tidyomics · stemangiola · Jul 10, 2025 · Oct 29, 2024 · Oct 29, 2024 · Apr 15, 2025
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySummarizedExperiment
 Title: Brings SummarizedExperiment to the Tidyverse 
-Version: 1.15.1
+Version: 1.19.1
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: The tidySummarizedExperiment package provides a set of tools for creating and
@@ -55,7 +55,7 @@ Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, Transcription, Transcriptomics
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 LazyDataCompression: xz
 URL: https://github.com/stemangiola/tidySummarizedExperiment

diff --git a/NAMESPACE b/NAMESPACE
@@ -60,6 +60,7 @@ importFrom(SummarizedExperiment,elementMetadata)
 importFrom(SummarizedExperiment,rbind)
 importFrom(SummarizedExperiment,rowData)
 importFrom(SummarizedExperiment,rowRanges)
+importFrom(cli,col_br_black)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
 importFrom(dplyr,distinct_at)

diff --git a/R/ggplot2_methods.R b/R/ggplot2_methods.R
@@ -1,7 +1,7 @@
 #' @name ggplot
 #' @rdname ggplot
 #' @inherit ggplot2::ggplot
-#' @title Create a new \code{ggplot} from a \code{tidyseurat}
+#' @title Create a new \code{ggplot} from a \code{SummarizedExperiment}
 #' @return `ggplot`
 #'
 #' @examples

diff --git a/README.Rmd b/README.Rmd
@@ -209,7 +209,7 @@ Here we plot the distribution of counts per sample.
 
 ```{r plot1}
 pasilla_tidy %>%
-    tidySummarizedExperiment::ggplot(aes(counts + 1, group=.sample, color=`type`)) +
+    ggplot(aes(counts + 1, group=.sample, color=`type`)) +
     geom_density() +
     scale_x_log10() +
     my_theme

diff --git a/README.md b/README.md
@@ -2,33 +2,35 @@ tidySummarizedExperiment - part of tidytranscriptomics
 ================
 
 <!-- badges: start -->
- 
+
 [![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 [![R build
 status](https://github.com/stemangiola/tidySummarizedExperiment/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/stemangiola/tidySummarizedExperiment/actions)
 <!-- badges: end -->
 
-**Brings SummarizedExperiment to the tidyverse!** 
+**Brings SummarizedExperiment to the tidyverse!**
 
 website:
 [stemangiola.github.io/tidySummarizedExperiment/](https://stemangiola.github.io/tidySummarizedExperiment/)
 
-Another [nice introduction](https://carpentries-incubator.github.io/bioc-intro/60-next-steps/index.html) by carpentries-incubator.
+Another [nice
+introduction](https://carpentries-incubator.github.io/bioc-intro/60-next-steps/index.html)
+by carpentries-incubator.
 
 Please also have a look at
 
--   [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/)
-    for tidy manipulation of SingleCellExperiment objects
--   [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy
-    manipulation of Seurat objects
--   [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy
-    analysis of RNA sequencing data
--   [nanny](https://github.com/stemangiola/nanny) for tidy high-level
-    data analysis and manipulation
--   [tidygate](https://github.com/stemangiola/tidygate) for adding
-    custom gate information to your tibble
--   [tidyHeatmap](https://stemangiola.github.io/tidyHeatmap/) for
-    heatmaps produced with tidy principles
+- [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/)
+  for tidy manipulation of SingleCellExperiment objects
+- [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy
+  manipulation of Seurat objects
+- [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy analysis
+  of RNA sequencing data
+- [nanny](https://github.com/stemangiola/nanny) for tidy high-level data
+  analysis and manipulation
+- [tidygate](https://github.com/stemangiola/tidygate) for adding custom
+  gate information to your tibble
+- [tidyHeatmap](https://stemangiola.github.io/tidyHeatmap/) for heatmaps
+  produced with tidy principles
 
 # Introduction
 
@@ -43,9 +45,9 @@ tidyverse worlds.
 
 ## Functions/utilities available
 
-| SummarizedExperiment-compatible Functions | Description                                                                        |
-|-------------------------------------------|------------------------------------------------------------------------------------|
-| `all`                                     | After all `tidySummarizedExperiment` is a SummarizedExperiment object, just better |
+| SummarizedExperiment-compatible Functions | Description |
+|----|----|
+| `all` | After all `tidySummarizedExperiment` is a SummarizedExperiment object, just better |
 
 | tidyverse Packages | Description                                 |
 |--------------------|---------------------------------------------|
@@ -98,7 +100,7 @@ pasilla_tidy
 ```
 
     ## # A SummarizedExperiment-tibble abstraction: 102,193 × 5
-    ## [90m# Transcripts=14599 | Samples=7 | Assays=counts[39m
+    ## # Features=14599 | Samples=7 | Assays=counts
     ##    .feature    .sample counts condition type      
     ##    <chr>       <chr>    <int> <chr>     <chr>     
     ##  1 FBgn0000003 untrt1       0 untreated single_end
@@ -111,7 +113,7 @@ pasilla_tidy
     ##  8 FBgn0000024 untrt1      10 untreated single_end
     ##  9 FBgn0000028 untrt1       0 untreated single_end
     ## 10 FBgn0000032 untrt1    1446 untreated single_end
-    ## # … with 40 more rows
+    ## # ℹ 40 more rows
 
 **But it is a SummarizedExperiment object after all**
 
@@ -136,7 +138,7 @@ pasilla_tidy %>%
 ```
 
     ## # A SummarizedExperiment-tibble abstraction: 1 × 5
-    ## [90m# Transcripts=1 | Samples=1 | Assays=counts[39m
+    ## # Features=1 | Samples=1 | Assays=counts
     ##   .feature    .sample counts condition type      
     ##   <chr>       <chr>    <int> <chr>     <chr>     
     ## 1 FBgn0000003 untrt1       0 untreated single_end
@@ -149,7 +151,7 @@ pasilla_tidy %>%
 ```
 
