Generating Venn diagrams from % of variance via ggVennDiagram

venn_diagrams

library(ggVennDiagram)
library(RColorBrewer)
library(tidyverse)
library(glue)

venn_3d <- function (
    total_variance = 100, # total number of items
    unique_x1 = 0.3, # 30% unique to X1
    unique_x2 = 0.3, # 30% unique to X2
    unique_y = 0.3, # 30% unique to Y
    shared_x1_x2 = 0.05, # % shared between X1 and X2
    shared_x1_y = 0.05, # % shared between X1 and Y
    shared_x2_y = 0.05, # % shared between X2 and Y
    shared_all = 0.1 # 10% shared across X1, X2, and Y
    ){

  # computing the number of elements for each component
  n_unique_x1 <- total_variance * unique_x1
  n_unique_x2 <- total_variance * unique_x2
  n_unique_y <- total_variance * unique_y
  n_shared_x1_x2 <- round(total_variance * shared_x1_x2)
  n_shared_x1_y <- round(total_variance * shared_x1_y)
  n_shared_x2_y <- round(total_variance * shared_x2_y)
  n_shared_all <- round(total_variance * shared_all)
  
  # generating numbers for each component
  x1_unique_numbers <- seq(1, n_unique_x1)
  x2_unique_numbers <- seq(max(x1_unique_numbers) + 1, max(x1_unique_numbers) + n_unique_x2)
  y_unique_numbers <- seq(max(x2_unique_numbers) + 1, max(x2_unique_numbers) + n_unique_y)
  shared_x1_x2_numbers <- seq(max(y_unique_numbers) + 1, max(y_unique_numbers) + n_shared_x1_x2)
  shared_x1_y_numbers <- seq(max(shared_x1_x2_numbers) + 1, max(shared_x1_x2_numbers) + n_shared_x1_y)
  shared_x2_y_numbers <- seq(max(shared_x1_y_numbers) + 1, max(shared_x1_y_numbers) + n_shared_x2_y)
  shared_all_numbers <- seq(max(shared_x2_y_numbers) + 1, max(shared_x2_y_numbers) + n_shared_all)
  
  # combining into lists for x1, x2, and y
  x <- list(
    Y = c(y_unique_numbers, shared_x1_y_numbers, shared_x2_y_numbers, shared_all_numbers),
    X1 = c(x1_unique_numbers, shared_x1_x2_numbers, shared_x1_y_numbers, shared_all_numbers),
    X2 = c(x2_unique_numbers, shared_x1_x2_numbers, shared_x2_y_numbers, shared_all_numbers)
    )
  
  # 3D Venn diagram
  # ggVennDiagram(
  #   x,
  #   label = "none",
  #   edge_size = 0.5,
  #   show_intersect = FALSE
  #   ) +
  #   theme(legend.position = "none") +
  #   scale_fill_distiller(palette = fill_palette) +
  #   # adding custom labels for subsets
  #   annotate(
  #     geom = "text", x = 2, y = 1.5,
  #     label = glue("a: {format(round(shared_x1_y, 2), nsmall = 2)}"),
  #     size = 4, color = "white"
  #     ) +
  #   annotate(
  #     geom = "text", x = -0.25, y = -2.5,
  #     label = glue("b: {format(round(shared_x2_y, 2), nsmall = 2)}"),
  #     size = 4, color = "white") +
  #   annotate(
  #     geom = "text", x = 2, y = -1.5,
  #     label = glue("c: {format(round(shared_all, 2), nsmall = 2)}"),
  #     size = 4, color = "white") +
  #   annotate(
  #     geom = "text", x = -1.5, y = 1,
  #     label = glue("d: {format(round(unique_y, 2), nsmall = 2)}"),
  #     size = 4, color = "white")
  
  # custom made Venn diagram
  # see https://gaospecial.github.io/ggVennDiagram/articles/fully-customed.html
  venn <- Venn(x)
  data <- process_data(venn)
  ggplot() +
    geom_polygon(aes(X, Y, fill = as.factor(id), group = id), data = venn_regionedge(data) ) +
    geom_path(
      aes(x = X, y = Y, group = id),
      data = venn_setedge(data),
      show.legend = FALSE,
      linewidth = 1
      ) +
    geom_text(
      aes(x = X, y = Y, label = name),
      data = venn_setlabel(data),
      size = 5
      ) +
    # adding custom labels for subsets
    annotate(
      geom = "text", x = 2, y = 1.5,
      label = glue("a: {format(round(shared_x1_y, 2), nsmall = 2)}"),
      size = 5
      ) +
    annotate(
      geom = "text", x = -0.25, y = -2.6,
      label = glue("b: {format(round(shared_x2_y, 2), nsmall = 2)}"),
      size = 5
      ) +
    annotate(
      geom = "text", x = 2, y = -1.5,
      label = glue("c: {format(round(shared_all, 2), nsmall = 2)}"),
      size = 5
      ) +
    annotate(
      geom = "text", x = -1.5, y = 0.75,
      label = glue("d: {format(round(unique_y, 2), nsmall = 2)}"),
      size = 5
      ) +
    scale_fill_brewer(palette = "Spectral") +
    coord_equal() +
    theme_void() +
    theme(legend.position = "none")
  
}

venn_4d <- function (
    total_variance = 100,
    unique_x1 = 0.2,
    unique_x2 = 0.2,
    unique_x3 = 0.2,
    unique_y = 0.2,
    shared_x1_x2 = 0.05,
    shared_x1_y = 0.05,
    shared_x2_y = 0.05,
    shared_x1_x3 = 0.05,
    shared_x2_x3 = 0.05,
    shared_x3_y = 0.05,
    shared_all = 0.05,
    labels = FALSE,
    alpha = 1
    ) {
  
