diff --git a/DESCRIPTION b/DESCRIPTION
index aa6ae2c..3702877 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,4 +26,4 @@ LazyData: true
 VignetteBuilder: knitr
 Suggests:
     knitr
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1.9000
diff --git a/NAMESPACE b/NAMESPACE
index 61251e7..ef26143 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,upset)
 export(elements)
 export(fromExpression)
 export(fromList)
diff --git a/R/Matrix.R b/R/Matrix.R
index da39416..b828672 100644
--- a/R/Matrix.R
+++ b/R/Matrix.R
@@ -38,11 +38,11 @@ Create_layout <- function(setup, mat_color, mat_col, matrix_dot_alpha){
       Matrix_layout$Intersection[i] <- paste(Matrix_layout$x[i], "yes", sep ="")
     }
     else{
-      
+
       Matrix_layout$color[i] <- "gray83"
       Matrix_layout$alpha[i] <- matrix_dot_alpha
       Matrix_layout$Intersection[i] <- paste(i, "No", sep = "")
-    } 
+    }
   }
   if(is.null(mat_col) == F){
     for(i in 1:nrow(mat_col)){
@@ -58,7 +58,7 @@ Create_layout <- function(setup, mat_color, mat_col, matrix_dot_alpha){
   return(Matrix_layout)
 }
 
-## Create data set to shade matrix 
+## Create data set to shade matrix
 MakeShading <- function(Mat_data, color){
   y <- unique(Mat_data$y)
   y <- (y[which(y %% 2 != 0)])
@@ -76,23 +76,23 @@ MakeShading <- function(Mat_data, color){
 ## Generate matrix plot
 Make_matrix_plot <- function(Mat_data,Set_size_data, Main_bar_data, point_size, line_size, text_scale, labels,
                              shading_data, shade_alpha){
-  
+
   if(length(text_scale) == 1){
-    name_size_scale <- text_scale 
+    name_size_scale <- text_scale
   }
   if(length(text_scale) > 1 && length(text_scale) <= 6){
     name_size_scale <- text_scale[5]
   }
-  
-  Matrix_plot <- (ggplot() 
+
+  Matrix_plot <- (ggplot()
                   + theme(panel.background = element_rect(fill = "white"),
                           plot.margin=unit(c(-0.2,0.5,0.5,0.5), "lines"),
                           axis.text.x = element_blank(),
                           axis.ticks.x = element_blank(),
                           axis.ticks.y = element_blank(),
-                          axis.text.y = element_text(colour = "gray0", 
+                          axis.text.y = element_text(colour = "gray0",
                                                      size = 7*name_size_scale, hjust = 0.4),
-                          panel.grid.major = element_blank(), 
+                          panel.grid.major = element_blank(),
                           panel.grid.minor = element_blank())
                   + xlab(NULL) + ylab("   ")
                   + scale_y_continuous(breaks = c(1:nrow(Set_size_data)),
@@ -103,10 +103,10 @@ Make_matrix_plot <- function(Mat_data,Set_size_data, Main_bar_data, point_size,
                                                               ymin = "y_min", ymax = "y_max"),
                               fill = shading_data$shade_color, alpha = shade_alpha)
                   + geom_point(data= Mat_data, aes_string(x= "x", y= "y"), colour = Mat_data$color,
-                               size= point_size, alpha = Mat_data$alpha)
+                               size= point_size, alpha = Mat_data$alpha, shape=16)
                   + geom_line(data= Mat_data, aes_string(group = "Intersection", x="x", y="y",
