documation updates

Author: zhanchen

NEWS

@@ -0,0 +1,25 @@
+# tidyprint NEWS
+
+## tidyprint 0.99.3 (2024-12-19)
+
+### NEW FEATURES
+- Initial Bioconductor submission
+- Custom print methods for SummarizedExperiment objects
+- Tidyverse-aligned console displays for genomic data
+- Alternative tibble abstractions for large genomic datasets
+- Unified messaging utilities for the tidyomics ecosystem
+- Support for multiple print designs: SummarizedExperiment, tidyprint_1, tidySummarizedExperiment, and plyxp
+- Automatic package detection for contextualized messaging
+
+### IMPROVEMENTS
+- Enhanced readability and usability within tidy workflows
+- Consistent display formatting across different data sizes
+- Improved discoverability and interpretation of genomic data
+
+### BUG FIXES
+- None in this initial release
+
+### DOCUMENTATION
+- Comprehensive vignette with Introduction section
+- Complete man pages for all exported functions
+- Package-level documentation

R/tibble_methods.R

@@ -1,3 +1,41 @@
+#' Convert SummarizedExperiment to tibble
+#'
+#' Converts a \link[SummarizedExperiment]{SummarizedExperiment} object to a tibble
+#' format, combining assay data with sample and feature metadata in a long format
+#' suitable for tidyverse workflows.
+#'
+#' @param x A \code{SummarizedExperiment} object to convert.
+#' @param ... Additional arguments passed to internal conversion functions.
+#' @param .name_repair Treatment of problematic column names. See
+#'   \code{\link[tibble]{as_tibble}} for details.
+#' @param rownames Either \code{NULL} or a string giving the name of a column
+#'   to use as rownames. See \code{\link[tibble]{as_tibble}} for details.
+#'
+#' @return A tibble containing the assay data combined with sample and feature
+#'   metadata. The structure includes:
+#'   \itemize{
+#'     \item Feature identifiers (from \code{rownames} or \code{rowData})
+#'     \item Sample identifiers (from \code{colnames} or \code{colData})
+#'     \item Assay values (one column per assay)
+#'     \item Sample metadata (from \code{colData})
+#'     \item Feature metadata (from \code{rowData})
+#'   }
+#'
+#' @details
+#' This method provides a bridge between Bioconductor's SummarizedExperiment
+#' objects and tidyverse data manipulation workflows. The conversion creates
+#' a long-format tibble where each row represents a feature-sample combination,
+#' making it suitable for filtering, grouping, and other tidyverse operations.
+#'
+#' @seealso \link[SummarizedExperiment]{SummarizedExperiment}, \link[tibble]{as_tibble}
+#'
+#' @examples
+#' \dontrun{
+#'   library(tidyprint)
+#'   data(se_airway)
+#'   as_tibble(se_airway)
+#' }
+#'
 #' @importFrom purrr reduce
 #' @importFrom purrr map map2
 #' @importFrom tidyr spread

