NEWS

---

OmicFlow 1.7.0 (2026-10-11)

Added

• Added additional parameters via ... to be passed to pairwise_adonis and pairwise_anosim (.e.g. parallel = 10 can be called now).
• Added tryCatch and better error handling in omics$sample_subset, omics$feature_subset and omics$samplepair_subset.
• Added R/dependencies.R file as placeholder to prevent NAMESPACE declaration issue by R6 class (reducing namespace imports).
• Added is.color internal util function to check for valid color input.
• Added a pairwise_test as an util that uses matrixTests functions, and implements t.test, t.equalvar and wilcox with paired option.

Changed

• Re-factoring and improved roxygen2 code, documentation style and error handling.
• Replaced jsonlite by yyjsonr functionality, much faster and cleaner code.
• Replaced tests/testthat/input/metagenomics/biom_with_taxonomy_json.biom with one from BIOM v2 example.
• #43 Re-combined foldchange into omics and option to use different fold-change computations via argument method and aggregate_method.
• replaced ggpubr by ggplot2 functions in diversity_plot.
• #42 replaced rstatix by inbuilt pairwise_wilcox_test, added also tests for the util.
• Added colorblind coloring and replaced "groups" to actual col_name in omics$ordination
• #41 Extended countData to handle data.tables with both feature and sample columns.
• Moved omics$validate() from public to private, since it is only used as an internal function in $new()

Fixed

• omics$feature_merge is optional in omics$foldchange
• omics$removeNAs uses stats::complete.cases instead of na.omit
• Added extra error handling in metagenomics when biomData is used.
• feature_names in metagenomics that do not match supplied taxonomies are automatically removed. FEATURE_ID is fixed as first column.

Deprecated

• diversity_plot is replaced by stats_boxplot. The original diversity_plot is scheduled for deprecation.
• Scheduled deprecation of arguments for the future, such as:
  • col_name to be replaced by groups in composition_plot, colormap, boxjitter_test, omics$alpha_diversity
  • col_name to be replaced by add_cols in omics$composition
  • group_by to be replaced by split_by in omics$foldchange, omics$alpha_diversity and boxjitter_test.
  • method for labelling is removed in boxjitter_plot, instead an argument test can be specified to perform a pairwise statistcal tests on the groups.

OmicFlow 1.6.0 (2026-05-19)

Added

• #34 Extra argument group_by in foldchange.

Changed

• #33 Combined two methods into a single omics$scale(), added euclidean method and aitchison. Improved all dissimilarity metrics (except for UniFrac) by 2x speed & 7x less memory, UniFrac is 4x faster.
• #36 Created foldchange method in omics abstract class and in metagenomics subclass
• Adapted & tested autoFlow with new changes

Fixed

• #35 changed removezeros by using @p of CsparseMatrix
• #37 omics$reset works with omics$copy

Deprecated

• #36 Moved foldchange from namespace to omics$foldchange and metagenomics$foldchange

OmicFlow 1.5.1 (2026-02-27)

Added

• Extended unit-tests to uncovered code sections.

Changed

• Added error handling when none SAMPLE_IDs are matching during private$sync

Fixed

• #31 colormap doesn't return any NAs.
• #30 Placed FEATURE_ID as first column.
• #29 replaced position_nudge with position_jitter
• foldchange was matching sub-strings, fixed by changing it to exact matching.

OmicFlow 1.5.0 (2026-01-26)

Added

• #23 active bindings on data types, in place modification and automatic synchronisation between other data types by default via private function sync.
• #23 featureData is now always created as placeholder.

Changed

• #23 omics classes are now cloneable.
• #23 removeZeros() function is now private.
• #26 clarified initialize and field tags.
• #27 Both denseMatrix as sparseMatrix are converted to CsparseMatrix, compatible to omics$normalize, omics$feature_merge, diversity, hill_taxa and C-functions.
• Replaced tmp_link and tmp_restore with inline code. Seems like private$.countData doesn't work with a private function.
• Improved the cli formatting and visualisation of different arguments.
• print() inherited for each sub-class from omics and uses cli::cli_inform instead of cat
• #21 introduced custom half boxplot/point in diversity_plot, now also added group_by to perform grouped statistical tests.
• Replaced read_rarefraction_qiime by check_table from private function of class omics.
• autoFlow compatible to denseMatrix formats, applies fdr correction in other omics layers, report can be set to False, removed nmds.

Fixed

• #25 changed default value of initialize function.

Deprecated

• Removed tmp_restore and tmp_link
• Utils function read_rarefraction_qiime

OmicFlow 1.4.2 (2025-11-30)

Fixed

• geom_boxplot global function note for CRAN

OmicFlow 1.4.1

Added

• #20 rankstat has now an unique option.