                                                          colour = "color"), size = line_size)
                   + scale_color_identity())
   Matrix_plot <- ggplot_gtable(ggplot_build(Matrix_plot))
   return(Matrix_plot)
-}
\ No newline at end of file
+}
diff --git a/R/UpSet.plot.R b/R/UpSet.plot.R
index 4e3ac5e..27ab9d8 100644
--- a/R/UpSet.plot.R
+++ b/R/UpSet.plot.R
@@ -11,13 +11,13 @@
 Make_base_plot <- function(Main_bar_plot, Matrix_plot, Size_plot, labels, hratios, att_x, att_y,
                            Set_data, exp, position, start_col, att_color, QueryData,
                            attribute_plots, legend, query_legend, boxplot, names, set_metadata,
-                           set_metadata_plots){
-  
+                           set_metadata_plots, newpage){
+
   end_col <- ((start_col + as.integer(length(labels))) - 1)
   Set_data <- Set_data[which(rowSums(Set_data[ ,start_col:end_col]) != 0), ]
   Main_bar_plot$widths <- Matrix_plot$widths
   Matrix_plot$heights <- Size_plot$heights
-  if(is.null(set_metadata) ==F){
+  if(!is.null(set_metadata)){
     ncols <- 0
     for(i in 1:length(set_metadata_plots)){
       ncols <- ncols + set_metadata$plots[[i]]$assign
@@ -25,33 +25,33 @@ Make_base_plot <- function(Main_bar_plot, Matrix_plot, Size_plot, labels, hratio
     }
     set_metadata$ncols <- ncols
   }
-  if(is.null(legend)==F){
+  if(!is.null(legend)) {
     legend$widths <- Matrix_plot$widths
   }
-  if(is.null(boxplot) == F){
+  if(!is.null(boxplot)){
     for(i in seq_along(boxplot)){
       boxplot[[i]]$widths <- Matrix_plot$widths
     }
   }
-  
+
   size_plot_height <- (((hratios[1])+0.01)*100)
   if((hratios[1] > 0.7 || hratios[1] < 0.3) ||
      (hratios[2] > 0.7 || hratios[2] < 0.3)) warning("Plot might be out of range if ratio > 0.7 or < 0.3")
-  if(is.null(attribute_plots) == T && is.null(boxplot) == T){
+  if(is.null(attribute_plots) && is.null(boxplot)){
     NoAttBasePlot(legend, size_plot_height, Main_bar_plot, Matrix_plot, hratios, Size_plot, query_legend,
-                  set_metadata, set_metadata_plots)
+                  set_metadata, set_metadata_plots, newpage=newpage)
   }
-  else if(is.null(attribute_plots) == F && is.null(boxplot) == T){
+  else if(!is.null(attribute_plots) && is.null(boxplot)){
     plots <- GenerateCustomPlots(attribute_plots, Set_data, QueryData, att_color, att_x, att_y, names)
     #      for(i in seq_along(plots)){
     #        attribute_plots$plots[[i]]$plot <- plots[[i]]
     #      }
     BaseCustomPlot(attribute_plots, plots, position, size_plot_height, Main_bar_plot, Matrix_plot, Size_plot,
-                   hratios, legend, query_legend, set_metadata, set_metadata_plots)
+                   hratios, legend, query_legend, set_metadata, set_metadata_plots, newpage=newpage)
   }
-  else if(is.null(boxplot)==F && is.null(attribute_plots) == T){
+  else if(!is.null(boxplot) && is.null(attribute_plots)){
     BaseBoxPlot(boxplot, position, size_plot_height, Main_bar_plot, Matrix_plot, Size_plot,
-                hratios, set_metadata, set_metadata_plots)
+                hratios, set_metadata, set_metadata_plots, newpage=newpage)
   }
 }
 
@@ -62,11 +62,12 @@ vplayout <- function(x,y){
 
 ## Generates UpSet plot with boxplots representing distributions of attributes
 BaseBoxPlot <- function(box_plot, position, size_plot_height, Main_bar_plot, Matrix_plot,
