Address CRAN comments

DESCRIPTION

@@ -6,9 +6,10 @@ URL: https://github.com/const-ae/ggupset
 BugReports: https://github.com/const-ae/ggupset/issues
 Authors@R: person("Constantin", "Ahlmann-Eltze", email = "[email protected]", role = c("aut", "cre"))
 Description: Replace the standard x-axis in 'ggplots' with a combination matrix
-  to visualize complex set overlaps. UpSet has introduced a new way to visualize
-  the overlap of sets, this package provides a simple way to produce such plots
-  using ggplot. In addition it can convert any categorical axis into a combination
+  to visualize complex set overlaps. 'UpSet' has introduced a new way to visualize
+  the overlap of sets as an alternative to Venn diagrams. 
+  This package provides a simple way to produce such plots using 'ggplot2'. 
+  In addition it can convert any categorical axis into a combination
   matrix axis.
 License: GPL-3
 Encoding: UTF-8

R/scale_upset.R

@@ -8,10 +8,24 @@
 #' @param sep String the is used to delimit the elements in each list entry.
 #'   Default: "-".
 #' @param ... additional arguments that are passed on to
-#'   \code{ggplot2::scale_discrete}
+#'   \code{ggplot2::scale_x_discrete}
 #' @param position either "top" or "bottom" to specify where the
 #'   x axis drawn. Default: "bottom"
 #'
+#' @seealso \code{\link[ggplot2]{discrete_scale}}
+#' @examples
+#' library(ggplot2)
+#' ggplot(tidy_movies[1:100, ], aes(x=Genres)) +
+#'   geom_bar() +
+#'   scale_x_mergelist() +
+#'   theme(axis.text.x = element_text(angle = 90, hjust=1, vjust = 0.5))
+#'
+#' ggplot(tidy_movies[1:100, ], aes(x=Genres)) +
+#'   geom_bar() +
+#'   scale_x_mergelist(sep = " & ", name = "Merged Movie Genres", position = "top") +
+#'   theme(axis.text.x = element_text(angle = 90, hjust=0, vjust = 0.5))
+#'
+#'
 #' @export
 scale_x_mergelist <- function(sep="-", ..., position = "bottom"){
   sc <- discrete_scale(c("x", "xmin", "xmax", "xend"), "position_d", identity, ...,

R/theme_combmatrix.R

@@ -39,6 +39,25 @@
 #'   Default: "#E0E0E0"
 #' @param ... additional arguments that are passed to \code{theme()}
 #'
+#'
+#' @examples
+#' library(ggplot2)
+#' # Ensure that the y-axis label is next to the axis by setting
+#' # combmatrix.label.make_space to FALSE
+#' ggplot(tidy_movies[1:100, ], aes(x=Genres)) +
+#'   geom_bar() +
+#'   scale_x_upset() +
+#'   theme_combmatrix(combmatrix.label.text = element_text(color = "black", size=15),
+#'                    combmatrix.label.make_space = FALSE,
+#'                    plot.margin = unit(c(1.5, 1.5, 1.5, 65), "pt"))
+#'
+#'  # Change the color of the background stripes
+#'  ggplot(tidy_movies[1:100, ], aes(x=Genres)) +
+#'    geom_bar() +
+#'    scale_x_upset() +
+#'    theme_combmatrix(combmatrix.panel.striped_background = TRUE,
+#'                     combmatrix.panel.striped_background.color.one = "grey")
+#'
 #' @export
 theme_combmatrix <- function(
   combmatrix.label.make_space = TRUE,

README.Rmd

@@ -26,8 +26,8 @@ Plot a combination matrix instead of the standard x-axis and create UpSet plots
 You can install the released version of ggupset from [CRAN](https://CRAN.R-project.org) with:
 
 ``` r
-# Package not yet on CRAN
-# install.packages("ggupset")
+# Download package from CRAN
+install.packages("ggupset")
 
 # Or get the latest version directly from GitHub
 devtools::install_github("const-ae/ggupset")
@@ -211,7 +211,7 @@ df_complex_conditions %>%
     geom_jitter(aes(color=KO), width=0.1) +
     geom_smooth(method = "lm", aes(group = paste0(KO, "-", DrugA))) +
     scale_x_upset(order_by = "degree",
-                  levels=c("KO", "WT", "Drug", "8h", "24h", "48h"),
+                  sets = c("KO", "WT", "Drug", "8h", "24h", "48h"),
                   position="top", name = "") +
     theme_combmatrix(combmatrix.label.text = element_text(size=12),
                      combmatrix.label.extra_spacing = 5)

README.md

@@ -13,8 +13,8 @@ Installation
 You can install the released version of ggupset from [CRAN](https://CRAN.R-project.org) with:
 
