Merge pull request #162 from krassowski/more-examples

Add new examples, ggplot2 3.4.0 compatibility, prepare release

.gitignore

@@ -5,6 +5,7 @@ docs/
 .virtual_documents/
 cran_package/
 data/
+*.ipynb
 
 # History files
 .Rhistory

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ComplexUpset
 Type: Package
 Title: Create Complex UpSet Plots Using 'ggplot2' Components
-Version: 1.3.3
+Version: 1.3.4
 Authors@R: person(
   "Michał", "Krassowski", email = "[email protected]", role = c("aut", "cre"),
   comment = c(ORCID = "0000-0002-9638-7785"))
@@ -29,5 +29,5 @@ Imports:
     scales,
     colorspace
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,3 +1,14 @@
+# Version 1.3.4
+
+2022-11-11
+
+Enhancements:
+- Accept `tibble`s in `arrange_venn`, thanks @maximilian-heeg! #159
+
+Maintenance:
+- Pass `width=0.9` to workaround change of behaviour in ggplot2 3.4 overextending the width of bars highlighted with `upset_query`
+- Fix deprecation warnings for ggplot 3.4 `size` to `linewidth` transition
+
 # Version 1.3.3
 
 2021-12-07

R/upset.R

@@ -196,7 +196,7 @@ matrix_background_stripes = function(data, stripes, orient='horizontal') {
 #' @param colors a vector of colors to repeat as many times as needed for the fill of stripes, or a named vector specifying colors for values of the variable mapped to the color aesthetics in the mapping argument
 #' @param data the dataset describing the sets with a column named `set` and any other columns as needed for mapping
 #' @export
-upset_stripes = function(mapping=aes(), geom=geom_segment(size=7), colors=c('white', 'grey95'), data=NULL) {
+upset_stripes = function(mapping=aes(), geom=geom_segment(linewidth=7), colors=c('white', 'grey95'), data=NULL) {
     stripes = list(
         mapping=mapping,
         geom=geom,
@@ -265,6 +265,7 @@ upset_mode = function(mode) {
 #' @param mapping additional aesthetics for `geom_bar()`
 #' @param mode region selection mode, defines which intersection regions will be accounted for when computing the size. See `get_size_mode()` for accepted values.
 #' @param position position passed to `geom_bar()`
+#' @param width bar width, by default set to 90%
 #' @inheritDotParams ggplot2::geom_bar
 #' @export
 intersection_size = function(
@@ -276,6 +277,7 @@ intersection_size = function(
     text_mapping=aes(),
     mode='distinct',
     position=position_stack(),
+    width=0.9,  # required to workaround an upstream bug in `resolution()` when `upset_query` is used.
     ...
 ) {
   size = get_size_mode(mode)
@@ -334,6 +336,7 @@ intersection_size = function(
           geom='bar',
           position=position,
           na.rm=TRUE,
+          width=width,
           ...
       )
   )
@@ -397,6 +400,7 @@ intersection_ratio = function(
   text_mapping=aes(),
   mode='distinct',
   denominator_mode='union',
+  width=0.9,  # required to workaround an upstream bug in `resolution()` when `upset_query` is used.
   ...
 ) {
   size = get_size_mode(mode)
@@ -454,6 +458,7 @@ intersection_ratio = function(
       # does not work, see
       # https://github.com/tidyverse/ggplot2/issues/3532
       na.rm=TRUE,
+      width=width,
       ...
   ))
 
@@ -868,7 +873,7 @@ scale_if_missing = function(annotation, axis, scale) {
         list(scale)
     }
 }
-                          
+
 #' Prepare layers for sets sizes plot
 #'
 #' @param geom a geom_point call, allowing to specify parameters (e.g. `geom=geom_point(shape='square')`)

README.md

@@ -10,7 +10,7 @@ Quick links: [Documentation](https://krassowski.github.io/complex-upset/) | [Ins
 
 ## Showcase
 
-Get all the goodies of `UpSetR`, but with full extensibility of `ggplot2`. 
+Get all the goodies of `UpSetR`, but with full extensibility of `ggplot2`.
 
 ![Example UpSet plot](https://raw.githubusercontent.com/krassowski/complex-upset/master/movies.png)
 
@@ -109,13 +109,13 @@ The list is not meant to be exhaustive, but representative of applications to di
 
 ## Testing
 
-The unit tests are run with testhat, and the visual "doppelganger" tests use vdiffr.
+The unit tests are run with `testhat`, and the visual "doppelganger" tests use `vdiffr`.
 
 The test cases for visual tests are auto-generated from the examples in the documentation; after changing or adding an example, please run:
 
 - `scripts/prepare_for_tests.sh` to generate updated test cases, and
 - `scripts/manage_visual_tests.sh` to validate the generated images.
 
-## Acknowledgments
+## Acknowledgements
 
 Originally developed in course of a DPhil programme in Women's & Reproductive Health at [OxfordNuffieldWRH](https://github.com/OxfordNuffieldWRH).