-                        Size_plot, hratios, set_metadata, set_metadata_plots){
+                        Size_plot, hratios, set_metadata, set_metadata_plots, newpage){
+
   if(length(box_plot) > 2){
     return(warning("UpSet can only show 2 box plots at a time"))
   }
-  if(is.null(position) == T || position == tolower("bottom")){
+  if(is.null(position) || position == tolower("bottom")){
     bar_top <- 1
     matrix_bottom <- 100
     att_top <- 101
@@ -77,7 +78,7 @@ BaseBoxPlot <- function(box_plot, position, size_plot_height, Main_bar_plot, Mat
       gridrow <- 145
     }
   }
-  if((is.null(position) == F) && (position != tolower("bottom"))){
+  if((!is.null(position)) && (position != tolower("bottom"))){
     if(length(box_plot)==1){
       size_plot_height <- (size_plot_height + 35)
       bar_top <- 36
@@ -94,13 +95,13 @@ BaseBoxPlot <- function(box_plot, position, size_plot_height, Main_bar_plot, Mat
       gridrow <- 150
     }
   }
-  if(is.null(set_metadata) == T){
+  if(is.null(set_metadata)){
     matrix_and_mainbar_right <- 100
     matrix_and_mainbar_left <- 21
     size_bar_right <- 20
     size_bar_left <- 1
   }
-  else if(is.null(set_metadata) == F){
+  else if(!is.null(set_metadata)){
     matrix_and_mainbar_right <- set_metadata$ncols + 100
     matrix_and_mainbar_left <- set_metadata$ncols + 21
     size_bar_right <- set_metadata$ncols + 20
@@ -108,7 +109,9 @@ BaseBoxPlot <- function(box_plot, position, size_plot_height, Main_bar_plot, Mat
     metadata_right <- set_metadata$ncols
     metadata_left <- 1
   }
-  grid.newpage()
+  if (newpage) {
+    grid.newpage()
+  }
   if(length(box_plot) == 1){
     pushViewport(viewport(layout = grid.layout(135,matrix_and_mainbar_right)))
   }
@@ -123,7 +126,7 @@ BaseBoxPlot <- function(box_plot, position, size_plot_height, Main_bar_plot, Mat
   pushViewport(vp)
   grid.draw(arrangeGrob(Size_plot))
   popViewport()
-  if(is.null(set_metadata) == F){
+  if(!is.null(set_metadata)){
     for(i in 1:length(set_metadata_plots)){
       if(i != 1){
         metadata_left <- 1+metadata_right
@@ -133,7 +136,7 @@ BaseBoxPlot <- function(box_plot, position, size_plot_height, Main_bar_plot, Mat
         metadata_left <- 1
         metadata_right <- set_metadata$plots[[i]]$assign
       }
-      
+
       vp = vplayout(size_plot_height:matrix_bottom, metadata_left:metadata_right)
       pushViewport(vp)
       grid.draw(arrangeGrob(set_metadata_plots[[i]]))
@@ -154,10 +157,10 @@ BaseBoxPlot <- function(box_plot, position, size_plot_height, Main_bar_plot, Mat
 
 ## Generates UpSet plot when no attributes are selected to be plotted
 NoAttBasePlot <- function(legend, size_plot_height, Main_bar_plot, Matrix_plot, hratios,
-                          Size_plot, query_legend, set_metadata, set_metadata_plots){
+                          Size_plot, query_legend, set_metadata, set_metadata_plots, newpage){
   top <- 1
   bottom <- 100
-  if((is.null(legend) == F) && (query_legend != tolower("none"))){
+  if((!is.null(legend)) && (query_legend != tolower("none"))){
     if(query_legend == tolower("top")){
       top <- 3
       bottom <- 102
@@ -170,13 +173,13 @@ NoAttBasePlot <- function(legend, size_plot_height, Main_bar_plot, Matrix_plot,
       legend_bottom <- 103