Fixed

• #22 private$check_matrix checks if any zero's are present before creating a sparseMatrix.
• #20 omics$compositon Doesn't show Others when there are none.
• #24 volcano_plot only sizes the points if there are significant features found.

Deprecated

• #21 Removed gghalves in diversity_plot

OmicFlow 1.4.0 (2025-10-29)

Added

• #14 unifrac for both weighted/unweighted and normalized options.
• #14 bray for both weighted/unweighted options.
• #14 jaccard for both weighted/unweighted options.
• #14 jsd for both weighted/unweighted options.
• #14 cosine for both weighted/unweighted options.
• #14 canberra for both weighted/unweighted options.
• #14 manhattan for both weighted/unweighted options.
• omics$distance as wrapper for all new dissimilarity metrics.
• #18 pairwise_adonis2 and pairwise_anosim now allow custom permutation designs from permute R package.
• Unit tests for dissimilarity metrics

Changed

• metagenomics and proteomics classes now align the countData (rows) and featureData by the treeData tip.labels.
• omics$ordination uses now omics$distance to compute dissimilarity metrics (previously computed via rbiom).
• Example data loaded from inst/extdata instead of re-using mock.rds object.

Fixed

• #15 Fixed flipped log2 values when condition A or B is zero.
• #17 Docker is built via pak from github instead of CRAN.

Deprecated

• #13 Removed viridis dependency, purrr:map is replaced by lapply
• Removed rbiom and it's dependency slam.

OmicFlow 1.3.2 (2025-09-20)

Deprecated

• testthat removed autoflow test

OmicFlow 1.3.1 (2025-09-04)

Added

• rhub yaml to check for additional platforms

Fixed

• testthat now uses seed & tempdir() to meet CRAN policy
• report.md now also displays volcano plots
• omics$autoFlow() saves report html in correct current path

OmicFlow 1.3.0 (2025-09-01)

Added

• Docker support for R package autoflow #10

Changed

• autoFlow and report.md now contain downloadable data #11
• Renamed feature_glom to feature_merge
• Added @returns documentation in manuals
• Updated citations.md
• Finalized readme.md

Fixed

• working directory is set to current working directory in rmarkdown::render (compatible in docker/bioconda etc.)

OmicFlow 1.2.1

Added

• Included github actions workflow for covr code coverage and R CMD build check.
• github MIT license
• created folder inst/extdata with test data

Changed

• testthat now only checks presence of write_biom and autoFlow files.
• All other testthat functions are replaced by snapshot testing, issues #2 and #3

Fixed

• on.exit now solves issue during error occurance that class items are changed, issue #3.

OmicFlow 1.2.0

Added

• included exec folder with autoFlow.R function to be called from the command line #8.
• New private functions check_matrix and check_table for loading of files or existing data structures, issue #6.

Changed

• autoFlow.R now has option to select sub-class from the command line.

OmicFlow 1.1.0

Added

• included inst folder with report.Rmd and css.styles
• autoFlow now automatically loads report.Rmd from inst folder #3.
• Test displayed on plots changes based on boolean paired value.

Changed

• refactoring of autoflow, handles now both paired and unpaired data #3.
• combine_conditions automatically check if comparison is significant and updates the list with new conditions.
• updated manuals
• foldchange.R now handles zero's and doesn't return Inf values

OmicFlow 1.0.7

Added

• volcano_plot now offers option to visualize only abundant bacteria

Fixed

• Wrong order of normalization and feature aggregation #7

OmicFlow 1.0.6

Changed

• Updated documentation according to issues #2 and #4

Fixed

• Improved regex pattern in json file, now checks and doesnt allow for spaces.

Deprecated

• removed personal files, cleaned up directory.

OmicFlow 1.0.5

Added

• Included @examples in documentation #4.

OmicFlow 1.0.4

Fixed

• Performed unit-testing #2, #3.

OmicFlow 1.0.3

Added

• Created a citation.md for all used R packages in bibtex format
• Added more error handling and documentation to functions/methods #2.

Changed

• Updated documentation, manual #2

Deprecated

• Removed non-used functions

OmicFlow 1.0.2

Added

• created column_exist for efficient error handling of missing/empty columns in tables

Fixed

• write_biom is now functional and tested compared to python API biom-format.
• feature_filter is not compatible with newer version of feature_glom
• featureData now replaces empty strings with NA, compatible with metaData.

OmicFlow 1.0.1

Fixed

• write_biom is now functional and tested compared to python API biom-format

OmicFlow 1.0.0

Added

• samplepair_subset finds automatically pairs and subsets class.
• created metadata validation based on json schema, function validate.
• additional error handling is added with cli R package.

