parameter to change intersection number colors

Author: JakeConway

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: UpSetR
 Title: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
 Version: 1.4.0
-Date: 2016-1-3
+Date: 2019-5-9
 URL: http://github.com/hms-dbmi/UpSetR
 BugReports: http://github.com/hms-dbmi/UpSetR/issues
 Authors@R: c(
     person("Jake", "Conway", email = "[email protected]", role = "cre"),
     person("Nils", "Gehlenborg", email = "[email protected]", role = "aut"))
 Description: Creates visualizations of intersecting sets using a novel matrix
     design, along with visualizations of several common set, element and attribute
-    related tasks.
+    related tasks (Conway 2017) <doi:10.1093/bioinformatics/btx364>.
 Depends:
     R (>= 3.0)
 Imports:
@@ -26,4 +26,4 @@ LazyData: true
 VignetteBuilder: knitr
 Suggests:
     knitr
-RoxygenNote: 6.1.0
+RoxygenNote: 7.0.2

R/MainBar.R

@@ -60,8 +60,8 @@ 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){
+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
 
@@ -128,9 +128,15 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
                             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")){
-    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$color))
+    if(is.null(number.colors)) {
+      Main_bar_plot <- (Main_bar_plot + geom_text(aes_string(label = "freq"), size = 2.2*intersection_size_number_scale, vjust = -1,
+                                                  angle = number_angles, colour = Main_bar_data$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
@@ -188,6 +194,9 @@ Make_main_bar <- function(Main_bar_data, Q, show_num, ratios, customQ, number_an
                     + 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)
 }

R/SizeBar.R

@@ -30,7 +30,7 @@ log2_reverse_trans <- function(){
   trans_new(paste0("reverselog2-", format(2), "reverse"), trans, inv,
             log_breaks(base = 2), domain = c(1e-100, Inf))
 }
-
+globalVariables(c("y"))
 ## 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){
@@ -64,9 +64,9 @@ 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
+    num.size <- (set_size.number_size/2.845276)*x_axis_tick_label_scale
   } else {
-    num.size <- (7/ggplot2:::.pt)*x_axis_tick_label_scale
+    num.size <- (7/2.845276)*x_axis_tick_label_scale
   }
 
   Size_plot <- (ggplot(data = Set_size_data, aes_string(x ="x", y = "y"))

R/upset.R

@@ -14,6 +14,7 @@
 #'        will be the specific intersections listed.
 #' @param matrix.color Color of the intersection points
 #' @param main.bar.color Color of the main bar plot
+#' @param plot.title Title of UpSetR plot
 #' @param mainbar.y.label The y-axis label of the intersection size bar plot
 #' @param mainbar.y.max The maximum y value of the intersection size bar plot scale. May be useful when aligning multiple UpSet plots horizontally.
 #' @param sets.bar.color Color of set size bar plot
@@ -28,6 +29,7 @@
 #' @param decreasing How the variables in order.by should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)
 #' @param show.numbers Show numbers of intersection sizes above bars
 #' @param number.angles The angle of the numbers atop the intersection size bars
+#' @param number.colors The colors of the numbers atop the intersection size bars
 #' @param group.by How the data should be grouped ("degree" or "sets")
 #' @param cutoff The number of intersections from each set (to cut off at) when aggregating by sets
 #' @param queries Unified query of intersections, elements, and custom row functions. Entered as a list that contains a list of
@@ -117,9 +119,9 @@
 #' @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,
-                  sets.bar.color = "gray23", sets.x.label = "Set Size", point.size = 2.2, line.size = 0.7,
+                  sets.bar.color = "gray23", plot.title = NA, sets.x.label = "Set Size", point.size = 2.2, line.size = 0.7,
                   mb.ratio = c(0.70,0.30), expression = NULL, att.pos = NULL, att.color = main.bar.color, order.by = c("freq", "degree"),
-                  decreasing = c(T, F), show.numbers = "yes", number.angles = 0, group.by = "degree",cutoff = NULL,
+                  decreasing = c(T, F), show.numbers = "yes", number.angles = 0, number.colors=NULL, 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){
@@ -255,8 +257,8 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
   if(is.null(ShadingData) == TRUE){
   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))
+  Main_bar <- suppressMessages(Make_main_bar(All_Freqs, Bar_Q, show.numbers, mb.ratio, customQBar, number.angles, number.colors, EBar_data, mainbar.y.label,
+                            mainbar.y.max, scale.intersections, text.scale, attribute.plots, plot.title))
   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,
@@ -292,7 +294,7 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, keep.order = F
 }
 
 #' @export
-print.upset <- function(x, newpage = TRUE) {
+print.upset <- function(x, ..., newpage = TRUE) {
   Make_base_plot(
     Main_bar_plot = x$Main_bar,
     Matrix_plot = x$Matrix,
@@ -318,6 +320,6 @@ print.upset <- function(x, newpage = TRUE) {
 }
 
 #' @export
-summary.upset <- function(x) {
+summary.upset <- function(...) {
     cat("An object of class `upset`. Call print() to show.")
 }