     }
   }
-  if(is.null(set_metadata) == T){
+  if(is.null(set_metadata)){
     matrix_and_mainbar_right <- 100
     matrix_and_mainbar_left <- 21
     size_bar_right <- 20
     size_bar_left <- 1
   }
-  else if(is.null(set_metadata) == F){
+  else if(!is.null(set_metadata)){
     matrix_and_mainbar_right <- set_metadata$ncols + 100
     matrix_and_mainbar_left <- set_metadata$ncols + 21
     size_bar_right <- set_metadata$ncols + 20
@@ -184,8 +187,10 @@ NoAttBasePlot <- function(legend, size_plot_height, Main_bar_plot, Matrix_plot,
     metadata_right <- set_metadata$ncols
     metadata_left <- 1
   }
-  grid.newpage()
-  if((is.null(legend) == F) && (query_legend != tolower("none"))){
+  if (newpage) {
+    grid.newpage()
+  }
+  if((!is.null(legend)) && (query_legend != tolower("none"))){
     if(query_legend == tolower("top")){
       pushViewport(viewport(layout = grid.layout(102, matrix_and_mainbar_right)))
     }
@@ -193,7 +198,7 @@ NoAttBasePlot <- function(legend, size_plot_height, Main_bar_plot, Matrix_plot,
       pushViewport(viewport(layout = grid.layout(103, matrix_and_mainbar_right)))
     }
   }
-  else if((is.null(legend) == T)|| (query_legend == tolower("none"))){
+  else if((is.null(legend))|| (query_legend == tolower("none"))){
     pushViewport(viewport(layout = grid.layout(100,matrix_and_mainbar_right)))
   }
   vp = vplayout(top:bottom, matrix_and_mainbar_left:matrix_and_mainbar_right)
@@ -204,7 +209,7 @@ NoAttBasePlot <- function(legend, size_plot_height, Main_bar_plot, Matrix_plot,
   pushViewport(vp)
   grid.draw(arrangeGrob(Size_plot))
   popViewport()
-  if(is.null(set_metadata) == F){
+  if(!is.null(set_metadata)){
     for(i in 1:length(set_metadata_plots)){
       if(i != 1){
         metadata_left <- 1+metadata_right
@@ -214,14 +219,14 @@ NoAttBasePlot <- function(legend, size_plot_height, Main_bar_plot, Matrix_plot,
         metadata_left <- 1
         metadata_right <- set_metadata$plots[[i]]$assign
       }
-      
+
       vp = vplayout(size_plot_height:bottom, metadata_left:metadata_right)
       pushViewport(vp)
       grid.draw(arrangeGrob(set_metadata_plots[[i]]))
       popViewport()
     }
   }
-  if((is.null(legend) == F) && (query_legend != tolower("none"))){
+  if((!is.null(legend)) && (query_legend != tolower("none"))){
     vp = vplayout(legend_top:legend_bottom, matrix_and_mainbar_left:matrix_and_mainbar_right)
     pushViewport(vp)
     grid.draw(arrangeGrob(legend))
@@ -231,19 +236,19 @@ NoAttBasePlot <- function(legend, size_plot_height, Main_bar_plot, Matrix_plot,
 
 ## Function that plots out the list of plots generated from custom plot input
 BaseCustomPlot <- function(attribute_plots, plots, position, size_plot_height, Main_bar_plot, Matrix_plot,
-                           Size_plot, hratios, legend, q_legend, set_metadata, set_metadata_plots){
+                           Size_plot, hratios, legend, q_legend, set_metadata, set_metadata_plots, newpage){
   bar_top <- 1
   matrix_bottom <- 100
   custom_top <- 101
   custom_bottom <- (attribute_plots$gridrows + 100)
-  
-  if(is.null(set_metadata) == T){
+
+  if(is.null(set_metadata)){
     matrix_and_mainbar_right <- 100
     matrix_and_mainbar_left <- 21
     size_bar_right <- 20
     size_bar_left <- 1
   }
-  else if(is.null(set_metadata) == F){