Changed

• metataxonomics is now called metagenomics sub-class, supports both hdf5, json formats.
• metagenomics class first loads omics class and then fills up any additional information.
• ordination plot now only shows ecclipses on T distribution.

Deprecated

• Removed find_pairs

OmicFlow 0.9.5

Changed

• unpaired_fold and paired_fold are now combined into a single function foldchange.

Deprecated

• Removed doParallel and foreach from foldchange computation.

OmicFlow 0.9.4

Changed

• feature_glom now handles multiple columns or single ones.
• metataxonomics sub-class now automatically renames the last taxonomy columns.

OmicFlow 0.9.3

Added

• read_sparseTable now efficiently reads in tsv, txt, csv, url or compressed files cleans it before creating a sparseMatrix

OmicFlow 0.9.2

Added

• error-handling for treeData

Changed

• Extra check for metadata & countdata alignment based of sample-ids
• Improved visualizations of triplot, using ggplot functions
• tools class is now called omics class.
• diversity_plot now only shows significant pvalues, supports p.adjust methods

OmicFlow 0.9.1

Changed

• feature_glom can now be repeated multiple times without throwing an error.
• Replaced ggpubr::compare_means by rstatix::pairwise_wilcox_test, makes it more flexible.

OmicFlow 0.9.0

Added

• Created new preoteomics-class.R
• Added basic cli error-handling in abstract class

OmicFlow 0.8.3

Fixed

• Labelling issue of features in feature_glom. More robust and equal fast method.

OmicFlow 0.8.2

Added

• Finalized docker image for autoFlow.R, placed it on docker hub.

OmicFlow 0.8.1

Changed

• autoflow now takes optionally pre-computed alpha or beta diversity in table format.

OmicFlow 0.8.0

Added

• Added documentation to all functions based on roxygen2 requirements.
• Created write_biom function in sub-class metataxonomics

Changed

• Finalised autoFlow.R standalone function, with docker image
• differential_feature_expression now uses sparseMatrix
• Updated manuals

Fixed

• Error handling in tools class
• autoFlow now handles missing data, including all other methods of tools class

OmicFlow 0.7.0

Added

• Created hill_taxa.R that implements sparseMatrix.

Changed

• Finalised autoFlow.R standalone function, with docker image
• differential_feature_expression now uses sparseMatrix

OmicFlow 0.6.0

Added

• Created new diversity function that uses sparseMatrix and uses 5x less memory.

Deprecated

• Removed vegan::diversity

OmicFlow 0.5.0

Changed

• countData class item now uses sparseMatrix instead of data.table

OmicFlow 0.4.1

Added

• testthat R scripts for metataxonomics-class.R

Fixed

• improved removeZeros for efficiency.

OmicFlow 0.4.0

Added

• Test data
• included documentation, focused on creating an R package

Changed

• alpha_diversity uses ggpubr R package
• Improved visualizations in differential_feature_expression

OmicFlow 0.3.1

Added

• created a fetch_colors function to get setNames from RColorBrewer.

Changed

• renamed shannon to alpha_diversity, more options for shannon metrics

OmicFlow 0.3.0

Added

• added dockerfile to use autoFlow

Changed

• Replaced single R scripts for autoFlow-class.R
• Applied foreach parallel in foldchange computation

Deprecated

• Removed single R scripts for automated analysis

OmicFlow 0.2.1

Fixed

• Added private functions within tools class; original_data, tmp_link and tmp_restore. Prevents modifications of tools components.

OmicFlow 0.2.0

Added

• Created a new foldchange plot that replaces DFE_plot
• Created differential_feature_expression within tools class
• Created a volcano_plot

Changed

• Created tools-class.R

Deprecated

• Removed deprecated phyloseq functions
• Removed DFE_plot

OmicFlow 0.1.0

Added

• Created a tools abstract class based on R6 OOP method, which uses data.table for efficiency.
• Created function removeZeros within class tools.
• Created function feature_subset within class tools.
• Created function sample_subset within class tools.
• Created function feature_glom within class tools.
• Created function transform within class tools.
• Created function composition within class tools.
• Created function shannon within class tools.
• Created function rankstat within class tools.
• Created function ordination within class tools.
• Differential Feature Analysis plot; fold_plot.R
• Started with metataxonomics sub-class for 16S metagenomics data
• Created print() similar to Phyloseq
• Created a reset() to undo changes
• Created a private generate_matrix from a biom file.
• Created an utils folder of new graph functions for composition_plot, ordination_plot, paired_fold, stats_plot, unpaired_fold