Allow user to keep order of sets entered using sets parameter. Fixes #46

R/upset.R

@@ -5,6 +5,7 @@
 #' @param nsets Number of sets to look at
 #' @param nintersects Number of intersections to plot
 #' @param sets Specific sets to look at (Include as combinations. Ex: c("Name1", "Name2"))
+#' @param keep.order Keep sets in the order entered using the sets parameter. The default is FALSE, which orders the sets by their sizes.
 #' @param set.metadata Metadata that offers insight to an attribute of the sets. Input should be a data frame where the first column is set names, and the 
 #'        remaining columns are attributes of those sets. To learn how to use this parameter it is highly suggested to view the set metadata vignette. The link
 #'        can be found on the package's GitHub page.
@@ -109,10 +110,10 @@
 #' @import grDevices
 #' @import scales       
 #' @export
-upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, 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, name.size = 7, mb.ratio = c(0.70,0.30),
-                  expression = NULL, att.pos = NULL, att.color = main.bar.color, order.by = c("freq", "degree"),
+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, name.size = 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,
                   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",
@@ -136,7 +137,9 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, set.metadata =
     Sets_to_remove <- Remove(data, first.col, last.col, Set_names)
     New_data <- Wanted(data, Sets_to_remove)
     Num_of_set <- Number_of_sets(Set_names)
-    Set_names <- order_sets(New_data, Set_names)
+    if(keep.order == F){
+      Set_names <- order_sets(New_data, Set_names)
+    }
     All_Freqs <- specific_intersections(data, first.col, last.col, intersections, order.by, group.by, decreasing,
                                         cutoff, main.bar.color, Set_names)
   }
@@ -148,7 +151,9 @@ upset <- function(data, nsets = 5, nintersects = 40, sets = NULL, set.metadata =
     Sets_to_remove <- Remove(data, first.col, last.col, Set_names)
     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)
+    }
     All_Freqs <- Counter(New_data, Num_of_set, first.col, Set_names, nintersects, main.bar.color,
                          order.by, group.by, cutoff, empty.intersections, decreasing)
   }

inst/doc/basic.usage.R

@@ -27,6 +27,9 @@ upset(movies, sets = c("Action", "Adventure", "Comedy", "Drama", "Mystery", "Thr
 ## ---- out.width="850px", fig.width=13, fig.height =7,tidy=TRUE, fig.align='center'----
 upset(movies, sets = c("Action", "Adventure", "Comedy", "Drama", "Mystery", "Thriller", "Romance", "War", "Western"), mb.ratio = c(0.55,0.45), order.by = c("degree", "freq"))
 
+## ---- out.width="850px", fig.width=13, fig.height =7, tidy=TRUE, fig.align='center'----
+upset(movies, sets = c("Action", "Adventure", "Comedy", "Drama", "Mystery", "Thriller", "Romance", "War", "Western"), mb.ratio = c(0.55,0.45), order.by = "freq", keep.order = TRUE)
+
 ## ---- out.width="850px", fig.width=13, fig.height =7,tidy=TRUE, fig.align='center'----
 upset(movies, nintersects = 70, group.by = "sets", cutoff = 7)
 

inst/doc/basic.usage.Rmd

@@ -59,7 +59,16 @@ upset(movies, sets = c("Action", "Adventure", "Comedy", "Drama", "Mystery", "Thr
 
 <br>
 
-Example 4: Grouping of Intersections
+Example 4: Keeping Order of Sets When Using Sets Parameter
+------------
+To keep the sets in the order entered using the `sets` parameter (Example 3), set the `keep.order` parameter to **TRUE**.
+```{r, out.width="850px", fig.width=13, fig.height =7, tidy=TRUE, fig.align='center'}
+upset(movies, sets = c("Action", "Adventure", "Comedy", "Drama", "Mystery", "Thriller", "Romance", "War", "Western"), mb.ratio = c(0.55,0.45), order.by = "freq", keep.order = TRUE)
+```
+
+<br>
+
+Example 5: Grouping of Intersections
 ------------
 Instead of the default method of grouping by degree, grouping by sets can be acheived using `group.by`. To set a cutoff for the number of intersections per group of sets use `cutoff`.
 ```{r, out.width="850px", fig.width=13, fig.height =7,tidy=TRUE, fig.align='center'}
@@ -68,7 +77,7 @@ upset(movies, nintersects = 70, group.by = "sets", cutoff = 7)
 
 <br>
 
-Example 5: Displaying Empty Intersections
+Example 6: Displaying Empty Intersections
 ------------
 There may be times where an intersection you are looking for is not present in the matrix. This may be due to not showing enough intersections which can be changes with `nintersects`, or it may be because the intersection contains no elements. To additionally show empty intersections turn on `empty.intersections`.
 ```{r, out.width="850px", fig.width=13, fig.height =7,tidy=TRUE, fig.align='center'}

vignettes/basic.usage.Rmd

@@ -59,7 +59,16 @@ upset(movies, sets = c("Action", "Adventure", "Comedy", "Drama", "Mystery", "Thr
 
 <br>
 
-Example 4: Grouping of Intersections
+Example 4: Keeping Order of Sets When Using Sets Parameter
+------------
+To keep the sets in the order entered using the `sets` parameter (Example 3), set the `keep.order` parameter to **TRUE**.
+```{r, out.width="850px", fig.width=13, fig.height =7, tidy=TRUE, fig.align='center'}
+upset(movies, sets = c("Action", "Adventure", "Comedy", "Drama", "Mystery", "Thriller", "Romance", "War", "Western"), mb.ratio = c(0.55,0.45), order.by = "freq", keep.order = TRUE)
+```
+
+<br>
+
+Example 5: Grouping of Intersections
 ------------
 Instead of the default method of grouping by degree, grouping by sets can be acheived using `group.by`. To set a cutoff for the number of intersections per group of sets use `cutoff`.
 ```{r, out.width="850px", fig.width=13, fig.height =7,tidy=TRUE, fig.align='center'}
@@ -68,7 +77,7 @@ upset(movies, nintersects = 70, group.by = "sets", cutoff = 7)
 
 <br>
 
-Example 5: Displaying Empty Intersections
+Example 6: Displaying Empty Intersections
 ------------
 There may be times where an intersection you are looking for is not present in the matrix. This may be due to not showing enough intersections which can be changes with `nintersects`, or it may be because the intersection contains no elements. To additionally show empty intersections turn on `empty.intersections`.
 ```{r, out.width="850px", fig.width=13, fig.height =7,tidy=TRUE, fig.align='center'}