Added support for tibbles and commas

DESCRIPTION

@@ -26,4 +26,4 @@ LazyData: true
 VignetteBuilder: knitr
 Suggests:
     knitr
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1

R/Helper.funcs.R

@@ -2,7 +2,7 @@
 FindStartEnd <- function(data){
   startend <- c()
   for(i in 1:ncol(data)){
-    column <- data[, i]
+    column <- data[[i]]
     column <- (levels(factor(column)))
     if((column[1] == "0") && (column[2] == "1" && (length(column) == 2))){
       startend[1] <- i
@@ -21,7 +21,7 @@ FindStartEnd <- function(data){
     }
   }
   for(i in ncol(data):1){
-    column <- data[ ,i]
+    column <- data[[i]]
     column <- (levels(factor(column)))
     if((column[1] == "0") && (column[2] == "1") && (length(column) == 2)){
       startend[2] <- i

R/MainBar.R

@@ -61,10 +61,10 @@ Counter <- function(data, num_sets, start_col, name_of_sets, nintersections, mba
 
 ## Generate main bar plot
 Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_angles,
-                          ebar, ylabel, ymax, scale_intersections, text_scale, attribute_plots){
-
+                          ebar, ylabel, ymax, scale_intersections, text_scale, attribute_plots, mainbar.comma, intersection.size.comma){
+  
   bottom_margin <- (-1)*0.65
-
+  
   if(is.null(attribute_plots) == FALSE){
     bottom_margin <- (-1)*0.45
   }
@@ -99,9 +99,9 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
   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(is.null(ymax)){
+    ten_perc <- ((max(Main_bar_data$freq)) * 0.1)
+    ymax <- max(Main_bar_data$freq) + ten_perc
   }
 
   if(ylabel == "Intersection Size" && scale_intersections != "identity"){
@@ -115,21 +115,33 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
     Main_bar_data$freq <- round(log10(Main_bar_data$freq), 2)
     ymax <- log10(ymax)
   }
+  labels_arg <- waiver()
+  if(mainbar.comma) labels_arg <- scales::comma
   Main_bar_plot <- (ggplot(data = Main_bar_data, aes_string(x = "x", y = "freq")) 
-                    + scale_y_continuous(trans = scale_intersections)
-                    + ylim(0, ymax)
+                    + scale_y_continuous(trans = scale_intersections, labels = labels_arg, limits = c(0, ymax))
                     + geom_bar(stat = "identity", width = 0.6,
                                fill = Main_bar_data$color)
                     + scale_x_continuous(limits = c(0,(nrow(Main_bar_data)+1 )), expand = c(0,0),
                                          breaks = NULL)
-                    + xlab(NULL) + ylab(ylabel) +labs(title = NULL)
+                    + xlab(NULL) + ylab(ylabel) + labs(title = NULL)
                     + theme(panel.background = element_rect(fill = "white"),
                             plot.margin = unit(c(0.5,0.5,bottom_margin,0.5), "lines"), panel.border = element_blank(),
-                            axis.title.y = element_text(vjust = -0.8, size = 8.3*y_axis_title_scale), axis.text.y = element_text(vjust=0.3,
-                                                                                                            size=7*y_axis_tick_label_scale)))
+                            axis.title.y = element_text(vjust = -0.8, 
+                                                        size = 8.3*y_axis_title_scale), 
+                            axis.text.y = element_text(vjust=0.3,size=7*y_axis_tick_label_scale))
+                    + scale_y_continuous(trans = scale_intersections, labels = labels_arg, limits = c(0, ymax))
+  )
   if((show_num == "yes") || (show_num == "Yes")){
-    Main_bar_plot <- (Main_bar_plot + geom_text(aes_string(label = "freq"), size = 2.2*intersection_size_number_scale, vjust = -1,
-                                                angle = number_angles, colour = Main_bar_data$color))
+    if(!intersection.size.comma){
+      Main_bar_plot <- (Main_bar_plot + geom_text(aes_string(label = "freq"), size = 2.2*intersection_size_number_scale, 
+                                                  vjust = 0.5, hjust = -0.1,
+                                                  angle = number_angles, colour = Main_bar_data$color))
+    } else{
+      Main_bar_plot <- (Main_bar_plot + geom_text(aes(label = scales::comma(freq)), size = 2.2*intersection_size_number_scale, 
+                                                  vjust = 0.5, hjust = -0.1,
+                                                  angle = number_angles, colour = Main_bar_data$color))
+    }
+
   }
   bInterDat <- NULL
   pInterDat <- NULL