+  else if(!is.null(set_metadata)){
     matrix_and_mainbar_right <- set_metadata$ncols + 100
     matrix_and_mainbar_left <- set_metadata$ncols + 21
     size_bar_right <- set_metadata$ncols + 20
@@ -251,15 +256,17 @@ BaseCustomPlot <- function(attribute_plots, plots, position, size_plot_height, M
     metadata_right <- set_metadata$ncols
     metadata_left <- 1
   }
-  
-  if((is.null(legend) == F) && (q_legend == tolower("bottom"))){custom_bottom <- (custom_bottom + 5)}
-  if((is.null(legend) == F) && (q_legend == tolower("top"))){
+
+  if((!is.null(legend)) && (q_legend == tolower("bottom"))){custom_bottom <- (custom_bottom + 5)}
+  if((!is.null(legend)) && (q_legend == tolower("top"))){
     bar_top <- bar_top + 5
     matrix_bottom <- matrix_bottom + 5
     custom_top <- custom_top + 5
     custom_bottom <- custom_bottom + 5
   }
-  grid.newpage()
+  if (newpage) {
+    grid.newpage()
+  }
   pushViewport(viewport(layout = grid.layout(custom_bottom,matrix_and_mainbar_right)))
   vp = vplayout(bar_top:matrix_bottom, matrix_and_mainbar_left:matrix_and_mainbar_right)
   pushViewport(vp)
@@ -269,7 +276,7 @@ BaseCustomPlot <- function(attribute_plots, plots, position, size_plot_height, M
   pushViewport(vp)
   grid.draw(arrangeGrob(Size_plot))
   popViewport()
-  if(is.null(set_metadata) == F){
+  if(!is.null(set_metadata)){
     for(i in 1:length(set_metadata_plots)){
       if(i != 1){
         metadata_left <- 1+metadata_right
@@ -279,14 +286,14 @@ BaseCustomPlot <- function(attribute_plots, plots, position, size_plot_height, M
         metadata_left <- 1
         metadata_right <- set_metadata$plots[[i]]$assign
       }
-      
+
       vp = vplayout(size_plot_height:matrix_bottom, metadata_left:metadata_right)
       pushViewport(vp)
       grid.draw(arrangeGrob(set_metadata_plots[[i]]))
       popViewport()
     }
   }
-  if((is.null(legend) == F) && (q_legend == tolower("bottom"))){
+  if((!is.null(legend)) && (q_legend == tolower("bottom"))){
     vp = vplayout(custom_top:(custom_bottom - 5), 1:matrix_and_mainbar_right)
     pushViewport(vp)
     grid.draw(do.call(arrangeGrob, c(plots, ncol = attribute_plots$ncols)))
@@ -296,7 +303,7 @@ BaseCustomPlot <- function(attribute_plots, plots, position, size_plot_height, M
     grid.draw(arrangeGrob(legend))
     popViewport()
   }
-  else if((is.null(legend) == F) && (q_legend == tolower("top"))){
+  else if((!is.null(legend)) && (q_legend == tolower("top"))){
     vp = vplayout(custom_top:custom_bottom, 1:matrix_and_mainbar_right)
     pushViewport(vp)
     grid.draw(do.call(arrangeGrob, c(plots, ncol = attribute_plots$ncols)))
@@ -317,4 +324,4 @@ BaseCustomPlot <- function(attribute_plots, plots, position, size_plot_height, M
 
 # printCustom <- function(attribute_plots){
 #   print(attribute_plots$plot, vp = vplayout(attribute_plots$rows, attribute_plots$cols), newpage = F)
-# }
\ No newline at end of file
+# }
diff --git a/R/scatter_plot.R b/R/scatter_plot.R
index 6a9bfd7..8a0144c 100644
--- a/R/scatter_plot.R
+++ b/R/scatter_plot.R
@@ -4,11 +4,11 @@
 #' @param mydata A data set containing intersection data provided internally
 #' @param x The x aesthetic for the scatter plot
 #' @param y The y aesthetic for the scatter plot
-#' @note See examples section for upset function on how to use custom.plot parameter. 
