upset plot with set size bars in right side

Question

The UpSetR R package offers a wonderful method to upgrade the traditional Venn-diagram when multiple components/sets are to be compared. However, the upset plot in R (using UpSetR package) plots the set size (horizontal bars) on the left side of the plot. Is there any way to make them on the right side?

score 2 · Accepted Answer · answered Sep 27 '19 at 13:04

It is not easy to move horizontal bars from the left to the right side.
You need to modify the Make_size_plot and the NoAttBasePlot of the UpSetR package as suggested below (before each modified line of code I wrote # Modified for your convenience).

library(UpSetR)
library(grid)
library(gridExtra)
library(ggplot2)

NoAttBasePlot <- function (legend, size_plot_height, Main_bar_plot, Matrix_plot, 
    hratios, Size_plot, query_legend, set_metadata, set_metadata_plots, 
    newpage) {
    top <- 1
    bottom <- 100
    if ((!is.null(legend)) && (query_legend != tolower("none"))) {
        if (query_legend == tolower("top")) {
            top <- 3
            bottom <- 102
            legend_top <- 1
            legend_bottom <- 3
            size_plot_height <- (size_plot_height + 2)
        }
        else if (query_legend == tolower("bottom")) {
            legend_top <- 101
            legend_bottom <- 103
        }
    }
    if (is.null(set_metadata)) {
        matrix_and_mainbar_right <- 100
        matrix_and_mainbar_left <- 21
        size_bar_right <- 20
        size_bar_left <- 1
    }
    else if (!is.null(set_metadata)) {
        matrix_and_mainbar_right <- set_metadata$ncols + 100
        matrix_and_mainbar_left <- set_metadata$ncols + 21
        size_bar_right <- set_metadata$ncols + 20
        size_bar_left <- set_metadata$ncols + 1
        metadata_right <- set_metadata$ncols
        metadata_left <- 1
    }
    if (newpage) {
        grid::grid.newpage()
    }
    if ((!is.null(legend)) && (query_legend != tolower("none"))) {
        if (query_legend == tolower("top")) {
            pushViewport(viewport(layout = grid.layout(102, matrix_and_mainbar_right)))
        }
        else if (query_legend == tolower("bottom")) {
            pushViewport(viewport(layout = grid.layout(103, matrix_and_mainbar_right)))
        }
    }
    else if ((is.null(legend)) || (query_legend == tolower("none"))) {
        pushViewport(viewport(layout = grid.layout(100, matrix_and_mainbar_right)))
    }
    # Modified
    vp = UpSetR:::vplayout(top:bottom, 1:(matrix_and_mainbar_right-matrix_and_mainbar_left))
    pushViewport(vp)
    grid.draw(arrangeGrob(Main_bar_plot, Matrix_plot, heights = hratios))
    popViewport()
    # Modified
    vp = UpSetR:::vplayout(size_plot_height:bottom, (matrix_and_mainbar_right-matrix_and_mainbar_left-1):96)
    pushViewport(vp)
    grid.draw(arrangeGrob(Size_plot))
    popViewport()
    if (!is.null(set_metadata)) {
        for (i in 1:length(set_metadata_plots)) {
            if (i != 1) {
                metadata_left <- 1 + metadata_right
                metadata_right <- metadata_right + set_metadata$plots[[i]]$assign
            }
            else {
                metadata_left <- 1
                metadata_right <- set_metadata$plots[[i]]$assign
            }
            vp = UpSetR:::vplayout(size_plot_height:bottom, metadata_left:metadata_right)
            pushViewport(vp)
            grid.draw(arrangeGrob(set_metadata_plots[[i]]))
            popViewport()
        }
    }
    if ((!is.null(legend)) && (query_legend != tolower("none"))) {
        vp = UpSetR:::vplayout(legend_top:legend_bottom, matrix_and_mainbar_left:matrix_and_mainbar_right)
        pushViewport(vp)
        grid.draw(arrangeGrob(legend))
        popViewport()
    }
}

