R/sp_vennDiagram.R

In Tong-Chen/ImageGP: For ImageGP cloud platform (https://www.bic.ac.cn/BIC)

#' Generating venDiagram plot
#'
#' @param data Data file (the first column is the name of genes or other things one want to compare, the second column is set name of each items, tab separated).
#' @inheritParams sp_readTable
#' @param supplyNumbers If you have the size of each set and the number overlaps between or among each set,  please give TRUE here.
#' @param title Title for the picture.
#' @param label1 The name for label1. One string in your second column. If not supplied, the program will try to do venn plot for all sets or first 5 sets.
#' @param label2 The name for label2.
#' @param label3 The name for label3.
#' @param label4 The name for label4.
#' @param label5 The name for label5.
#' @param numVector List of numbers for venn plot(used when `supplyNumbers` is true).
#' For two-set venn, the format is "100, 110, 50" represents
#' (length_a, length_b, a_b_overlap).
#' For three-set venn, the format is "100, 110, 90, 50, 40, 40, 20"
#' represents (length_a, length_b, length_c,
#'            a_b_overlap,  b_c_overlap, a_c_overlap, a_b_c_overlap).
#' For four-set venn, the format is "100, 110, 90, 50, 40, 40, 20"
#' represents (length_a, length_b, length_c,
#'            a_b_overlap, a_c_overlap, a_d_overlap, b_c_overlap,
#'            b_d_overlap, c_d_overlap, abc_overlap, abd_overlap,
#'            acd_overlap, bcd_overlap, abcd_overlap).
#' @param labelVector List of label for venn plot(used when `supplyNumbers` is true).
#' Format: c('a', 'b')" for two-set and c('a', 'b', 'c') for three-set.
#' @param manual_color_vector Color for each area. Ussally the number of colors should
#' be equal to the number of labels (however the program will make them equal).
#' If you manually set colors for 4-way
#' venn diagram, the first color will be given to the
#' leftmost set, the second will be given to the rightmost
#' set, the third will be given to second leftmost and the forth
#' will be given to the second rightmost.
#' Colors like c('red', 'blue', '#6181BD') (number of colors not matter) or
#' a RColorBrewer color set like  "BrBG"     "PiYG"     "PRGn"     "PuOr"
#' "RdBu"     "RdGy"     "RdYlBu"   "RdYlGn"  "Spectral" "Accent"
#' "Dark2"    "Paired"   "Pastel1"  "Pastel2"  "Set1"
#' "Set2"    "Set3"     "Blues"    "BuGn"     "BuPu"
#' "GnBu"     "Greens"   "Greys"    "Oranges" "OrRd"     "PuBu"
#' "PuBuGn"   "PuRd"     "Purples"  "RdPu"     "Reds"
#' "YlGn"    "YlGnBu"   "YlOrBr"   "YlOrRd"
#' (check http://www.sthda.com/english/wiki/colors-in-r for more).
#' @inheritParams sp_manual_color_ggplot2
#' @param label_size Siez of category names. Default system default.
#' @param margin Number giving the amount of whitespace around the diagram in grid units. Default system default
#' @inheritParams base_plot_save
#' @param ...
#'
#' @return A grid object.
#' @export
#'
#' @examples
#'
#'
#' vennDiagram_test_data <- data.frame(elements=c("1","2","2","2","3"), sets=c("A","A","B","C","C"))
#' sp_vennDiagram(data = vennDiagram_test_data, label1 = "A",label2 = "B", label3 = "C")
#'
#'
#'
#' sp_vennDiagram( supplyNumbers = TRUE,  numVector=c (120, 110, 50), labelVector=c('a','b'))
#'
#'
#'
#' ## Not run:
#' vennDiagram_data = "vennDiagram.data"
#' sp_vennDiagram(data = vennDiagram_data, label1 = "Set1",label2 = "Set2")
#' ## End(Not run)
#'
sp_vennDiagram <- function (data,
                            supplyNumbers = FALSE,
                            header = FALSE,
                            title = NULL,
                            label1 = NULL,
                            label2 = NULL,
                            label3 = NULL,
                            label4 = NULL,
                            label5 = NULL,
                            color_for_circumference = "transparent",
                            numVector = c(),
                            labelVector = c(),
                            manual_color_vector = c("dodgerblue",
                                        "goldenrod1",
                                        "darkorange1",
                                        "seagreen3",
                                        "orchid3"),
                            alpha = 0.5,
                            label_size = NULL,
                            margin = NULL,
                            filename = NULL,
                            debug = FALSE,
                            ...) {

  options(stringsAsFactors = FALSE)

  if (debug) {
    argg <- c(as.list(environment()), list(...))
    print(argg)
  }

