Fix size bar number positioning and give leverage over set size scale maximum

Author: Jake Conway

R/SizeBar.R

@@ -32,7 +32,8 @@ 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){
+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)
 #   }
@@ -62,16 +63,22 @@ Make_size_plot <- function(Set_size_data, sbar_color, ratios, ylabel, scale_sets
     }
   }
 
+  if(!is.null(set_size.number_size)) {
+    num.size <- (set_size.number_size/ggplot2:::.pt)*x_axis_tick_label_scale
+  } else {
+    num.size <- (7/ggplot2:::.pt)*x_axis_tick_label_scale
+  }
+  
   Size_plot <- (ggplot(data = Set_size_data, aes_string(x ="x", y = "y"))
                 + geom_bar(stat = "identity",colour = sbar_color, width = 0.4,
                            fill = sbar_color, position = "identity")
-                + scale_x_continuous(limits = c(0.5, (nrow(Set_size_data)+0.5)),
+                + scale_x_continuous(limits = c(0.5, (nrow(Set_size_data) + 0.5)),
                                      breaks = c(0, max(Set_size_data)),
                                      expand = c(0,0))
                 + theme(panel.background = element_rect(fill = "white"),
                         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, angle = set_size_angle,
+                        axis.text.x = element_text(size = 7*x_axis_tick_label_scale,
                                                    vjust = 1, hjust = 0.5),
                         axis.line = element_line(colour = "gray0"),
                         axis.line.y = element_blank(),
@@ -84,17 +91,32 @@ Make_size_plot <- function(Set_size_data, sbar_color, ratios, ylabel, scale_sets
                 + coord_flip())
 
   if(set_size.show == TRUE){
-    Size_plot <- (Size_plot + geom_text(aes(label=y,vjust=0.5,hjust=0.1),size=(7/ggplot2:::.pt)*x_axis_tick_label_scale))
+    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"){
-    Size_plot <- (Size_plot + scale_y_continuous(trans = log10_reverse_trans()))
+    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()))
+    } else {
+      Size_plot <- (Size_plot + scale_y_continuous(trans = log10_reverse_trans()))
+    }
   }
   else if (scale_sets == "log2"){
-    Size_plot <- (Size_plot + scale_y_continuous(trans = log2_reverse_trans()))
+    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()))
+    } else {
+      Size_plot <- (Size_plot + scale_y_continuous(trans = log2_reverse_trans()))
+    }
   }
   else{
-    Size_plot <- (Size_plot + scale_y_continuous(trans = "reverse"))
+    if(!is.null(set_size.scale_max)) {
+      Size_plot <- (Size_plot + scale_y_continuous(limits = c(set_size.scale_max, 0),
+                                                   trans = "reverse"))
+    } else {
+      Size_plot <- (Size_plot + scale_y_continuous(trans = "reverse"))
+    }
   }
 
   Size_plot <- ggplot_gtable(ggplot_build(Size_plot))

R/upset.R

@@ -53,6 +53,8 @@
 #'        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.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.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
 #' Hadley Wickham's apply function. To further analyze the data contained in the intersections, the user may select additional attribute plots
@@ -120,7 +122,7 @@ 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 , set_size.show = FALSE ){
+                  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)
   first.col <- startend[1]
@@ -257,8 +259,9 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
                             mainbar.y.max, scale.intersections, text.scale, attribute.plots))
   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)
-
+  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)
+  
   # 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)
@@ -287,6 +290,7 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
       set.metadata.plots = set.metadata.plots)
   )
 }
+
 #' @export
 print.upset <- function(x, newpage = TRUE) {
   Make_base_plot(