R/tidyprint-package.R

@@ -0,0 +1,53 @@
+#' tidyprint: Custom Print Methods for SummarizedExperiment
+#'
+#' Provides customized print methods for \link[SummarizedExperiment]{SummarizedExperiment} objects
+#' to enhance readability and usability within a tidy workflow. It offers
+#' consistent, tidyverse-aligned console displays, including alternative
+#' tibble abstractions for large genomic data to improve discoverability and
+#' interpretation. The package also includes unified, contextual messaging
+#' utilities intended for the 'tidyomics' ecosystem.
+#'
+#' @section Key Features:
+#' \itemize{
+#'   \item \strong{Custom Print Methods}: Alternative display formats for SummarizedExperiment objects
+#'   \item \strong{Tidyverse Integration}: Seamless integration with tidyverse workflows
+#'   \item \strong{Scalable Visualization}: Adaptive displays for large genomic datasets
+#'   \item \strong{Standardized Messaging}: Consistent messaging utilities for the tidyomics ecosystem
+#' }
+#'
+#' @section Print Designs:
+#' The package provides multiple print designs for SummarizedExperiment objects:
+#' \itemize{
+#'   \item \code{"SummarizedExperiment"}: Standard Bioconductor summary display
+#'   \item \code{"tidyprint_1"}: Compact tibble abstraction with adaptive separator rows
+#'   \item \code{"tidySummarizedExperiment"}: Legacy tidySummarizedExperiment style
+#'   \item \code{"plyxp"}: Compact top/bottom row display
+#' }
+#'
+#' @section Messaging System:
+#' The \code{\link{tidy_message}} function provides standardized, visually appealing
+#' messages for packages within the tidyomics ecosystem. It automatically detects
+#' the calling package to provide contextualized messaging.
+#'
+#' @section Data Conversion:
+#' The \code{\link[=as_tibble.SummarizedExperiment]{as_tibble}} method converts
+#' SummarizedExperiment objects to tibble format, combining assay data with
+#' sample and feature metadata in a long format suitable for tidyverse workflows.
+#'
+#' @author Chen Zhan \email{[email protected]}
+#'
+#' @seealso
+#' \itemize{
+#'   \item \link[SummarizedExperiment]{SummarizedExperiment} - The core Bioconductor class
+#'   \item \link[tibble]{as_tibble} - Base tibble conversion methods
+#'   \item \link{print.SummarizedExperiment} - Custom print methods
+#'   \item \link{tidy_message} - Messaging utilities
+#' }
+#'
+#' @references
+#' tidyprint: Custom Print Methods for SummarizedExperiment
+#' \url{https://github.com/tidyomics/tidyprint}
+#'
+#' @name tidyprint-package
+#' @aliases tidyprint-package tidyprint
+NULL

README.md

@@ -7,10 +7,47 @@ tidyprint
 
 <!-- badges: end -->
 
+## Introduction
+
 **tidyprint** is an R package that provides a centralised tidy display
 strategy for biological data (e.g. SummarizedExperiment) and centralised
-messaging styles for the `tidyomics` packages. To facilitate the
-discussion about data display, we compare here four data displays:
+messaging styles for the `tidyomics` packages. This package addresses a
+critical need in the Bioconductor ecosystem for improved data
+visualization and user experience when working with genomic data.
+
+**tidyprint** fills this important gap by:
+
+1.  **Enhancing Data Discoverability**: Large genomic datasets often
+    contain millions of features and thousands of samples, making it
+    difficult to quickly understand data structure and content.
+    tidyprint provides intuitive, compact visualizations that help
+    researchers immediately grasp their data’s dimensions and key
+    characteristics.
+
+2.  **Improving Workflow Integration**: The package seamlessly
+    integrates with existing Bioconductor infrastructure while providing
+    output formats that are familiar to users of modern R data science
+    tools, particularly the tidyverse ecosystem.
+
+3.  **Supporting Reproducible Research**: By standardizing how
+    SummarizedExperiment objects are displayed across different analysis
+    contexts, tidyprint promotes consistency in scientific communication
+    and documentation.
+
+4.  **Addressing Scalability Challenges**: As genomic datasets continue
+    to grow in size and complexity, traditional display methods become
+    inadequate. tidyprint’s adaptive display strategies ensure that
+    users can effectively explore data regardless of scale.
+
+5.  **Fostering Community Standards**: The package establishes
+    conventions for data display that can be adopted across the
+    Bioconductor ecosystem, promoting consistency and reducing the
+    learning curve for new users.
+
+### Package Overview
+
+To facilitate the discussion about data display, we compare here four
+data displays:
 
 1.  **SummarizedExperiment**: Standard R/SummarizedExperiment printing
     style.
@@ -23,7 +60,7 @@ it easy to switch between these printing styles.
 
