSE
        }

        if(!(is.null(selection_legend)) & sum(selection_vector) > 0){
                legend(legend_pos,
                       legend = c(selection_legend),
                       bg = "white",
                       col = c(selection_color), pch = 19, cex = 1)
        }

}