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Changelog

Source: NEWS.md

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 (2025-11-30)

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 (2025-10-23)

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 (2025-09-03)

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 (2025-08-13)

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 (2025-08-05)

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 (2025-08-03)

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 (2025-08-02)

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 (2025-07-29)

Added

  • volcano_plot now offers option to visualize only abundant bacteria

Fixed

  • Wrong order of normalization and feature aggregation #7

OmicFlow 1.0.6 (2025-07-28)

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 (2025-07-27)

Added

  • Included @examples in documentation #4.

OmicFlow 1.0.4 (2025-07-24)

Fixed

  • Performed unit-testing #2, #3.

OmicFlow 1.0.3 (2025-07-23)

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 (2025-07-22)

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 (2025-07-18)

Fixed

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

OmicFlow 1.0.0 (2025-07-17)

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 (2025-06-11)

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 (2025-06-03)

Changed

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

OmicFlow 0.9.3 (2025-05-08)

Added

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

OmicFlow 0.9.2 (2025-03-27)

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 (2025-03-11)

Changed

OmicFlow 0.9.0 (2025-02-24)

Added

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

OmicFlow 0.8.3 (2025-01-14)

Fixed

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

OmicFlow 0.8.2 (2025-01-02)

Added

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

OmicFlow 0.8.1 (2024-12-17)

Changed

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

OmicFlow 0.8.0 (2024-12-16)

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 (2024-11-28)

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 (2024-11-25)

Added

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

Deprecated

OmicFlow 0.5.0 (2024-11-14)

Changed

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

OmicFlow 0.4.1 (2024-11-8)

Added

  • testthat R scripts for metataxonomics-class.R

Fixed

  • improved removeZeros for efficiency.

OmicFlow 0.4.0 (2024-10-21)

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 (2024-10-13)

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 (2024-10-11)

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 (2024-10-07)

Fixed

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

OmicFlow 0.2.0 (2024-09-25)

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 (2024-09-17)

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