add label comma options

DESCRIPTION

@@ -26,4 +26,4 @@ LazyData: true
 VignetteBuilder: knitr
 Suggests:
     knitr
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1

R/MainBar.R

@@ -61,11 +61,11 @@ 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){
+
 
-
   bottom_margin <- (-1)*0.65
-
+  
   if(is.null(attribute_plots) == FALSE){
     bottom_margin <- (-1)*0.45
   }
@@ -101,8 +101,8 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
 
   #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
+    ten_perc <- ((max(Main_bar_data$freq)) * 0.1)
+    ymax <- max(Main_bar_data$freq) + ten_perc
   }
 
   if(ylabel == "Intersection Size" && scale_intersections != "identity"){
@@ -117,8 +117,11 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
     }
   }
 
+  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)
+                    + scale_y_continuous(trans = scale_intersections, labels = labels_arg)
                     + ylim(0, ymax)
                     + geom_bar(stat = "identity", width = 0.6,
                                fill = Main_bar_data$color)
@@ -128,7 +131,7 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
                     + theme(panel.background = element_rect(fill = "white"),
                             plot.margin = unit(c(0.5,0.5,bottom_margin,0.5), "lines"), panel.border = element_blank(),
                             axis.title.y = element_text(vjust = -0.8, size = 8.3*y_axis_title_scale), axis.text.y = element_text(vjust=0.3,
-                                                                                                            size=7*y_axis_tick_label_scale)))
+                                                                                                                                 size=7*y_axis_tick_label_scale)))
   if((show_num == "yes") || (show_num == "Yes")){
     Main_bar_plot <- (Main_bar_plot + geom_text(aes_string(label = "freq"), size = 2.2*intersection_size_number_scale, vjust = -1,
                                                 angle = number_angles, colour = Main_bar_data$color))
@@ -186,6 +189,9 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
                                                  position = position_jitter(width = 0.2, height = 0.2),
                                                  colour = pElemDat$color, size = 2, shape = 17))
   }
+  if(mainbar.comma){
+    Main_bar_plot <- (Main_bar_plot + scale_y_continuous(labels = scales::comma))
+  }
 
   Main_bar_plot <- (Main_bar_plot 
                     + geom_vline(xintercept = 0, color = "gray0")

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
@@ -32,16 +32,16 @@ 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){
-#   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, sets.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]
@@ -83,17 +83,19 @@ 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(scale_sets == "log10"){
-    Size_plot <- (Size_plot + scale_y_continuous(trans = log10_reverse_trans()))
+    Size_plot <- (Size_plot + scale_y_continuous(trans = log10_reverse_trans(), labels = labels_arg))
   }
   else if (scale_sets == "log2"){
-    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{
-    Size_plot <- (Size_plot + scale_y_continuous(trans = "reverse"))
+    Size_plot <- (Size_plot + scale_y_continuous(trans = "reverse", labels = labels_arg))
   }
 
   Size_plot <- ggplot_gtable(ggplot_build(Size_plot))
   return(Size_plot)
 }
-

R/upset.R

@@ -52,6 +52,8 @@
 #' @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 sets.comma Logical, format numeric labels with commas
+#' @param mainbar.comma Logical, format numeric labels with commas
 #' @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
 #' Hadley Wickhams apply function. To further analyze the data contained in the intersections, the user may select additional attribute plots
@@ -119,7 +121,7 @@ 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 ){
+                  scale.sets = "identity", text.scale = 1, set_size.angles = 0, sets.comma = F, mainbar.comma = F){
 
   startend <-FindStartEnd(data)
   first.col <- startend[1]
@@ -154,7 +156,7 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
     New_data <- Wanted(data, Sets_to_remove)
     Num_of_set <- Number_of_sets(Set_names)
     if(keep.order == F){
-    Set_names <- order_sets(New_data, Set_names)
+      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)
@@ -244,20 +246,20 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
     set.metadata <- output[[2]]
 
     if(is.null(ShadingData) == FALSE){
-    shade.alpha <- unique(ShadingData$alpha)
+      shade.alpha <- unique(ShadingData$alpha)
     }
   }
   if(is.null(ShadingData) == TRUE){
-  ShadingData <- MakeShading(Matrix_layout, shade.color)
+    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))
   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)
+  Sizes <- Make_size_plot(Set_sizes, sets.bar.color, mb.ratio, sets.x.label, scale.sets, text.scale, set_size.angles, sets.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,
                  legend, query.legend, BoxPlots, Set_names, set.metadata, set.metadata.plots)
 
-}
+}