diff --git a/R/.ipynb_checkpoints/MainBar-checkpoint.R b/R/.ipynb_checkpoints/MainBar-checkpoint.R
new file mode 100644
index 0000000..d35ce92
--- /dev/null
+++ b/R/.ipynb_checkpoints/MainBar-checkpoint.R
@@ -0,0 +1,208 @@
+#' @importFrom plyr count
+
+## 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){
+  temp_data <- list()
+  Freqs <- data.frame()
+  end_col <- as.numeric(((start_col + num_sets) -1))
+  #gets indices of columns containing sets used
+  for( i in 1:num_sets){
+    temp_data[i] <- match(name_of_sets[i], colnames(data))
+  }
+  Freqs <- data.frame(count(data[ ,as.integer(temp_data)]))
+  colnames(Freqs)[1:num_sets] <- name_of_sets
+  #Adds on empty intersections if option is selected
+  if(is.null(empty_intersects) == F){
+    empty <- rep(list(c(0,1)), times = num_sets)
+    empty <- data.frame(expand.grid(empty))
+    colnames(empty) <- name_of_sets
+    empty$freq <- 0
+    all <- rbind(Freqs, empty)
+    Freqs <- data.frame(all[!duplicated(all[1:num_sets]), ], check.names = F)
+  }
+  #Remove universal empty set
+  Freqs <- Freqs[!(rowSums(Freqs[ ,1:num_sets]) == 0), ]
+  #Aggregation by degree
+  if(tolower(aggregate) == "degree"){
+    for(i in 1:nrow(Freqs)){
+      Freqs$degree[i] <- rowSums(Freqs[ i ,1:num_sets])
+    }
+    order_cols <- c()
+    for(i in 1:length(order_mat)){
+      order_cols[i] <- match(order_mat[i], colnames(Freqs))
+    }
+    # if(length(order_cols)==2 && order_cols[1]>order_cols[2]){decrease <- rev(decrease)}
+    for(i in 1:length(order_cols)){
+      logic <- decrease[i]
+      Freqs <- Freqs[order(Freqs[ , order_cols[i]], decreasing = logic), ]
+    }
+  }
+  #Aggregation by sets
+  else if(tolower(aggregate) == "sets")
+  {
+    Freqs <- Get_aggregates(Freqs, num_sets, order_mat, cut)
+  }
+  #delete rows used to order data correctly. Not needed to set up bars.
+  delete_row <- (num_sets + 2)
+  Freqs <- Freqs[ , -delete_row]
+  for( i in 1:nrow(Freqs)){
+    Freqs$x[i] <- i
+    Freqs$color <- mbar_color
+  }
+  if(is.na(nintersections)){
+    nintersections = nrow(Freqs)
+  }
+  Freqs <- Freqs[1:nintersections, ]
+  Freqs <- na.omit(Freqs)
+  return(Freqs)
+}
+
+## Generate main bar plot
+Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_angles, number.colors,
+                          ebar, ylabel, ymax, scale_intersections, text_scale, attribute_plots, plot.title){
+
+  bottom_margin <- (-1)*0.65
+
+  if(is.null(attribute_plots) == FALSE){
+    bottom_margin <- (-1)*0.45
+  }
+  
+  if(length(text_scale) > 1 && length(text_scale) <= 6){
+    y_axis_title_scale <- text_scale[1]
+    y_axis_tick_label_scale <- text_scale[2]
+    intersection_size_number_scale <- text_scale[6]
+  }
+  else{
+    y_axis_title_scale <- text_scale
+    y_axis_tick_label_scale <- text_scale
+    intersection_size_number_scale <- text_scale
+  }
+  
+  if(is.null(Q) == F){
+    inter_data <- Q
+    if(nrow(inter_data) != 0){
+      inter_data <- inter_data[order(inter_data$x), ]
+    }
+    else{inter_data <- NULL}
+  }
+  else{inter_data <- NULL}
+  
+  if(is.null(ebar) == F){
+    elem_data <- ebar
+    if(nrow(elem_data) != 0){
+      elem_data <- elem_data[order(elem_data$x), ]
+    }
+    else{elem_data <- NULL}
+  }
+  else{elem_data <- NULL}
+  
+  #ten_perc creates appropriate space above highest bar so number doesnt get cut off
+  if(is.null(ymax) == T){
+  ten_perc <- ((max(Main_bar_data$freq)) * 0.1)
+  ymax <- max(Main_bar_data$freq) + ten_perc
+  }
+  
+  if(ylabel == "Intersection Size" && scale_intersections != "identity"){
+    ylabel <- paste("Intersection Size", paste0("( ", scale_intersections, " )"))
+  }
+  if(scale_intersections == "log2"){
+    Main_bar_data$freq <- round(log2(Main_bar_data$freq), 2)
+    elem_data$freq <- round(log2(elem_data$freq), 2)
+    inter_data$freq <- round(log2(inter_data$freq), 2)
+    customQ$freq2 <- round(log2(customQ$freq2), 2)
+    ymax <- log2(ymax)
+  }
+  if(scale_intersections == "log10"){
+    Main_bar_data$freq <- round(log10(Main_bar_data$freq), 2)
+    elem_data$freq <- round(log10(elem_data$freq), 2)
+    inter_data$freq <- round(log10(inter_data$freq), 2)
+    customQ$freq2 <- round(log10(customQ$freq2), 2)
+    ymax <- log10(ymax)
+  }
+  Main_bar_plot <- (ggplot(data = Main_bar_data, aes_string(x = "x", y = "freq")) 
+                    + scale_y_continuous(trans = scale_intersections)
+                    + ylim(0, ymax)
+                    + geom_bar(stat = "identity", width = 0.6,
+                               fill = Main_bar_data$color)
+                    + scale_x_continuous(limits = c(0,(nrow(Main_bar_data)+1 )), expand = c(0,0),
+                                         breaks = NULL)
+                    + xlab(NULL) + ylab(ylabel) +labs(title = NULL)
+                    + theme(panel.background = element_rect(fill = "white"),
