From ae6e6736964cfd9b06b407d1ad1f7ee50ffee1df Mon Sep 17 00:00:00 2001
From: Alexis Derumigny <aderumigny@gmail.com>
Date: Wed, 18 Oct 2023 16:20:27 +0200
Subject: [PATCH] Add a possibility to allow the univ empty set

---
 R/MainBar.R  | 10 +++++++---
 R/upset.R    |  6 ++++--
 man/upset.Rd |  3 +++
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/R/MainBar.R b/R/MainBar.R
index e9cf791..f67ac10 100644
--- a/R/MainBar.R
+++ b/R/MainBar.R
@@ -3,7 +3,7 @@
 ## Counts the frequency of each intersection being looked at and sets up data for main bar plot.
 ## Also orders the data for the bar plot and matrix plot
 Counter <- function(data, num_sets, start_col, name_of_sets, nintersections, mbar_color, order_mat,
-                    aggregate, cut, empty_intersects, decrease){
+                    aggregate, cut, empty_intersects, decrease, keep.universal.empty.set = FALSE){
   temp_data <- list()
   Freqs <- data.frame()
   end_col <- as.numeric(((start_col + num_sets) -1))
@@ -22,8 +22,12 @@ Counter <- function(data, num_sets, start_col, name_of_sets, nintersections, mba
     all <- rbind(Freqs, empty)
     Freqs <- data.frame(all[!duplicated(all[1:num_sets]), ], check.names = F)
   }
-  #Remove universal empty set
-  Freqs <- Freqs[!(rowSums(Freqs[ ,1:num_sets]) == 0), ]
+  
+  if (!keep.universal.empty.set){
+    # Remove universal empty set
+    Freqs <- Freqs[!(rowSums(Freqs[ ,1:num_sets]) == 0), ]
+  }
+  
   #Aggregation by degree
   if(tolower(aggregate) == "degree"){
     for(i in 1:nrow(Freqs)){
diff --git a/R/upset.R b/R/upset.R
index 20c09c8..8c4e22a 100644
--- a/R/upset.R
+++ b/R/upset.R
@@ -42,6 +42,7 @@
 #' @param shade.alpha Transparency of shading in matrix
 #' @param matrix.dot.alpha Transparency of the empty intersections points in the matrix
 #' @param empty.intersections Additionally display empty sets up to nintersects
+#' @param keep.universal.empty.set Additionally displays the universal empty set (i.e. the set \code{c()} for which no choices are selected)
 #' @param color.pal Color palette for attribute plots
 #' @param boxplot.summary Boxplots representing the distribution of a selected attribute for each intersection. Select attributes by entering a character vector of attribute names (e.g. c("Name1", "Name2")).
 #'        The maximum number of attributes that can be entered is 2.
@@ -123,7 +124,7 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
                   mb.ratio = c(0.70,0.30), expression = NULL, att.pos = NULL, att.color = main.bar.color, order.by = c("freq", "degree"),
                   decreasing = c(T, F), show.numbers = "yes", number.angles = 0, number.colors=NULL, group.by = "degree",cutoff = NULL,
                   queries = NULL, query.legend = "none", shade.color = "gray88", shade.alpha = 0.25, matrix.dot.alpha =0.5,
-                  empty.intersections = NULL, color.pal = 1, boxplot.summary = NULL, attribute.plots = NULL, scale.intersections = "identity",
+                  empty.intersections = NULL, keep.universal.empty.set = FALSE, color.pal = 1, boxplot.summary = NULL, attribute.plots = NULL, scale.intersections = "identity",
                   scale.sets = "identity", text.scale = 1, set_size.angles = 0 , set_size.show = FALSE, set_size.numbers_size = NULL, set_size.scale_max = NULL){
 
   startend <-FindStartEnd(data)
@@ -162,7 +163,8 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
     Set_names <- order_sets(New_data, Set_names)
     }
     All_Freqs <- Counter(New_data, Num_of_set, first.col, Set_names, nintersects, main.bar.color,
-                         order.by, group.by, cutoff, empty.intersections, decreasing)
+                         order.by, group.by, cutoff, empty.intersections, decreasing,
+                         keep.universal.empty.set = keep.universal.empty.set)
   }
   Matrix_setup <- Create_matrix(All_Freqs)
   labels <- Make_labels(Matrix_setup)
diff --git a/man/upset.Rd b/man/upset.Rd
index 7947d64..51362de 100644
--- a/man/upset.Rd
+++ b/man/upset.Rd
@@ -38,6 +38,7 @@ upset(
   shade.alpha = 0.25,
   matrix.dot.alpha = 0.5,
   empty.intersections = NULL,
+  keep.universal.empty.set = FALSE,
   color.pal = 1,
   boxplot.summary = NULL,
   attribute.plots = NULL,
@@ -125,6 +126,8 @@ See examples section on how to do this.}
 
 \item{empty.intersections}{Additionally display empty sets up to nintersects}
 
+\item{keep.universal.empty.set}{Additionally displays the universal empty set (i.e. the set \code{c()} for which no choices are selected)}
+
 \item{color.pal}{Color palette for attribute plots}
 
 \item{boxplot.summary}{Boxplots representing the distribution of a selected attribute for each intersection. Select attributes by entering a character vector of attribute names (e.g. c("Name1", "Name2")).