R/SizeBar.R

@@ -6,7 +6,7 @@ FindSetFreqs <- function(data, start_col, num_sets, set_names, keep_order){
   temp_data <- as.data.frame(colSums(temp_data))
   colnames(temp_data) <- c("y")
   if(keep_order == FALSE){
-  temp_data <- temp_data[order(temp_data$y, decreasing = T), ]
+    temp_data <- temp_data[order(temp_data$y, decreasing = T), ]
   }
   else{
     temp_data <- temp_data$y
@@ -32,17 +32,17 @@ log2_reverse_trans <- function(){
 }
 
 ## Generate set size plot
-Make_size_plot <- function(Set_size_data, sbar_color, ratios, ylabel, scale_sets, text_scale, set_size_angle, set_size.show, set_size.scale_max,
-                           set_size.number_size){
-#   if(ratios[1] < 0.4){
-#     m <- (-0.05)
-#   }
-#   else if((ratios[1] > 0.4) & (ratios[1] < 0.46)){
-#     m <- (-0.03)
-#   }
-#   else{
-#     m <- 0
-#   }
+Make_size_plot <- function(Set_size_data, sbar_color, ratios, ylabel, scale_sets, text_scale, set_size_angle, set_size_x_axis.angles, set_size.show, set_size.scale_max,
+                           set_size.number_size, sets.comma, set_size.number_comma){
+  #   if(ratios[1] < 0.4){
+  #     m <- (-0.05)
+  #   }
+  #   else if((ratios[1] > 0.4) & (ratios[1] < 0.46)){
+  #     m <- (-0.03)
+  #   }
+  #   else{
+  #     m <- 0
+  #   }
 
   if(length(text_scale) > 1 && length(text_scale) <= 6){
     x_axis_title_scale <- text_scale[3]
@@ -79,7 +79,11 @@ Make_size_plot <- function(Set_size_data, sbar_color, ratios, ylabel, scale_sets
                         plot.margin=unit(c(-0.11,-1.3,0.5,0.5), "lines"),
                         axis.title.x = element_text(size = 8.3*x_axis_title_scale),
                         axis.text.x = element_text(size = 7*x_axis_tick_label_scale,
-                                                   vjust = 1, hjust = 0.5),
+                                                   vjust = 1, 
+                                                   # hjust = 0.5,
+                                                   hjust = 1,
+                                                   angle = set_size_x_axis.angles
+                        ),
                         axis.line = element_line(colour = "gray0"),
                         axis.line.y = element_blank(),
                         axis.line.x = element_line(colour = "gray0", size = 0.3),
@@ -90,32 +94,47 @@ Make_size_plot <- function(Set_size_data, sbar_color, ratios, ylabel, scale_sets
                 + xlab(NULL) + ylab(ylabel)
                 + coord_flip())
 
+  labels_arg <- waiver()
+  if(sets.comma) labels_arg <- scales::comma
+
   if(set_size.show == TRUE){
-    Size_plot <- (Size_plot + geom_text(aes(label=y,vjust=0.5,hjust=1.2, angle = set_size_angle), size=num.size))
+    if(set_size.number_comma){
+      Size_plot <- (Size_plot + geom_text(aes(label = scales::comma(y), vjust=0.5,hjust=1.2, angle = set_size_angle), size=num.size))
+    } else{
+      Size_plot <- (Size_plot + geom_text(aes(label=y,vjust=0.5,hjust=1.2, angle = set_size_angle), size=num.size)) 
+    }
   }
-    
+
   if(scale_sets == "log10"){
     if(!is.null(set_size.scale_max)) {
       Size_plot <- (Size_plot + scale_y_continuous(limits = c(set_size.scale_max, 0), 
-                                                   trans = log10_reverse_trans()))
+                                                   trans = log10_reverse_trans(),
+                                                   labels = labels_arg))
     } else {
-      Size_plot <- (Size_plot + scale_y_continuous(trans = log10_reverse_trans()))
+      Size_plot <- (Size_plot + scale_y_continuous(limits = c(max(Set_size_data) + 0.1*max(Set_size_data), 0),
+                                                   trans = log10_reverse_trans(),
+                                                   labels = labels_arg))
     }
   }
   else if (scale_sets == "log2"){
     if(!is.null(set_size.scale_max)) {
       Size_plot <- (Size_plot + scale_y_continuous(limits = c(set_size.scale_max, 0), 
-                                                   trans = log2_reverse_trans()))
+                                                   trans = log2_reverse_trans(),
+                                                   labels = labels_arg))
     } else {
-      Size_plot <- (Size_plot + scale_y_continuous(trans = log2_reverse_trans()))
+      Size_plot <- (Size_plot + scale_y_continuous(trans = log2_reverse_trans(),
+                                                   labels = labels_arg))
     }
   }
   else{
     if(!is.null(set_size.scale_max)) {
       Size_plot <- (Size_plot + scale_y_continuous(limits = c(set_size.scale_max, 0),
-                                                   trans = "reverse"))
+                                                   trans = "reverse",
+                                                   labels = labels_arg))
     } else {
-      Size_plot <- (Size_plot + scale_y_continuous(trans = "reverse"))
+      Size_plot <- (Size_plot + scale_y_continuous(limits = c(max(Set_size_data) + 0.1*max(Set_size_data), 0),
+                                                   trans = "reverse",
+                                                   labels = labels_arg))
     }
   }
 