+#' @note See examples section for upset function on how to use custom.plot parameter.
 #' @export
 scatter_plot <- function(mydata, x, y){
-  att_plot <- (ggplot(data = mydata, aes_string(x = x, y = y, colour = "color")) 
-               + geom_point() + scale_color_identity()
+  att_plot <- (ggplot(data = mydata, aes_string(x = x, y = y, colour = "color"))
+               + geom_point(shape=16) + scale_color_identity()
                + theme(panel.background = element_rect(fill = "white"),
                        plot.title = element_text(vjust = 1.3),
                        panel.grid.minor = element_blank(),
@@ -16,4 +16,4 @@ scatter_plot <- function(mydata, x, y){
                        axis.title.y = element_text(vjust = 1.3, size = 8.3),
                        axis.title.x = element_text(size = 8.3),
                        plot.margin=unit(c(0.5,0,0,1), "cm")))
-}
\ No newline at end of file
+}
diff --git a/R/upset.R b/R/upset.R
index 2212308..dddb8ec 100644
--- a/R/upset.R
+++ b/R/upset.R
@@ -6,7 +6,7 @@
 #' @param nintersects Number of intersections to plot. If set to NA, all intersections will be plotted.
 #' @param sets Specific sets to look at (Include as combinations. Ex: c("Name1", "Name2"))
 #' @param keep.order Keep sets in the order entered using the sets parameter. The default is FALSE, which orders the sets by their sizes.
-#' @param set.metadata Metadata that offers insight to an attribute of the sets. Input should be a data frame where the first column is set names, and the 
+#' @param set.metadata Metadata that offers insight to an attribute of the sets. Input should be a data frame where the first column is set names, and the
 #'        remaining columns are attributes of those sets. To learn how to use this parameter it is highly suggested to view the set metadata vignette. The link
 #'        can be found on the package's GitHub page.
 #' @param intersections Specific intersections to include in plot entered as a list of lists.
@@ -42,7 +42,7 @@
 #' @param empty.intersections Additionally display empty sets up to nintersects
 #' @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. 
+#'        The maximum number of attributes that can be entered is 2.
 #' @param attribute.plots Create custom ggplot using intersection data represented in the main bar plot. Prior to adding custom plots, the UpSet plot is set up in a 100 by 100 grid.
 #'        The attribute.plots parameter takes a list that contains the number of rows that should be allocated for the custom plot, and a list of plots with specified positions.
 #'        nrows is the number of rows the custom plots should take up. There is already 100 allocated for the custom plot. plots takes a list that contains a function that returns
@@ -83,7 +83,7 @@
 #'             + geom_point() + scale_color_identity()
 #'             + theme_bw() + theme(plot.margin = unit(c(0,0,0,0), "cm")))
 #' }
-#' 
+#'
 #' attributeplots <- list(gridrows = 55,
 #'                   plots = list(list(plot = plot1, x= "ReleaseDate",  queries = FALSE),
 #'                          list(plot = plot1, x= "ReleaseDate", queries = TRUE),
@@ -103,14 +103,14 @@
 #'                     list(query = intersects, params = list("Drama"), color= "red"),
 #'                     list(query = elements, params = list("ReleaseDate", 1990, 1991, 1992))),
 #'       main.bar.color = "yellow")
-#'       
+#'
 #' @import gridExtra
 #' @import ggplot2
 #' @import utils
 #' @import stats
 #' @import methods
 #' @import grDevices
-#' @import scales       
+#' @import scales
 #' @export
 upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F, set.metadata = NULL, intersections = NULL,
                   matrix.color = "gray23", main.bar.color = "gray23", mainbar.y.label = "Intersection Size", mainbar.y.max = NULL,
@@ -120,11 +120,11 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
                   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",
                   scale.sets = "identity", text.scale = 1, set_size.angles = 0 ){
-  
+
   startend <-FindStartEnd(data)
   first.col <- startend[1]
   last.col <- startend[2]
-  
+
   if(color.pal == 1){
     palette <- c("#1F77B4", "#FF7F0E", "#2CA02C", "#D62728", "#9467BD", "#8C564B", "#E377C2",
                  "#7F7F7F", "#BCBD22", "#17BECF")
@@ -133,7 +133,7 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
     palette <- c("#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00",
                  "#CC79A7")
   }
-  
+
   if(is.null(intersections) == F){
     Set_names <- unique((unlist(intersections)))
     Sets_to_remove <- Remove(data, first.col, last.col, Set_names)
@@ -182,7 +182,7 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
       }
     }
   }
-  
+
   BoxPlots <- NULL
   if(is.null(boxplot.summary) == F){
     BoxData <- IntersectionBoxPlot(All_Freqs, New_data, first.col, Set_names)
@@ -191,7 +191,7 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
       BoxPlots[[i]] <- BoxPlotsPlot(BoxData, boxplot.summary[i], att.color)
     }
   }
-  
+
   customAttDat <- NULL
   customQBar <- NULL
   Intersection <- NULL
@@ -218,7 +218,7 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
   else{
     Matrix_col <- NULL
   }
-  
+
   Matrix_layout <- Create_layout(Matrix_setup, matrix.color, Matrix_col, matrix.dot.alpha)
   Set_sizes <- FindSetFreqs(New_data, first.col, Num_of_set, Set_names, keep.order)
   Bar_Q <- NULL
@@ -234,18 +234,20 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
                                palette)
   }
   AllQueryData <- combineQueriesData(QInter_att_data, QElem_att_data, customAttDat, att.x, att.y)
-  
+
   ShadingData <- NULL
-  
+
   if(is.null(set.metadata) == F){
     ShadingData <- get_shade_groups(set.metadata, Set_names, Matrix_layout, shade.alpha)
     output <- Make_set_metadata_plot(set.metadata, Set_names)
     set.metadata.plots <- output[[1]]
     set.metadata <- output[[2]]
-    
+
     if(is.null(ShadingData) == FALSE){
     shade.alpha <- unique(ShadingData$alpha)
     }
+  } else {
+    set.metadata.plots <- NULL
   }
   if(is.null(ShadingData) == TRUE){
   ShadingData <- MakeShading(Matrix_layout, shade.color)
@@ -255,9 +257,62 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
   Matrix <- Make_matrix_plot(Matrix_layout, Set_sizes, All_Freqs, point.size, line.size,
                              text.scale, labels, ShadingData, shade.alpha)
   Sizes <- Make_size_plot(Set_sizes, sets.bar.color, mb.ratio, sets.x.label, scale.sets, text.scale, set_size.angles)
-  
-  Make_base_plot(Main_bar, Matrix, Sizes, labels, mb.ratio, att.x, att.y, New_data,
-                 expression, att.pos, first.col, att.color, AllQueryData, attribute.plots,
-                 legend, query.legend, BoxPlots, Set_names, set.metadata, set.metadata.plots)
-  
-}
\ No newline at end of file
+
+  # Make_base_plot(Main_bar, Matrix, Sizes, labels, mb.ratio, att.x, att.y, New_data,
+  #                expression, att.pos, first.col, att.color, AllQueryData, attribute.plots,
+  #                legend, query.legend, BoxPlots, Set_names, set.metadata, set.metadata.plots)
+
+  structure(class = "upset",
+    .Data=list(
