R/Venn.R

In ComputationalProteomics/OmicLoupe: OmicLoupe: Taking a closer look at omics

Venn <- R6::R6Class(
    
    public = list(
        
        simple_venn = function(col1, col2, dereplicate=TRUE, title="Venn", colors=NULL, verbose=FALSE, labels=c("left", "right"), legend.position="right") {
            
            if (dereplicate) {
                col1 <- unique(col1)
                col2 <- unique(col2)
            }
            
            df.venn <- data.frame(
                x = c(-0.5, 0.5), y = c(0, 0),
                labels = labels
            )
            
            joint_count <- length(intersect(col1, col2))
            left_count <- length(col1) - joint_count
            right_count <- length(col2) - joint_count
            # ses$prot_des_prot %>% get_uniques_from_rdf("Protein")
            if (verbose) {
                message("Overlapping features: ", intersect(col1, col2))
                message("Left only features: ", setdiff(col1, col2))
                message("Right only features: ", setdiff(col2, col1))
            }
            
            df.vdc <- data.frame(
                x=c(-1.5, 1.5, 0),
                y=c(0, 0, 0),
                label=c(left_count, right_count, joint_count)
            )
            
            self$do_ggvenn(df.venn, df.vdc, legend.position=legend.position, title=title)
        },
        
        count_venn = function(left_count, right_count, joint_count, title="Venn", colors=NULL, verbose=FALSE, labels=c("left", "right"), legend.position="right") {
            
            df.venn <- data.frame(
                x = c(-0.5, 0.5), y = c(0, 0),
                labels = labels
            )
            
            df.vdc <- data.frame(
                x=c(-1.5, 1.5, 0),
                y=c(0, 0, 0),
                label=c(left_count-joint_count, right_count-joint_count, joint_count)
            )
            
            self$do_ggvenn(df.venn, df.vdc, legend.position=legend.position, title=title)
        },
        
        do_ggvenn = function(df.venn, df.vdc, legend.position='none', colors=NULL, title="No title") {
            
            
            if (is.null(colors)) {
                colors <- c("#A0D398", "#FDF9BD")
            }
            
            plt <- ggplot2::ggplot(data=df.venn) +
                ggforce::geom_circle(
                    ggplot2::aes_string(x0 = "x", y0 = "y", r = 1.5, fill = "labels"),
                    alpha = 0.3,
                    size = 0.5,
                    colour = 'darkgray'
                ) +
                ggplot2::coord_fixed() +
                ggplot2::theme_void() +
                ggplot2::scale_fill_manual(values = colors) +
                ggplot2::scale_colour_manual(values = colors, guide = FALSE) +
                ggplot2::labs(fill = NULL) +
                ggplot2::annotate("text", x = df.vdc$x, y = df.vdc$y, label = df.vdc$label, size = 5) +
                ggplot2::ggtitle(title) + 
                theme(plot.title = element_text(hjust = 0.5))
            
            if (!is.null(labels)) {
                plt <- plt + ggplot2::theme(legend.position = legend.position, legend.direction='vertical')
            }
            
            plt
        },
        
        do_paired_expression_venn = function(col1_w_fold, col2_w_fold, title="", colors=c("#CCCCCC", "#CCCCCC"), highlight="A&B", contrast_names=c("Ref. contrast", "Comp. contrast")) {

            both_sig_names <- intersect(col1_w_fold %>% names(), col2_w_fold %>% names())
            
            joint_count <- length(both_sig_names)
            if (joint_count > 0) {
                joint_contra_count <- length(which(sign(unlist(col1_w_fold[both_sig_names])) != sign(unlist(col2_w_fold[both_sig_names]))))
            }
            else {
                joint_contra_count <- 0
            }
            joint_same_count <- joint_count - joint_contra_count
            left_count <- length(col1_w_fold) - joint_count
            right_count <- length(col2_w_fold) - joint_count
            
            labels <- c(
                as.character(left_count),
                as.character(right_count),
                sprintf("%s same fold dir.", joint_same_count),
                sprintf("%s reverse fold dir.", joint_contra_count),
                contrast_names[1],
                contrast_names[2]
            )
            
