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. 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:
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.
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.
Supporting Reproducible Research: By standardizing how SummarizedExperiment objects are displayed across different analysis contexts, tidyprint promotes consistency in scientific communication and documentation.
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.
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.
Installation
You need the remotes package to install from GitHub. If
you don’t have it, install it via:
install.packages("remotes")Then install tidyprint from GitHub:
remotes::install_github("tidyomics/tidyprint")When available in Bioconductor, install with:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tidyprint")Demo
Below is an example demonstrating how to use
tidyprint with a sample
SummarizedExperiment object.
SummarizedExperiment
The standard SummarizedExperiment display:
airway
#> class: RangedSummarizedExperiment
#> dim: 63677 8
#> metadata(1): ''
#> assays(1): counts
#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
#> ENSG00000273493
#> rowData names(10): gene_id gene_name ... seq_coord_system symbol
#> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
#> colData names(9): SampleName cell ... Sample BioSampleOpting In and Out of Tidy Print
By default, tidyprint does not change the standard SummarizedExperiment print format. You can opt in to use the tidy print format, and opt out at any time. The setting can be configured for the current R session only, or saved to persist across sessions.
airway
#> class: RangedSummarizedExperiment
#> dim: 63677 8
#> metadata(1): ''
#> assays(1): counts
#> rownames(63677): ENSG00000000003 ENSG00000000005 ... ENSG00000273492
#> ENSG00000273493
#> rowData names(10): gene_id gene_name ... seq_coord_system symbol
#> colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521
#> colData names(9): SampleName cell ... Sample BioSampleOpt In to Tidy Print
To enable the tidy print format, use tidy_print_on(). By
default, this only affects the current R session:
# Enable tidy print for current session only
tidy_print_on()
#> ℹ tidyprint says: Tidy print enabled for this session only. Use tidy_print_on(remember = TRUE) to save this setting for future sessions.
airway
#> ! tidyprint says: R option 'tidyprint.use_tidy_print' (TRUE) overrides cache value (FALSE). Use tidy_print_on(remember = TRUE) to update cache.
#> # A SummarizedExperiment-tibble abstraction: Features=63677 | Samples=8 |
#> # Assays=counts
#> # |----------------- COVARIATES ---------------|
#> .feature .sample | counts | SampleName cell dex albut Run avgLength
#> <chr> <chr> | <chr> | <fct> <fct> <fct> <fct> <fct> <chr>
#> 1 ENSG0000… SRR103… | 679 | GSM1275862 N613… untrt untrt SRR1… 126
#> 2 ENSG0000… SRR103… | 0 | GSM1275862 N613… untrt untrt SRR1… 126
#> 3 ENSG0000… SRR103… | 467 | GSM1275862 N613… untrt untrt SRR1… 126
#> 4 ENSG0000… SRR103… | 260 | GSM1275862 N613… untrt untrt SRR1… 126
#> 5 ENSG0000… SRR103… | 60 | GSM1275862 N613… untrt untrt SRR1… 126
#> -------- ------- - ------ - ---------- ---- --- ----- --- ---------
#> 509412 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
#> 509413 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
#> 509414 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
#> 509415 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
#> 509416 ENSG0000… SRR103… | 0 | GSM1275875 N061… trt untrt SRR1… 98
#> # ℹ 14 more variables: Experiment <fct>, Sample <fct>, BioSample <fct>,
#> # `|` <|>, gene_id <chr>, gene_name <chr>, entrezid <chr>,
#> # gene_biotype <chr>, gene_seq_start <chr>, gene_seq_end <chr>,
#> # seq_name <chr>, seq_strand <chr>, seq_coord_system <chr>, symbol <chr>If you want the setting to persist across R sessions, use
remember = TRUE:
# Enable tidy print and remember the setting
tidy_print_on(remember = TRUE)
airway # Will display with tidy format in all future sessionsWhen remember = TRUE, the setting is saved to a cache
file in your R configuration directory, so it will automatically be
enabled when you start new R sessions.
Opt Out of Tidy Print
To return to the standard SummarizedExperiment print format, use
tidy_print_off(). By default, this only affects the current
session:
# Disable tidy print for current session only
tidy_print_off()
airway # Will display with standard formatTo permanently disable tidy print and clear any saved preference:
# Disable tidy print and remember the setting
tidy_print_off(remember = TRUE)
airway # Will display with standard format in all future sessionsMessaging function
We integrated a messaging function providing standardized, visually appealing messages for packages within the tidyomics ecosystem. It automatically detects the calling package to provide contextualized messaging, such as “tidyprint says” or “tidybulk says”, enhancing consistency and readability across projects.
To use the tidy_message function:
tidyprint::tidy_message('message to print')
#> ℹ Console says: message to printYou can specify the type of message as
info (default)
success
warning
danger
demo_tidy_message()
#> ℹ tidyprint says: This is an informational message send within tidyprint package.
#> ✔ tidyprint says: Operation completed successfully!
#> ! tidyprint says: Potential issue detected.
#> ✖ tidyprint says: Operation failed.The above code demonstrates calling tidy_message within
a package function, showing the name of package.
Session info
sessionInfo()
#> R Under development (unstable) (2026-01-03 r89269)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] tidyprint_0.99.9 airway_1.31.0
#> [3] SummarizedExperiment_1.41.0 Biobase_2.71.0
#> [5] GenomicRanges_1.63.1 Seqinfo_1.1.0
#> [7] IRanges_2.45.0 S4Vectors_0.49.0
#> [9] BiocGenerics_0.57.0 generics_0.1.4
#> [11] MatrixGenerics_1.23.0 matrixStats_1.5.0
#> [13] tidyr_1.3.2 dplyr_1.1.4
#> [15] BiocStyle_2.39.0
#>
#> loaded via a namespace (and not attached):
#> [1] utf8_1.2.6 sass_0.4.10 SparseArray_1.11.10
#> [4] stringi_1.8.7 lattice_0.22-7 digest_0.6.39
#> [7] magrittr_2.0.4 evaluate_1.0.5 grid_4.6.0
#> [10] bookdown_0.46 fastmap_1.2.0 rprojroot_2.1.1
#> [13] jsonlite_2.0.0 Matrix_1.7-4 BiocManager_1.30.27
#> [16] fansi_1.0.7 purrr_1.2.0 textshaping_1.0.4
#> [19] jquerylib_0.1.4 abind_1.4-8 cli_3.6.5
#> [22] rlang_1.1.6 XVector_0.51.0 withr_3.0.2
#> [25] DelayedArray_0.37.0 cachem_1.1.0 yaml_2.3.12
#> [28] otel_0.2.0 S4Arrays_1.11.1 tools_4.6.0
#> [31] vctrs_0.6.5 R6_2.6.1 lifecycle_1.0.4
#> [34] stringr_1.6.0 fs_1.6.6 htmlwidgets_1.6.4
#> [37] ragg_1.5.0 pkgconfig_2.0.3 desc_1.4.3
#> [40] pkgdown_2.2.0 pillar_1.11.1 bslib_0.9.0
#> [43] glue_1.8.0 systemfonts_1.3.1 xfun_0.55
#> [46] tibble_3.3.0 tidyselect_1.2.1 knitr_1.51
#> [49] htmltools_0.5.9 rmarkdown_2.30 compiler_4.6.0