 ``` r
-# Package not yet on CRAN
-# install.packages("ggupset")
+# Download package from CRAN
+install.packages("ggupset")
 
 # Or get the latest version directly from GitHub
 devtools::install_github("const-ae/ggupset")
@@ -29,12 +29,12 @@ This is a basic example which shows you how to solve a common problem:
 # Load helper packages
 library(ggplot2)
 library(tidyverse)
-#> ── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
+#> ── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
 #> ✔ tibble  1.4.2     ✔ purrr   0.2.5
 #> ✔ tidyr   0.8.2     ✔ dplyr   0.7.8
 #> ✔ readr   1.2.1     ✔ stringr 1.4.0
 #> ✔ tibble  1.4.2     ✔ forcats 0.3.0
-#> ── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
+#> ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
 #> ✖ dplyr::filter() masks stats::filter()
 #> ✖ dplyr::lag()    masks stats::lag()
 
@@ -249,7 +249,7 @@ df_complex_conditions %>%
     geom_jitter(aes(color=KO), width=0.1) +
     geom_smooth(method = "lm", aes(group = paste0(KO, "-", DrugA))) +
     scale_x_upset(order_by = "degree",
-                  levels=c("KO", "WT", "Drug", "8h", "24h", "48h"),
+                  sets = c("KO", "WT", "Drug", "8h", "24h", "48h"),
                   position="top", name = "") +
     theme_combmatrix(combmatrix.label.text = element_text(size=12),
                      combmatrix.label.extra_spacing = 5)

cran-comments.md

@@ -1,4 +1,14 @@
 
+## Resubmission
+This is a resubmission in this version I have:
+
+* Put single quotes around 'ggplot2' and 'UpSet'
+
+* Added examples to the documentation of `scale_x_mergelist()` and 
+ `theme_combmatrix()`
+
+* Added more automatic tests
+
 ## Test environments
 
 * linux ubuntu: r 3.5.2

tests/testthat/test-axis_combmatrix.R

@@ -8,122 +8,70 @@ test_that("Plotting works as expected", {
   mtcars$comb <- paste0("gears: ", mtcars$gear, "-cyl: ", mtcars$cyl)
   mtcars$list_col <- lapply(seq_len(nrow(mtcars)), function(idx) c(paste0("gear: ", mtcars$gear[idx]), paste0("cyl: ", mtcars$cyl[idx])))
 
-  expect_silent(
+  expect_silent({
     ggplot(mtcars, aes(x=comb)) +
       geom_bar() +
       axis_combmatrix(sep="-")
-  )
 
-  ggplot(mtcars, aes(x=comb)) +
-    geom_bar() +
-    axis_combmatrix(sep="-")
 
-  ggplot(mtcars, aes(x=comb)) +
-    geom_bar() +
-    scale_x_discrete(position = "top") +
-    axis_combmatrix(sep="-")
+    ggplot(mtcars, aes(x=comb)) +
+      geom_bar() +
+      axis_combmatrix(sep="-")
 
-  ggplot(mtcars, aes(x=list_col)) +
-    geom_bar() +
-    scale_x_mergelist() +
-    axis_combmatrix(sep = "-")
+    ggplot(mtcars, aes(x=comb)) +
+      geom_bar() +
+      scale_x_discrete(position = "top") +
+      axis_combmatrix(sep="-")
 
-  ggplot(mtcars, aes(x=list_col)) +
-    geom_bar() +
-    scale_x_upset()
+    ggplot(mtcars, aes(x=list_col)) +
+      geom_bar() +
+      scale_x_mergelist() +
+      axis_combmatrix(sep = "-")
 
-  ggplot(mtcars, aes(x=list_col)) +
-    geom_bar() +
-    scale_x_upset(n_sets = 6)
+    ggplot(mtcars, aes(x=list_col)) +
+      geom_bar() +
+      scale_x_upset()
 
+    ggplot(mtcars, aes(x=list_col)) +
+      geom_bar() +
+      scale_x_upset(n_sets = 6)
 
-  ggplot(mtcars, aes(x=list_col)) +
-    geom_bar() +
-    scale_x_upset(intersections = list(c("gear: 3", "cyl: 8"), c("gear: 4", "cyl: 4"), c("cyl: 4", "gear: 3")))
 
+    ggplot(mtcars, aes(x=list_col)) +
+      geom_bar() +
+      scale_x_upset(intersections = list(c("gear: 3", "cyl: 8"), c("gear: 4", "cyl: 4"), c("cyl: 4", "gear: 3")))
 