R/upset.R

@@ -51,9 +51,14 @@
 #' @param scale.sets The scale to be used for the set sizes. Options: "identity", "log10", "log2"
 #' @param text.scale Numeric, value to scale the text sizes, applies to all axis labels, tick labels, and numbers above bar plot. Can be a universal scale, or a vector containing individual scales
 #'        in the following format: c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars)
-#' @param set_size.angles Numeric, angle to rotate the set size plot x-axis text
+#' @param set_size.angles Numeric, angle to rotate the set size plot text
+#' @param set_size_x_axis.angles Numeric, angle to rotate the set size plot x-axis text
+#' @param sets.comma Logical, format numeric labels with commas
+#' @param mainbar.comma Logical, format numeric labels with commas
+#' @param intersection.size.comma Logical, format numeric labels with commas. Ignored if show.numbers is not "yes".
 #' @param set_size.show Logical, display the set sizes on the set size bar chart
 #' @param set_size.numbers_size If set_size.show is TRUE, adjust the size of the numbers
+#' @param set_size.number_comma Logical, format numeric labels with commas. Ignored if set_size.show is FALSE.
 #' @param set_size.scale_max Increase the maximum of set size scale
 #' @details Visualization of set data in the layout described by Lex and Gehlenborg in \url{http://www.nature.com/nmeth/journal/v11/n8/abs/nmeth.3033.html}.
 #' UpSet also allows for visualization of queries on intersections and elements, along with custom queries queries implemented using
@@ -122,7 +127,8 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
                   decreasing = c(T, F), show.numbers = "yes", number.angles = 0, 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",
-                  scale.sets = "identity", text.scale = 1, set_size.angles = 0 , set_size.show = FALSE, set_size.numbers_size = NULL, set_size.scale_max = NULL){
+                  scale.sets = "identity", text.scale = 1, set_size.angles = 0 , set_size_x_axis.angles = 0, set_size.show = FALSE, set_size.numbers_size = NULL, set_size.scale_max = NULL,
+                  sets.comma = F, mainbar.comma = F, intersection.size.comma = F, set_size.number_comma = F){
 
   startend <-FindStartEnd(data)
   first.col <- startend[1]
@@ -256,11 +262,11 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
   ShadingData <- MakeShading(Matrix_layout, shade.color)
   }
   Main_bar <- suppressMessages(Make_main_bar(All_Freqs, Bar_Q, show.numbers, mb.ratio, customQBar, number.angles, EBar_data, mainbar.y.label,
-                            mainbar.y.max, scale.intersections, text.scale, attribute.plots))
+                            mainbar.y.max, scale.intersections, text.scale, attribute.plots, mainbar.comma, intersection.size.comma))
   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,set_size.show,
-                          set_size.scale_max, set_size.numbers_size)
+  Sizes <- Make_size_plot(Set_sizes, sets.bar.color, mb.ratio, sets.x.label, scale.sets, text.scale, set_size.angles, set_size_x_axis.angles, set_size.show,
+                          set_size.scale_max, set_size.numbers_size, sets.comma, set_size.number_comma)
 
   # 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,