since UpsetR doesn't report back the elements for the ploted groups this function was created to to just that. See (https://github.com/hms-dbmi/UpSetR/issues/85)

upsetR_group_overlap.R

# source of this function: https://github.com/hms-dbmi/UpSetR/issues/85#issuecomment-327900647
fromList <- function (input) {
  # Same as original fromList()...
  elements <- unique(unlist(input))
  data <- unlist(lapply(input, function(x) {
      x <- as.vector(match(elements, x))
      }))
  data[is.na(data)] <- as.integer(0)
  data[data != 0] <- as.integer(1)
  data <- data.frame(matrix(data, ncol = length(input), byrow = F))
  data <- data[which(rowSums(data) != 0), ]
  names(data) <- names(input)
  # ... Except now it conserves your original value names!
  row.names(data) <- elements
  return(data)
}

overlapGroups <- function (listInput, sort = TRUE) {
  # listInput could look like this:
  # $one
  # [1] "a" "b" "c" "e" "g" "h" "k" "l" "m"
  # $two
  # [1] "a" "b" "d" "e" "j"
  # $three
  # [1] "a" "e" "f" "g" "h" "i" "j" "l" "m"
  listInputmat    <- fromList(listInput) == 1
  #     one   two three
  # a  TRUE  TRUE  TRUE
  # b  TRUE  TRUE FALSE
  #...
  # condensing matrix to unique combinations elements
  listInputunique <- unique(listInputmat)
  grouplist <- list()
  # going through all unique combinations and collect elements for each in a list
  for (i in 1:nrow(listInputunique)) {
    currentRow <- listInputunique[i,]
    myelements <- which(apply(listInputmat,1,function(x) all(x == currentRow)))
    attr(myelements, "groups") <- currentRow
    grouplist[[paste(colnames(listInputunique)[currentRow], collapse = ":")]] <- myelements
    myelements
    # attr(,"groups")
    #   one   two three 
    # FALSE FALSE  TRUE 
    #  f  i 
    # 12 13 
  }
  if (sort) {
    grouplist <- grouplist[order(sapply(grouplist, function(x) length(x)), decreasing = TRUE)]
  }
  attr(grouplist, "elements") <- unique(unlist(listInput))
  return(grouplist)
  # save element list to facilitate access using an index in case rownames are not named
}


# How to use:
# library(UpSetR)
# example of list input (list of named vectors)
#listInput <- list(one = letters[ c(1, 2, 3, 5, 7, 8, 11, 12, 13) ], 
#                  two = letters[ c(1, 2, 4, 5, 10) ], 
#                  three = letters[ c(1, 5, 6, 7, 8, 9, 10, 12, 13) ])

# li <- overlapGroups(listInput)

# list of all elements:
# attr(li, "elements")
#  [1] "a" "b" "c" "e" "g" "h" "k" "l" "m" "d" "j" "f" "i"

# which elements are in the biggest group?
# li[1]
# $`one:three`
# g h l m 
# 5 6 8 9 
# attr(,"groups")
#   one   two three 
#  TRUE FALSE  TRUE 

# names(li[[1]])
# [1] "g" "h" "l" "m"
# attr(li, "elements")[li[[1]]]
# [1] "g" "h" "l" "m"