  # increasing the number of colour in the "Spectral" palette
  # https://stackoverflow.com/questions/34106898/extending-rcolorbrewer-to-support-more-colors
  mycolors <- colorRampPalette(brewer.pal(11, "Spectral") )(15)
  
  # computing the number of elements for each component
  n_unique_x1 <- total_variance * unique_x1
  n_unique_x2 <- total_variance * unique_x2
  n_unique_x3 <- total_variance * unique_x3
  n_unique_y <- total_variance * unique_y
  n_shared_x1_x2 <- round(total_variance * shared_x1_x2)
  n_shared_x1_y <- round(total_variance * shared_x1_y)
  n_shared_x2_y <- round(total_variance * shared_x2_y)
  n_shared_x1_x3 <- round(total_variance * shared_x1_x3)
  n_shared_x2_x3 <- round(total_variance * shared_x2_x3)
  n_shared_x3_y <- round(total_variance * shared_x3_y)
  n_shared_all <- round(total_variance * shared_all)
  
  # generating numbers for each component
  x1_unique_numbers <- seq(1, n_unique_x1)
  x2_unique_numbers <- seq(max(x1_unique_numbers) + 1, max(x1_unique_numbers) + n_unique_x2)
  x3_unique_numbers <- seq(max(x2_unique_numbers) + 1, max(x2_unique_numbers) + n_unique_x3)
  y_unique_numbers <- seq(max(x3_unique_numbers) + 1, max(x3_unique_numbers) + n_unique_y)
  shared_x1_x2_numbers <- seq(max(y_unique_numbers) + 1, max(y_unique_numbers) + n_shared_x1_x2)
  shared_x1_y_numbers <- seq(max(shared_x1_x2_numbers) + 1, max(shared_x1_x2_numbers) + n_shared_x1_y)
  shared_x2_y_numbers <- seq(max(shared_x1_y_numbers) + 1, max(shared_x1_y_numbers) + n_shared_x2_y)
  shared_x1_x3_numbers <- seq(max(shared_x2_y_numbers) + 1, max(shared_x2_y_numbers) + n_shared_x1_x3)
  shared_x2_x3_numbers <- seq(max(shared_x1_x3_numbers) + 1, max(shared_x1_x3_numbers) + n_shared_x2_x3)
  shared_x3_y_numbers <- seq(max(shared_x2_x3_numbers) + 1, max(shared_x2_x3_numbers) + n_shared_x3_y)
  shared_all_numbers <- seq(max(shared_x3_y_numbers) + 1, max(shared_x3_y_numbers) + n_shared_all)
  
  # combining into lists for Y, X1, X2, and X3
  x <- list(
    Y = c(y_unique_numbers, shared_x1_y_numbers, shared_x2_y_numbers, shared_x3_y_numbers, shared_all_numbers),
    X1 = c(x1_unique_numbers, shared_x1_x2_numbers, shared_x1_y_numbers, shared_x1_x3_numbers, shared_all_numbers),
    X2 = c(x2_unique_numbers, shared_x1_x2_numbers, shared_x2_y_numbers, shared_x2_x3_numbers, shared_all_numbers),
    X3 = c(x3_unique_numbers, shared_x1_x3_numbers, shared_x2_x3_numbers, shared_x3_y_numbers, shared_all_numbers)
    )
  
  # creating the Venn diagram using ellipses
  venn <- Venn(x)
  data <- process_data(venn)
  
  ggplot() +
    geom_polygon(
      aes(X, Y, fill = as.factor(id), group = id),
      data = venn_regionedge(data), alpha = alpha
      ) +
    geom_path(
      aes(X, Y, group = id),
      data = venn_setedge(data),
      show.legend = FALSE,
      linewidth = 1
      ) +
    geom_text(
      aes(x = X, y = Y, label = name),
      data = venn_setlabel(data),
      size = 5
      ) + {
        if (labels) annotate(
          geom = "text", x = 0.32, y = 0.675,
          label = glue("a: {format(round(shared_x1_y, 2), nsmall = 2)}"),
          size = 5
          )
        } + {
          if (labels) annotate(
            geom = "text", x = 0.32, y = 0.425,
            label = glue("b: {format(round(shared_x2_y, 2), nsmall = 2)}"),
            size = 5
            )
          } + {
            if (labels) annotate(
              geom = "text", x = 0.4, y = 0.575,
              label = glue("d: {format(round(shared_x1_x2, 2), nsmall = 2)}"),
              size = 5
              ) } + {
                if (labels) annotate(
                  geom = "text", x = 0.2, y = 0.55,
                  label = glue("h: {format(round(unique_y, 2), nsmall = 2)}"),
                  size = 5
                  ) } + {
                    if (labels) annotate(
                      geom = "text", x = 0.5, y = 0.48,
                      label = glue("g: {format(round(shared_all, 2), nsmall = 2)}"),
                      size = 5
                      ) } + {
                      if (labels) annotate(
                        geom = "text", x = 0.425, y = 0.38,
                        label = glue("f: {format(round(shared_x2_x3, 2), nsmall = 2)}"),
                        size = 5
                        ) } + {
                        if (labels) annotate(
                          geom = "text", x = 0.575, y = 0.38,
                          label = glue("e: {format(round(shared_x1_x3, 2), nsmall = 2)}"),
                          size = 5
                          ) } + {
                          if (labels) annotate(
                            geom = "text", x = 0.5, y = 0.3,
                            label = glue("c: {format(round(shared_x3_y, 2), nsmall = 2)}"),
                            size = 5
                            ) } +
    scale_fill_manual(values = mycolors) +
    coord_equal() +
    theme_void() +
    theme(legend.position = "none")
  
}

# generating the intro 4-variable Venn diagram
venn_4d()