R/ggVennDiagram.R

In ggVennDiagram: A 'ggplot2' Implement of Venn Diagram

#' `ggVennDiagram`: an easy to use Venn diagram generator
#'
#' Venn diagram is frequently used in scientific studies of many fields.
#' This package incorporates state-of-art Venn plot tools and provides a set of
#' easy-to-use functions to plot Venn. By dealing with a user-provided list,
#' which contains the sets of Venn, `ggVennDiagram` returns a structured data that
#' can be used to plot Venn. The data contains three slots: 1) the edge of Venn sets;
#' 2) the separated regions of Venn sets; 3) the labels of Venn sets.
#' By help from the package `venn`, it is possible to draw Venn diagram up to 7 sets.
#'
#' @docType package
#' @name ggVennDiagram-package
NULL

#' shapes: shape data used to setup Venn plot
#'
#' a collection of geometric shapes, which defined the edge and label of sets in a Venn plot.
#' use `plot_shapes()` to see some of them.
#'
#' @format a tibble with 6 columns
#'
#'  * `nsets`: number of sets, from 1-7.
#'  * `type`: ellipse, circle or triangle
#'  - `shape_id`: to separate different shapes
#'  - `component`: each shape has two components, 'setEdge' and 'setLabel'
#'  - `id`: to separate edges/labels of a shape. For example, 4 sets shape will have ids of 1-4.
#'  - `xy`: coordinates
#' @md
#'
#' @source
#' - `venn:::sets`
#' - `library(VennDiagram)`
#' - [Wiki](https://upload.wikimedia.org/wikipedia/commons/5/56/6-set_Venn_diagram_SMIL.svg)
#' @md
#' @name vennplot-shapes
NULL

#' ggVennDiagram main parser
#'
#' @param x list of items
#' @param category.names default is names(x)
#' @param show_intersect if TRUE the text can be visualized by `plotly`
#' @param set_color color of set labels ("black")
#' @param set_size size of set labels (NA)
#' @param label format of region labels, select one from c("count","percent","both","none")
#' @param label_geom layer of region labels, choose from c("label", "text")
#' @param label_alpha set 0 to remove the background of region labels
#' @param label_color color of region labels ("black")
#' @param label_size size of region labels (NA)
#' @param label_percent_digit number of digits when formatting percent label (0)
#' @param label_txtWidth width of text used in showing intersect members, will be ignored unless show_intersection is TRUE (40)
#' @param edge_lty line type of set edges ("solid")
#' @param edge_size line width of set edges (1)
#' @param ... Other arguments passed on to downstream functions.
#'
#' @return A ggplot object
#' @export
#' @examples
#' library(ggVennDiagram)
#' x <- list(A=1:5,B=2:7,C=3:6,D=4:9)
#' ggVennDiagram(x)  # 4d venn
#' ggVennDiagram(x[1:3])  # 3d venn
#' ggVennDiagram(x[1:2])  # 2d venn
ggVennDiagram <- function(x, category.names=names(x),
                          show_intersect = FALSE,
                          set_color = "black",
                          set_size = NA,
                          label=c("both","count","percent","none"),
                          label_alpha=0.5,
                          label_geom=c("label","text"),
                          label_color = "black",
                          label_size = NA,
                          label_percent_digit = 0,
                          label_txtWidth = 40,
                          edge_lty = "solid",
                          edge_size = 1,
                          ...){

  if (!is.list(x)){
    stop(simpleError("ggVennDiagram() requires at least a list."))
  }
  names(x) <- category.names
  dimension <- length(x)
  label <- match.arg(label)
  label_geom <- match.arg(label_geom)
  if (dimension <= 7){
    plot_venn(x,
              show_intersect = show_intersect,
              set_color = set_color,
              set_size = set_size,
              label = label,
              label_alpha=label_alpha,
              label_geom = label_geom,
              label_color = label_color,
              label_size = label_size,
              label_percent_digit = label_percent_digit,
              label_txtWidth = label_txtWidth,
              edge_lty = edge_lty,
              edge_size = edge_size,
              ...)
  }
  else{
    stop("Only support 2-7 dimension Venn diagram.")
  }
}




#' plot codes
#'
#' @inheritParams ggVennDiagram
#'
#' @import ggplot2
#' @export
#'
#' @return ggplot object, or plotly object if show_intersect is TRUE
plot_venn <- function(x,
                      show_intersect,
                      set_color,
                      set_size,
                      label,
                      label_geom,
                      label_alpha,
                      label_color,
                      label_size,
                      label_percent_digit,
                      label_txtWidth,
                      edge_lty,
                      edge_size,
                      ...){
  venn <- Venn(x)
  data <- process_data(venn)
  p <- ggplot()

  region.params <- list(data = data@region, mapping = aes_string(fill = 'count'))

  edge.params <- list(data = data@setEdge, 
                      mapping = aes_string(color = 'id'), 
                      show.legend = FALSE)

  if (utils::packageVersion('ggplot2') >= '3.4.0'){
    edge.params$linetype <- edge_lty
    edge.params$linewidth <- edge_size
  }else{
    edge.params$lty <- edge_lty
    edge.params$size <- edge_size
  }

  text.params <- list(data = data@setLabel, 
                      mapping = aes_string(label = 'name'),
                      size = set_size,
                      color = set_color
                 )

  region.layer <- do.call('geom_sf', region.params)
  
  edge.layer <- do.call('geom_sf', edge.params)

  text.layer <- do.call('geom_sf_text', text.params)

  p <- p + region.layer + edge.layer + text.layer + theme_void()

  if (label != "none" & show_intersect == FALSE){
    region_label <- data@region %>%
      dplyr::filter(.data$component == "region") %>%
      dplyr::mutate(percent = paste(round(.data$count*100/sum(.data$count),
                                          digits = label_percent_digit),"%", sep="")) %>%
      dplyr::mutate(both = paste(.data$count,paste0("(",.data$percent,")"),sep = "\n"))
    if (label_geom == "label"){
      p <- p + geom_sf_label(aes_string(label=label),
                             data = region_label,
                             alpha=label_alpha,
                             color = label_color,
                             size = label_size,
                             lineheight = 0.85,
                             label.size = NA)
    }
    if (label_geom == "text"){
      p <- p + geom_sf_text(aes_string(label=label),
                            data = region_label,
                            alpha=label_alpha,
                            color = label_color,
                            size = label_size,
                            lineheight = 0.85)
    }
  }

  if (show_intersect == TRUE){
    items <- data@region %>%
      dplyr::rowwise() %>%
      dplyr::mutate(text = yulab.utils::str_wrap(paste0(.data$item, collapse = " "),
                                             width = label_txtWidth)) %>%
      sf::st_as_sf()
    label_coord = sf::st_centroid(items$geometry) %>% sf::st_coordinates()
    p <- ggplot(items) +
      geom_sf(aes_string(fill="count")) +
      geom_sf_text(aes_string(label = "name"),
                   data = data@setLabel,
                   inherit.aes = F) +
      geom_text(aes_string(label = "count", text = "text"),
                x = label_coord[,1],
                y = label_coord[,2],
                show.legend = FALSE) +
      theme_void()
    ax <- list(
      showline = FALSE
    )
    p <- plotly::ggplotly(p, tooltip = c("text")) %>%
      plotly::layout(xaxis = ax, yaxis = ax)
  }

  p
}