venn_diagram

library(VennDiagram)

venn.diagram(list(first = c("a", "b", "c"),
                  second = c("a", "c", "d"),
                  third = c("a", "d"))
             imagetype = "png",
             col = "transparent",
             filename = "example.png",
             height = 2000,
             width = 2000,
             fill = 1:2)

Real life example with overlap calculations

library(VennDiagram)
library(dplyr)
calculate.overlap(list(DE = read.csv2("output_data/diff_DE_PSC.csv") %>%
                          filter(FDR < 0.01) %>%
                          select(X) %>%
                          unlist %>% as.character(),
                       `_  EB` = read.csv2("output_data/diff_EB_PSC.csv") %>%
                          filter(FDR < 0.01) %>%
                          select(X) %>%
                          unlist %>% as.character(),
                       ECTO = read.csv2("output_data/diff_ECTO_PSC.csv") %>%
                          filter(FDR < 0.01) %>%
                          select(X) %>%
                          unlist %>% as.character(),
                       MESO = read.csv2("output_data/diff_MESO_PSC.csv") %>%
                          filter(FDR < 0.01) %>%
                          select(X) %>%
                          unlist %>% as.character(),
                      # `Other __` = read.csv2("output_data/diff_NoCLASS_PSC.csv") %>%
                       #   filter(FDR < 0.01) %>%
                        #  select(X) %>%
                         # unlist %>% as.character())
                      ) -> overlap

overlap



x <- list(DE = read.csv2("output_data/diff_DE_PSC.csv") %>%
             filter(FDR < 0.01) %>%
             select(X) %>%
             unlist %>% as.character(),
          `EB` = read.csv2("output_data/diff_EB_PSC.csv") %>%
             filter(FDR < 0.01) %>%
             select(X) %>%
             unlist %>% as.character(),
          ECTO = read.csv2("output_data/diff_ECTO_PSC.csv") %>%
             filter(FDR < 0.01) %>%
             select(X) %>%
             unlist %>% as.character(),
          MESO = read.csv2("output_data/diff_MESO_PSC.csv") %>%
             filter(FDR < 0.01) %>%
             select(X) %>%
             unlist %>% as.character()#,
          #`Other __` = read.csv2("output_data/diff_NoCLASS_PSC.csv") %>%
           #  filter(FDR < 0.01) %>%
            # select(X) %>%
             #unlist %>% as.character()
          )

get.venn.partitions(x) -> y
get.venn.partitions(x, force.unique = FALSE)

y[, 6] <- unlist(lapply(y[, 6], paste, collapse = " "))

write.csv2(y,
           file = "output_data/venn_4groups.csv",
           quote = FALSE,
           row.names = TRUE)