venn_diagram2.r

venn_diagram2 <- function(a, b, name_a = "A", name_b = "B", colors =  c("#e41a1c","#377eb8"), out = FALSE, file_name = "default.pdf", euler = FALSE){
  # Niels Hanson
  # Info: A function to create a venn digagram between three (3) overapping sets a, b, and c.
  # Requies: The VennDiagram R package, the program will try to download and install if you dont
  #          have it.
  # Inputs: a,b,c - vertical vectors or the first column of matrixes as sets of strings to be compared
  #         name_a, name_b, and name_c - names that you give to sets a, b, and c, respectively
  #         these will appear in the final image
  #         colors - a vector of colors defined in hex format ie. colors <- c("#B80830","#EACC33","#46E2D9")
  #         it might be a good idea that these mix well as the interlapping classes will be a mix of colors
  #         Colors must be specified in hex ie. "#123456", google "hex colors" for more info
  #         name_output - the name of the output image that will be put in R's current working directory
  #         you can set this yourself before running. ie. setwd("~/my-director/")
  
  # A: find all classes for set a, a_b, a_c, a_b_c
  # number in a, we will use this at the end for a sanity check
  
  # make sure that a,b,c are all sets, get rid of duplicates
  a <- intersect(a,a)
  b <- intersect(b,b)
  # length of a
  a_tot <- length(a)
  # length of b
  b_tot <- length(b)
  # number shared between a and b and c
  a_b <- intersect(a,b)
  a_b_tot <- length(a_b)
  a_b_tot
  a_only <- setdiff(a,b)
  a_only_tot <- length(a_only)
  b_only <- setdiff(b,a)
  b_only_tot <- length(b_only)
  
  # try to load VennDiagram else try to download it
  # More info: see Hanbo Chen and Paul C Boutros. BMC Bioinformatics 2011, 12:35 doi:10.1186/1471-2105-12-35
  try(library(VennDiagram), install.packages("VennDiagram")) 
  library(VennDiagram)
  
  
  # create the venn diagram and output into the current working directory
  temp <- list(
    name_a = c(1:length(a)),
    name_b = c((length(a_only)+1):((length(a_only))+length(b)))
  )
  names(temp) <- c(name_a,name_b)
  
  output <- venn.diagram(
    x = temp,
    filename = NULL,
    col = "black",
    fill = c(colors[1], colors[2]),
    alpha = 0.5,
    label.col = c("black"),
    cex = 2.5,
    fontfamily = "serif",
    fontface = "bold",
    cat.default.pos = "text",
    cat.col = c("black"),
    cat.cex = 2.5,
    cat.fontfamily = "serif",
    cat.dist = c(0.06, 0.06),
    cat.pos = c(-20, 14),
    euler.d = euler,
    scaled = euler
  );
  
  try(library("grid"), install.packages("grid")) 
  library(grid)
  if (out == TRUE) {
    # only produce ouptut files upon request
    png(filename = paste(file_name,'.png', sep=''))
    grid.draw(output)
    dev.off()       
    pdf(file = paste(file_name,'.pdf', sep=''), width=8, height=8)
    grid.draw(output)
    dev.off()
  } else {
    # just plot the figure
    grid.draw(output)
  }
  
  # pack all the sets up and return to the user
  out <- NULL;
  # a <- c(out, name_a, as.vector(a))
  # a_only <-  as.vector(a_only)
  # a_b <- as.vector(a_b)
  # b <- c(out,name_b,as.vector(b))
  # b_only <- c(out,paste(name_b,"only",sep="_"),as.vector(b_only))
  out <- list(a,a_only,a_b,b,b_only)
  names(out) <- c(name_a, 
                  paste(name_a,"only",sep="_"), 
                  paste(name_a,name_b,sep="_"),
                  name_b,
                  paste(name_b,"only",sep="_"))
  
  return(out)
  
}