R/tidyprint-package.R
tidyprint-package.RdProvides customized print methods for 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.
This package provides S3 methods and functions that enhance the display and manipulation of SummarizedExperiment objects. The main functions return:
print.SummarizedExperiment: Returns the input object invisibly
as_tibble.SummarizedExperiment: Returns a tibble with combined assay and metadata
tidy_message: Returns NULL invisibly (prints styled messages)
Custom Print Methods: Alternative display formats for SummarizedExperiment objects
Tidyverse Integration: Seamless integration with tidyverse workflows
Scalable Visualization: Adaptive displays for large genomic datasets
Standardized Messaging: Consistent messaging utilities for the tidyomics ecosystem
The package provides multiple print designs for SummarizedExperiment objects:
"SummarizedExperiment": Standard Bioconductor summary display
"tidyprint_1": Compact tibble abstraction with adaptive separator rows
"tidySummarizedExperiment": Legacy tidySummarizedExperiment style
"plyxp": Compact top/bottom row display
The tidy_message function provides standardized, visually appealing
messages for packages within the tidyomics ecosystem. It automatically detects
the calling package to provide contextualized messaging.
The 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.
tidyprint: Custom Print Methods for SummarizedExperiment https://github.com/tidyomics/tidyprint
SummarizedExperiment - The core Bioconductor class
as_tibble - Base tibble conversion methods
print.SummarizedExperiment - Custom print methods
tidy_message - Messaging utilities