            df.vdc <- data.frame(
                x=c(-1.5, 1.5, 0, 0, -1.8, 1.8),
                y=c(0, 0, 0, -0.3, 1.4, 1.4),
                label=labels
            )
            
            df.venn <- data.frame(x = c(-0.5, 0.5),
                                  y = c(0, 0),
                                  labels="gray",
                                  # labels = c("Contrast 1", "Contrast 2"),
                                  stringsAsFactors = FALSE)
            
            plt <- ggplot2::ggplot(data=df.venn) +
                ggforce::geom_circle(
                    ggplot2::aes_string(x0 = "x", y0 = "y", r = 1.5, fill="labels"), 
                    # ggplot2::aes_string(x0 = "x", y0 = "y", r = 1.5, fill = "labels"), 
                    alpha = 0.3, 
                    size = 0.5, 
                    colour = 'darkgray'
                ) +
                ggplot2::coord_fixed() +
                ggplot2::theme_void() +
                ggplot2::theme(legend.position = 'bottom', legend.direction='vertical')
            
            fill_color <- "darkgreen"
            
            if (!is.null(highlight)) {
                if (highlight == "A&B") {
                    colors <- c(fill_color, fill_color)
                }
                else if (highlight == "A|B") {
                    yvals <- seq(-sqrt(2), sqrt(2), 0.001)
                    xvals <- sqrt(2.25 - yvals^2) - 0.5
                    yvals <- c(yvals, rev(yvals))
                    xvals <- c(xvals, -xvals)
                    combo <- data.frame(x = xvals, y = yvals)
                    plt <- plt + ggplot2::geom_polygon(data=combo, aes(x=x, y=y), fill=fill_color, alpha=0.5) 
                }
                else if (highlight == "A") {
                    theta <- seq(70, 290, 10)
                    outer_x <- 1.5 * cos(theta * pi / 180)
                    outer_y <- 1.5 * sin(theta * pi / 180)
                    
                    inner_theta <- rev(seq(110, 250, 10))
                    inner_x <- 1.5 * cos(inner_theta * pi / 180)
                    inner_y <- 1.5 * sin(inner_theta * pi / 180)
                    
                    x <- c(inner_x+0.5, outer_x-0.5)
                    y <- c(inner_y, outer_y)
                    
                    combo <- data.frame(x = x, y = y)
                    plt <- plt + ggplot2::geom_polygon(data=combo, aes(x=x, y=y), fill=fill_color, alpha=0.5)
                }
                else if (highlight == "B") {
                    theta <- seq(70, 290, 10)
                    outer_x <- 1.5 * cos(theta * pi / 180)
                    outer_y <- 1.5 * sin(theta * pi / 180)
                    
                    inner_theta <- rev(seq(110, 250, 10))
                    inner_x <- 1.5 * cos(inner_theta * pi / 180)
                    inner_y <- 1.5 * sin(inner_theta * pi / 180)
                    
                    x <- c(-(inner_x+0.5), -(outer_x-0.5))
                    y <- c(inner_y, outer_y)
                    
                    combo <- data.frame(x = x, y = y)
                    plt <- plt + ggplot2::geom_polygon(data=combo, aes(x=x, y=y), fill=fill_color, alpha=0.5)
                    
                }
                else {
                    stop(sprintf("Unknown highlight: %s", highlight))
                }
            }
            
            plt <- plt + ggplot2::scale_fill_manual(values = colors) +
                ggplot2::scale_colour_manual(values = colors, guide = FALSE) +
                # ggplot2::labs(fill = NULL) +
                theme(legend.position="none") +
                ggplot2::annotate("text", x = df.vdc$x, y = df.vdc$y, label = df.vdc$label, size = 5) +
                ggplot2::ggtitle(title) +
                scale_x_continuous(expand=c(0.1, 0.1))
            
            # ggsave(plt, filename = "~/Desktop/out.png")
            
            plt
        }
    )
)

venn <- Venn$new()