  if (!sp.is.null(filename)) {
    base_plot_save(filename, ...)
  }

  if (!supplyNumbers)  {
    if ("character" %in% class(data)) {
      data <- sp_readTable(data, row.names = NULL, header = header)
    }else if (!"data.frame" %in% class(data)) {
      stop("Unknown input format for `data` parameter.")
    }

    data <- data[!is.na(data[,1]),]
    data[, 2] <- make.names(data[, 2])
    data <- unique(data)



    labelRecord = c(label1, label2, label3, label4, label5)
    labelRecord = labelRecord[labelRecord!="NULL"]

    if(length(labelRecord)==0){
      labelRecord = unique(data[,2])
      if(length(labelRecord)>5){
        labelRecord = labelRecord[1:5]
      }
    }

    # 移除log
    futile.logger::flog.threshold(futile.logger::ERROR, name = "VennDiagramLogger")

    num = length(labelRecord)

    generateVennData <- function(label, data){
      label = make.names(label)
      label_content <- data[data[, 2] == label, 1]
    }

    labelContent = lapply(labelRecord, generateVennData, data)

    names(labelContent) <- labelRecord


    color_v <- generate_color_list(manual_color_vector, num,alpha=alpha)
    #label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"),
    if(color_for_circumference != "transparent"){
      color_for_circumference <- generate_color_list(color_for_circumference, num, alpha=alpha)
    }

    main.pos = c(0.5, 1.05)
    cat.default.pos = "outer"
    cat.pos = 0
    cat.dist = 0.03
    if (sp.is.null(label_size)) {
      label_size = 1
    }
    if (sp.is.null(margin)) {
      margin = 0.01
    }
    if (num == 5) {
      cat.pos = c(0,225,270,135,90)
      cat.dist = 0.12
      if (sp.is.null(label_size)) {
        label_size = 0.6
      }
      main.pos = c(0.5, 1)
      if (sp.is.null(margin)) {
        margin = 0.05
      }
    } else if (num == 4 ){
      cat.pos = c(-15, 15, 0, 0)
      cat.dist = c(0.22, 0.22, 0.11, 0.11)
    } else if (num ==3 ){
      cat.pos = c(0,0,180)
    }
      p <- venn.diagram(
        x = labelContent,
        filename = NULL,
        col = color_for_circumference,
        lwd = 1,
        fill = color_v,
        #alpha = alpha,
        main = title,
        label.col = c("black"),
        cex = 1,
        cat.col = color_v,
        cat.cex = label_size,
        margin = margin,
        main.pos = main.pos,
        cat.default.pos = cat.default.pos,
        cat.pos = cat.pos,
        cat.dist = cat.dist
      )
  } else {
    #---venn plot for given numbers---------
    num <- length(labelVector)
    color_v <- generate_color_list(manual_color_vector, num)
    #label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"),
    if(color_for_circumference != "transparent"){
      color_for_circumference <- generate_color_list(color_for_circumference, num)
    }

    if (num == 2) {
      p <- draw.pairwise.venn(
        area1 = numVector[1],
        area2 = numVector[2],
        cross.area = numVector[3],
        category = labelVector,
        lwd = rep(1, 1),
        lty = rep(2, 2),
        col = color_for_circumference,
        fill = color_v,
        cat.col = color_v,
        ind = F
      )
    } else if (num == 3) {
      p <- draw.triple.venn(
        area1 = numVector[1],
        area2 = numVector[2],
        area3 = numVector[3],
        n12 = numVector[4],
        n23 = numVector[5],
        n13 = numVector[6],
        n123 = numVector[7],
        category = labelVector,
        col = color_for_circumference,
        fill = color_v,
        cat.col = color_v,
        reverse = FALSE,
        ind = F
      )
    } else if (num == 4) {
      p <- draw.quad.venn(
        area1 = numVector[1],
        area2 = numVector[2],
        area3 = numVector[3],
        area4 = numVector[4],
        n12 = numVector[5],
        n13 = numVector[6],
        n14 = numVector[7],
        n23 = numVector[8],
        n24 = numVector[9],
        n34 = numVector[10],
        n123 = numVector[11],
        n124 = numVector[12],
        n134 = numVector[13],
        n234 = numVector[14],
        n1234 = numVector[15],
        category = labelVector,
        col = color_for_circumference,
        fill = color_v,
        cat.col = color_v,
        reverse = FALSE,
        ind = F
      )
    } else if (num == 5) {
      stop("Unsupported 5 set venn diagram for input numbers.")
    }
  }

  if (!sp.is.null(filename)) {
    grid::grid.newpage()
    grid::grid.draw(p)
    dev.off()
  }
  grid::grid.newpage()
  grid::grid.draw(p)
}