+                            plot.margin = unit(c(0.5,0.5,bottom_margin,0.5), "lines"), panel.border = element_blank(),
+                            axis.title.y = element_text(vjust = -0.8, size = 8.3*y_axis_title_scale), axis.text.y = element_text(vjust=0.3,
+                                                                                                            size=7*y_axis_tick_label_scale)))
+  if((show_num == "yes") || (show_num == "Yes")){
+    if(is.null(number.colors)) {
+      Main_bar_plot <- (Main_bar_plot + geom_text(aes_string(label = "freq"), size = 2.2*intersection_size_number_scale, vjust = -1,
+                                                  angle = number_angles, colour = Main_bar_data$color))
+    } else {
+      Main_bar_plot <- (Main_bar_plot + geom_text(aes_string(label = "freq"), size = 2.2*intersection_size_number_scale, vjust = -1,
+                                                  angle = number_angles, colour = number.colors))
+    }
+  }
+
+  bInterDat <- NULL
+  pInterDat <- NULL
+  bCustomDat <- NULL
+  pCustomDat <- NULL
+  bElemDat <- NULL
+  pElemDat <- NULL
+  if(is.null(elem_data) == F){
+    bElemDat <- elem_data[which(elem_data$act == T), ]
+    bElemDat <- bElemDat[order(bElemDat$x), ]
+    pElemDat <- elem_data[which(elem_data$act == F), ]
+  }
+  if(is.null(inter_data) == F){
+    bInterDat <- inter_data[which(inter_data$act == T), ]
+    bInterDat <- bInterDat[order(bInterDat$x), ]
+    pInterDat <- inter_data[which(inter_data$act == F), ]
+  }
+  if(length(customQ) != 0){
+    pCustomDat <- customQ[which(customQ$act == F), ]
+    bCustomDat <- customQ[which(customQ$act == T), ]
+    bCustomDat <- bCustomDat[order(bCustomDat$x), ]
+  }
+  if(length(bInterDat) != 0){
+    Main_bar_plot <- Main_bar_plot + geom_bar(data = bInterDat,
+                                              aes_string(x="x", y = "freq"),
+                                              fill = bInterDat$color,
+                                              stat = "identity", position = "identity", width = 0.6)
+  }
+  if(length(bElemDat) != 0){
+    Main_bar_plot <- Main_bar_plot + geom_bar(data = bElemDat,
+                                              aes_string(x="x", y = "freq"),
+                                              fill = bElemDat$color,
+                                              stat = "identity", position = "identity", width = 0.6)
+  }
+  if(length(bCustomDat) != 0){
+    Main_bar_plot <- (Main_bar_plot + geom_bar(data = bCustomDat, aes_string(x="x", y = "freq2"),
+                                               fill = bCustomDat$color2,
+                                               stat = "identity", position ="identity", width = 0.6))
+  }
+  if(length(pCustomDat) != 0){
+    Main_bar_plot <- (Main_bar_plot + geom_point(data = pCustomDat, aes_string(x="x", y = "freq2"), colour = pCustomDat$color2,
+                                                 size = 2, shape = 17, position = position_jitter(width = 0.2, height = 0.2)))
+  }
+  if(length(pInterDat) != 0){
+    Main_bar_plot <- (Main_bar_plot + geom_point(data = pInterDat, aes_string(x="x", y = "freq"),
+                                                 position = position_jitter(width = 0.2, height = 0.2),
+                                                 colour = pInterDat$color, size = 2, shape = 17))
+  }
+  if(length(pElemDat) != 0){
+    Main_bar_plot <- (Main_bar_plot + geom_point(data = pElemDat, aes_string(x="x", y = "freq"),
+                                                 position = position_jitter(width = 0.2, height = 0.2),
+                                                 colour = pElemDat$color, size = 2, shape = 17))
+  }
+  
+  Main_bar_plot <- (Main_bar_plot 
+                    + geom_vline(xintercept = 0, color = "gray0")
+                    + geom_hline(yintercept = 0, color = "gray0"))
+  
+  if(!is.na(plot.title)) {
+    Main_bar_plot <- c(Main_bar_plot + ggtitle(plot.title))
+  }
+  Main_bar_plot <- ggplotGrob(Main_bar_plot)
+  return(Main_bar_plot)
+}
diff --git a/R/MainBar.R b/R/MainBar.R
index e9cf791..d35ce92 100644
--- a/R/MainBar.R
+++ b/R/MainBar.R
@@ -109,10 +109,16 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
   }
   if(scale_intersections == "log2"){
     Main_bar_data$freq <- round(log2(Main_bar_data$freq), 2)
+    elem_data$freq <- round(log2(elem_data$freq), 2)
+    inter_data$freq <- round(log2(inter_data$freq), 2)
+    customQ$freq2 <- round(log2(customQ$freq2), 2)
     ymax <- log2(ymax)
   }
   if(scale_intersections == "log10"){
     Main_bar_data$freq <- round(log10(Main_bar_data$freq), 2)
+    elem_data$freq <- round(log10(elem_data$freq), 2)
+    inter_data$freq <- round(log10(inter_data$freq), 2)
+    customQ$freq2 <- round(log10(customQ$freq2), 2)
     ymax <- log10(ymax)
   }
   Main_bar_plot <- (ggplot(data = Main_bar_data, aes_string(x = "x", y = "freq"))