     ## # A SummarizedExperiment-tibble abstraction: 58,396 × 5
-    ## [90m# Transcripts=14599 | Samples=4 | Assays=counts[39m
+    ## # Features=14599 | Samples=4 | Assays=counts
     ##    .feature    .sample counts condition type      
     ##    <chr>       <chr>    <int> <chr>     <chr>     
     ##  1 FBgn0000003 untrt1       0 untreated single_end
@@ -162,7 +164,7 @@ pasilla_tidy %>%
     ##  8 FBgn0000024 untrt1      10 untreated single_end
     ##  9 FBgn0000028 untrt1       0 untreated single_end
     ## 10 FBgn0000032 untrt1    1446 untreated single_end
-    ## # … with 40 more rows
+    ## # ℹ 40 more rows
 
 We can use `select` to choose columns.
 
@@ -184,7 +186,7 @@ pasilla_tidy %>%
     ##  8 untrt1 
     ##  9 untrt1 
     ## 10 untrt1 
-    ## # … with 102,183 more rows
+    ## # ℹ 102,183 more rows
 
 We can use `count` to count how many rows we have for each sample.
 
@@ -231,7 +233,7 @@ pasilla_tidy %>%
 ```
 
     ## # A SummarizedExperiment-tibble abstraction: 102,193 × 5
-    ## [90m# Transcripts=14599 | Samples=7 | Assays=counts[39m
+    ## # Features=14599 | Samples=7 | Assays=counts
     ##    .feature    .sample counts condition sequencing
     ##    <chr>       <chr>    <int> <chr>     <chr>     
     ##  1 FBgn0000003 untrt1       0 untreated single_end
@@ -244,7 +246,7 @@ pasilla_tidy %>%
     ##  8 FBgn0000024 untrt1      10 untreated single_end
     ##  9 FBgn0000028 untrt1       0 untreated single_end
     ## 10 FBgn0000032 untrt1    1446 untreated single_end
-    ## # … with 40 more rows
+    ## # ℹ 40 more rows
 
 We could use `mutate` to create a column. For example, we could create a
 new type column that contains single and paired instead of single_end
@@ -256,7 +258,7 @@ pasilla_tidy %>%
 ```
 
     ## # A SummarizedExperiment-tibble abstraction: 102,193 × 5
-    ## [90m# Transcripts=14599 | Samples=7 | Assays=counts[39m
+    ## # Features=14599 | Samples=7 | Assays=counts
     ##    .feature    .sample counts condition type  
     ##    <chr>       <chr>    <int> <chr>     <chr> 
     ##  1 FBgn0000003 untrt1       0 untreated single
@@ -269,7 +271,7 @@ pasilla_tidy %>%
     ##  8 FBgn0000024 untrt1      10 untreated single
     ##  9 FBgn0000028 untrt1       0 untreated single
     ## 10 FBgn0000032 untrt1    1446 untreated single
-    ## # … with 40 more rows
+    ## # ℹ 40 more rows
 
 We could use `unite` to combine multiple columns into a single column.
 
@@ -279,7 +281,7 @@ pasilla_tidy %>%
 ```
 
     ## # A SummarizedExperiment-tibble abstraction: 102,193 × 4
-    ## [90m# Transcripts=14599 | Samples=7 | Assays=counts[39m
+    ## # Features=14599 | Samples=7 | Assays=counts
     ##    .feature    .sample counts group               
     ##    <chr>       <chr>    <int> <chr>               
     ##  1 FBgn0000003 untrt1       0 untreated_single_end
@@ -292,7 +294,7 @@ pasilla_tidy %>%
     ##  8 FBgn0000024 untrt1      10 untreated_single_end
     ##  9 FBgn0000028 untrt1       0 untreated_single_end
     ## 10 FBgn0000032 untrt1    1446 untreated_single_end
-    ## # … with 40 more rows
+    ## # ℹ 40 more rows
 
 We can also combine commands with the tidyverse pipe `%>%`.
 
@@ -340,7 +342,7 @@ pasilla_tidy %>%
     ##  8 FBgn0000024 untrt1      10 untreated single_end      7    
     ##  9 FBgn0000028 untrt1       0 untreated single_end      0.429
     ## 10 FBgn0000032 untrt1    1446 untreated single_end   1085.   
-    ## # … with 86,503 more rows
+    ## # ℹ 86,503 more rows
 
 # Plotting
 
@@ -371,7 +373,7 @@ Here we plot the distribution of counts per sample.
 
 ``` r
 pasilla_tidy %>%
-    tidySummarizedExperiment::ggplot(aes(counts + 1, group=.sample, color=`type`)) +
+    ggplot(aes(counts + 1, group=.sample, color=`type`)) +
     geom_density() +
     scale_x_log10() +
     my_theme

diff --git a/inst/NEWS.rd b/inst/NEWS.rd
@@ -1,6 +1,12 @@
 \name{NEWS}
 \title{News for Package \pkg{tidySummarizedExperiment}}
 
+\section{Changes in version 1.16.0, Bioconductor 3.22 Release}{
+\itemize{
+    \item Updated documentation to properly reflect S3 method structure.
+    \item Simplified ggplot2 compatibility - S3 method continues to work with ggplot2 4.0.0.
+}}
+
 \section{Changes in version 1.4.0, Bioconductor 3.14 Release}{
 \itemize{
     \item Improved join_*() functions.

diff --git a/man/as_tibble.Rd b/man/as_tibble.Rd
diff --git a/man/formatting.Rd b/man/formatting.Rd
diff --git a/man/ggplot.Rd b/man/ggplot.Rd