Make_size_plot <- function (Set_size_data, sbar_color, ratios, ylabel, scale_sets, 
    text_scale, set_size_angle, set_size.show, set_size.scale_max, 
    set_size.number_size) {
    if (length(text_scale) > 1 && length(text_scale) <= 6) {
        x_axis_title_scale <- text_scale[3]
        x_axis_tick_label_scale <- text_scale[4]
    }
    else {
        x_axis_title_scale <- text_scale
        x_axis_tick_label_scale <- text_scale
    }
    if (ylabel == "Set Size" && scale_sets != "identity") {
        ylabel <- paste("Set Size", paste0("( ", 
            scale_sets, " )"))
        if (scale_sets == "log2") {
            Set_size_data$y <- log2(Set_size_data$y)
        }
        if (scale_sets == "log10") {
            Set_size_data$y <- log10(Set_size_data$y)
        }
    }
    if (!is.null(set_size.number_size)) {
        num.size <- (set_size.number_size/2.845276) * x_axis_tick_label_scale
    }
    else {
        num.size <- (7/2.845276) * x_axis_tick_label_scale
    }
    Size_plot <- (ggplot(data = Set_size_data, aes_string(x = "x", 
        y = "y")) + geom_bar(stat = "identity", colour = sbar_color, 
        width = 0.4, fill = sbar_color, position = "identity") + 
        scale_x_continuous(limits = c(0.5, (nrow(Set_size_data) + 
            0.5)), breaks = c(0, max(Set_size_data)), expand = c(0, 
            0)) + theme(panel.background = element_rect(fill = "white"), 
        plot.margin = unit(c(-0.11, -1.3, 0.5, 0.5), "lines"), 
        axis.title.x = element_text(size = 8.3 * x_axis_title_scale), 
        axis.text.x = element_text(size = 7 * x_axis_tick_label_scale, 
            vjust = 1, hjust = 0.5), axis.line = element_line(colour = "gray0"), 
        axis.line.y = element_blank(), axis.line.x = element_line(colour = "gray0", 
            size = 0.3), axis.text.y = element_blank(), axis.ticks.y = element_blank(), 
        panel.grid.minor = element_blank(), panel.grid.major = element_blank()) + 
        xlab(NULL) + ylab(ylabel) + coord_flip())
    if (set_size.show == TRUE) {
        Size_plot <- (Size_plot + geom_text(aes(label = y, vjust = 0.5, 
            hjust = 1.2, angle = set_size_angle), size = num.size))
    }
    if (scale_sets == "log10") {
        if (!is.null(set_size.scale_max)) {
            Size_plot <- (Size_plot + scale_y_continuous(limits = c(set_size.scale_max, 
                0), trans = log10_reverse_trans()))
        }
        else {
            Size_plot <- (Size_plot + scale_y_continuous(trans = log10_reverse_trans()))
        }
    }
    else if (scale_sets == "log2") {
        if (!is.null(set_size.scale_max)) {
            Size_plot <- (Size_plot + scale_y_continuous(limits = c(set_size.scale_max, 
                0), trans = log2_reverse_trans()))
        }
        else {
            Size_plot <- (Size_plot + scale_y_continuous(trans = log2_reverse_trans()))
        }
    }
    else {
        if (!is.null(set_size.scale_max)) {
            Size_plot <- (Size_plot + scale_y_continuous(limits = c(set_size.scale_max, 
                0), trans = "reverse"))
        }
        else {
            # Modified
            #Size_plot <- (Size_plot + scale_y_continuous(trans = "reverse"))
        }
    }
    Size_plot <- ggplot_gtable(ggplot_build(Size_plot))
    return(Size_plot)
}

assignInNamespace(x="NoAttBasePlot", value=NoAttBasePlot, ns="UpSetR")
assignInNamespace(x="Make_size_plot", value=Make_size_plot, ns="UpSetR")

movies <- read.csv(system.file("extdata", "movies.csv", package = "UpSetR"), 
                   header=TRUE, sep=";")
upset(movies, nsets = 7, nintersects = 30, mb.ratio = c(0.5, 0.5),
      order.by = c("freq", "degree"), decreasing = c(TRUE,FALSE))

That works perfectly. However, there is still one challenge. The set names (Adventure, Horror, ....) are still on the left side. — Alemu Assefa, Sep 28 '19 at 14:10
@AlemuAssefa OK. I will try to move set names of the right side. — Marco Sandri, Sep 28 '19 at 16:39

upset plot with set size bars in right side

1 Answers1