-  ggplot(mtcars, aes(x=list_col)) +
-    geom_bar() +
-    scale_x_upset(n_intersections = 5)
 
-  ggplot(mtcars, aes(x=list_col)) +
-    geom_bar() +
-    scale_x_upset(n_intersections = 5, sets=c(paste0("gear: ", c(3,4,5)), paste0("cyl: ", c(4,6,8,9))))
+    ggplot(mtcars, aes(x=list_col)) +
+      geom_bar() +
+      scale_x_upset(n_intersections = 5)
 
+    ggplot(mtcars, aes(x=list_col)) +
+      geom_bar() +
+      scale_x_upset(n_intersections = 5, sets=c(paste0("gear: ", c(3,4,5)), paste0("cyl: ", c(4,6,8,9))))
+  })
 })
 
 
-# test_that("Test for skipping", {
-#   skip("Ignore")
-#   library(tidyverse)
-#
-#   starwars %>%
-#     ggplot(aes(x=films)) +
-#     geom_bar() +
-#     scale_x_upset() +
-#     axis_combmatrix(sep = "-_-_-")
-#
-#   starwars %>%
-#     mutate(films_col = map_chr(films, paste0, collapse="-")) %>%
-#     ggplot(aes(x=films)) +
-#     geom_bar() +
-#     axis_combmatrix(sep = "-")
-#
-#
-#   starwars %>%
-#     mutate(films_col = map_chr(films, paste0, collapse="-")) %>%
-#     ggplot(aes(x=films_col, y=height)) +
-#     geom_boxplot() +
-#     axis_combmatrix(sep = "-") +
-#     # theme(axis.text.x = element_text(angle = 90))
-#     NULL
-#
-# })
-#
-#
-#
-# test_that("Test for skipping 2", {
-#   skip("Ignore")
-#
-#   library(ggplot2movies)
-#   library(tidyverse)
-#   tidy_movies <- movies %>%
-#     mutate(id = 1:n()) %>%
-#     gather(Genre, GenreMember, Action:Short) %>%
-#     filter(GenreMember == 1) %>%
-#     select(- GenreMember) %>%
-#     group_by_at(vars(-Genre)) %>%
-#     summarize(Genres = list(Genre)) %>%
-#     ungroup()
-#
-#
-#   tidy_movies %>%
-#     ggplot(aes(x=Genres)) +
-#       geom_bar() +
-#       scale_x_upset(n_intersections = 10)
-#
-#   tidy_movies %>%
-#     sample_n(1000) %>%
-#     ggplot(aes(x=Genres)) +
-#     geom_bar() +
-#     scale_x_upset(n_intersections = 10)
-#
-#   tidy_movies %>%
-#     sample_n(1000) %>%
-#     ggplot(aes(x=Genres, y=year)) +
-#     # geom_violin() +
-#     geom_boxplot() +
-#     scale_x_upset()
-#
-#   tidy_movies %>%
-#     # sample_n(1000) %>%
-#     mutate(Genres_col = map_chr(Genres, ~ paste0(sort(.x), collapse="-"))) %>%
-#     mutate(Genres_col = fct_infreq(as.factor(Genres_col))) %>%
-#     mutate(Genres_col = fct_lump(Genres_col, n=12)) %>%
-#     ggplot(aes(x=Genres_col, y=year)) +
-#       geom_violin() +
-#       # geom_jitter(width = 0.1, height=0, size=0.01) +
-#       axis_combmatrix(sep="-", levels = c("Drama", "Comedy", "Short", "Documentary", "Action", "Romance"))
-#       NULL
-#
-# })
+
+test_that("Plotting with tidy_movies works as expected 2", {
+  expect_silent({
+    ggplot(tidy_movies[1:100, ], aes(x=Genres)) +
+        geom_bar() +
+        scale_x_upset(n_intersections = 10)
+
+    ggplot(tidy_movies[1:100, ], aes(x=Genres)) +
+      geom_bar() +
+      scale_x_upset(n_intersections = 10)
+
+    ggplot(tidy_movies[1:100, ], aes(x=Genres, y=year)) +
+      geom_violin() +
+      scale_x_upset()
+
+    ggplot(tidy_movies[1:100, ], aes(x=sapply(Genres, paste0, collapse="-"), y=year)) +
+        geom_boxplot() +
+        geom_jitter(width = 0.1, height=0, size=1) +
+        axis_combmatrix(sep="-", levels = c("Drama", "Comedy", "Short", "Documentary", "Action", "Romance"))
+
+  })
+})