 ------------------------------------------------------------------------
 
-## 1. Installation
+## Installation
 
 You need the `remotes` package to install from GitHub. If you don’t have
 it, install it via:
@@ -48,12 +85,12 @@ BiocManager::install("tidyprint")
 
 ------------------------------------------------------------------------
 
-## 2. Demo
+## Demo
 
 Below is an example demonstrating how to use **tidyprint** with a sample
 `SummarizedExperiment` object.
 
-### 2.1 Load Required Packages
+### Load Required Packages
 
 ``` r
 library(dplyr)
@@ -113,7 +150,7 @@ airway
 **For comparative purposes we display the alternative visualisations we
 are trying to harmonise (now depreciated)**
 
-### 2.4 **tidySummarizedExperiment**
+### **tidySummarizedExperiment**
 
 Use the “tidySummarizedExperiment” design to view your data in a
 **tidy-friendly tibble** format:
@@ -142,7 +179,7 @@ airway %>% print(design = "tidySummarizedExperiment")
 #> #   seq_coord_system <int>, symbol <chr>, GRangesList <list>
 ```
 
-### 2.5 **plyxp**
+### **plyxp**
 
 For a more compact view (top and bottom rows), similar to a
 plyxp/tidyverse style:
@@ -168,7 +205,7 @@ airway %>% print(design = "plyxp")
 #> #   avgLength <int>, Experiment <fct>, Sample <fct>, BioSample <fct>
 ```
 
-# 3. Messaging function
+## Messaging function
 
 We integrated a messaging function providing standardized, visually
 appealing messages for packages within the tidyomics ecosystem. It
@@ -232,7 +269,7 @@ sessionInfo()
 #> [8] base     
 #> 
 #> other attached packages:
-#>  [1] tidyprint_0.99.0            airway_1.26.0              
+#>  [1] tidyprint_0.99.2            airway_1.26.0              
 #>  [3] SummarizedExperiment_1.36.0 Biobase_2.66.0             
 #>  [5] GenomicRanges_1.58.0        GenomeInfoDb_1.42.3        
 #>  [7] IRanges_2.40.1              S4Vectors_0.44.0           
@@ -243,17 +280,17 @@ sessionInfo()
 #> loaded via a namespace (and not attached):
 #>  [1] utf8_1.2.6              generics_0.1.4          SparseArray_1.6.2      
 #>  [4] stringi_1.8.7           lattice_0.22-6          digest_0.6.37          
-#>  [7] magrittr_2.0.3          evaluate_1.0.5          grid_4.4.3             
+#>  [7] magrittr_2.0.4          evaluate_1.0.5          grid_4.4.3             
 #> [10] fastmap_1.2.0           rprojroot_2.1.0         jsonlite_2.0.0         
 #> [13] Matrix_1.7-2            httr_1.4.7              fansi_1.0.6            
 #> [16] purrr_1.1.0             UCSC.utils_1.2.0        abind_1.4-8            
 #> [19] cli_3.6.5               rlang_1.1.6             crayon_1.5.3           
 #> [22] XVector_0.46.0          withr_3.0.2             DelayedArray_0.32.0    
 #> [25] yaml_2.3.10             S4Arrays_1.6.0          tools_4.4.3            
 #> [28] GenomeInfoDbData_1.2.13 vctrs_0.6.5             R6_2.6.1               
-#> [31] lifecycle_1.0.4         stringr_1.5.1           zlibbioc_1.52.0        
-#> [34] pkgconfig_2.0.3         pillar_1.11.0           glue_1.8.0             
+#> [31] lifecycle_1.0.4         stringr_1.5.2           zlibbioc_1.52.0        
+#> [34] pkgconfig_2.0.3         pillar_1.11.1           glue_1.8.0             
 #> [37] xfun_0.53               tibble_3.3.0            tidyselect_1.2.1       
 #> [40] rstudioapi_0.17.1       knitr_1.50              htmltools_0.5.8.1      
-#> [43] rmarkdown_2.29          compiler_4.4.3
+#> [43] rmarkdown_2.30          compiler_4.4.3
 ```