+      Main_bar = Main_bar,
+      Matrix = Matrix,
+      Sizes = Sizes,
+      labels = labels,
+      mb.ratio = mb.ratio,
+      att.x = att.x,
+      att.y = att.y,
+      New_data = New_data,
+      expression = expression,
+      att.pos = att.pos,
+      first.col = first.col,
+      att.color = att.color,
+      AllQueryData = AllQueryData,
+      attribute.plots = attribute.plots,
+      legend = legend,
+      query.legend = query.legend,
+      BoxPlots = BoxPlots,
+      Set_names = Set_names,
+      set.metadata = set.metadata,
+      set.metadata.plots = set.metadata.plots)
+  )
+}
+#' @export
+print.upset <- function(x, newpage = TRUE) {
+  Make_base_plot(
+    Main_bar_plot = x$Main_bar,
+    Matrix_plot = x$Matrix,
+    Size_plot = x$Sizes,
+    labels = x$labels,
+    hratios = x$mb.ratio,
+    att_x = x$att.x,
+    att_y = x$att.y,
+    Set_data = x$New_data,
+    exp = x$expression,
+    position = x$att.pos,
+    start_col = x$first.col,
+    att_color = x$att.color,
+    QueryData = x$AllQueryData,
+    attribute_plots = x$attribute.plots,
+    legend = x$legend,
+    query_legend = x$query.legend,
+    boxplot = x$BoxPlots,
+    names = x$Set_names,
+    set_metadata = x$set.metadata,
+    set_metadata_plots = x$set.metadata.plots,
+    newpage = newpage)
+}
+
+#' @export
+summary.upset <- function(x) {
+    cat("An object of class `upset`. Call print() to show.")
+}
diff --git a/man/elements.Rd b/man/elements.Rd
index 03b0dd1..d8420a0 100644
--- a/man/elements.Rd
+++ b/man/elements.Rd
@@ -19,4 +19,3 @@ A query paramter to visualize specific elements of interest if queries = active
 \note{
 See examples section of upset function on how to use this function in the queries parameter.
 }
-
diff --git a/man/fromExpression.Rd b/man/fromExpression.Rd
index 10f42fa..175947c 100644
--- a/man/fromExpression.Rd
+++ b/man/fromExpression.Rd
@@ -15,4 +15,3 @@ A function to convert an expression to a data frame compatible with UpSetR.
 \note{
 See "Basic Usage" vignette for an example on how to use this function in UpSetR.
 }
-
diff --git a/man/fromList.Rd b/man/fromList.Rd
index 63397bb..f5f4ce5 100644
--- a/man/fromList.Rd
+++ b/man/fromList.Rd
@@ -15,4 +15,3 @@ A function to convert a list of named vectors to a data frame compatible with Up
 \note{
 See "Basic Usage" vignette for an example on how to use this function in UpSetR.
 }
-
diff --git a/man/histogram.Rd b/man/histogram.Rd
index 7df7d80..006c7e9 100644
--- a/man/histogram.Rd
+++ b/man/histogram.Rd
@@ -17,4 +17,3 @@ A pre-made histogram that can be added to custom.plot paramter.
 \note{
 See examples section for upset function on how to use custom.plot parameter
 }
-
diff --git a/man/intersects.Rd b/man/intersects.Rd
index c20573b..beffc73 100644
--- a/man/intersects.Rd
+++ b/man/intersects.Rd
@@ -19,4 +19,3 @@ A query paramter to visualize elements contained in specific intersections
 \note{
 See examples section of upset function on how to use this function in the queries parameter.
 }
-
diff --git a/man/scatter_plot.Rd b/man/scatter_plot.Rd
index ef6a6bf..cff0be2 100644
--- a/man/scatter_plot.Rd
+++ b/man/scatter_plot.Rd
@@ -19,4 +19,3 @@ A pre-made scatter plot that can be added to the custom.plot paramter.
 \note{
 See examples section for upset function on how to use custom.plot parameter.
 }
-
diff --git a/man/upset.Rd b/man/upset.Rd
index 8f1dc7d..7740109 100644
--- a/man/upset.Rd
+++ b/man/upset.Rd
@@ -176,4 +176,3 @@ Original UpSet Website: \url{http://vcg.github.io/upset/about/}
 
 UpSetR github for additional examples: \url{http://github.com/hms-dbmi/UpSetR}
 }
-