NEWS

MOSuite 0.5.0

The multiOmicDataSet class has been moved to a new package, MOObject. (#277, @kelly-sovacool)
- Ensure backward compatibility by coercing legacy MOSuite MOO objects when read/loaded. (#281, @kelly-sovacool)
Harmonize Volcano Plot output dimensions as physical inches with 300 DPI defaults for Enhanced and Summary plots. (#274, @TJoshMeyer)

Align Volcano Plot threshold comparisons across labeling, coloring, and summary filtering, and use resolved column names for classification. (#266, @TJoshMeyer)
normalize_counts() now uses normalized counts instead of filtered counts for the correlation heatmap so it matches the PCA and histogram outputs. (#269, @phoman14)

Fix how plot_volcano_summary() & plot_volcano_enhanced handle detecting column names for features, significance, and fold-change. plot_volcano_summary() plot now uses plot_volcano_enhanced() for rendering. (#239, @phoman14)

Update PCA label, point-size, and histogram behavior. (#230, @phoman14)
Add optional count log-transform controls for PCA plots. (#234, @phoman14)
Add a post-clean CPM histogram output in clean_raw_counts(). (#234, @phoman14)
Improvements to plot colors: (#223, @phoman14)
- Align plot color defaults with the MOSuite Code Ocean capsule defaults while preserving fallback random colors when a requested palette is too short.
- Improve top and bottom legend wrapping and automatic legend text sizing for PCA and histogram plots with many or long labels.
- Add optional group coloring to plot_read_depth() and the clean_raw_counts() read-depth output while preserving the single-color default when no group is selected.
New function display_colors() shows a multiOmicDataSet's chosen color palettes, and get_colors_lst() now takes a palette vector rather than function for simplicity. (#236, @kelly-sovacool)
New report template & helper function: render_report(). (#120, @kelly-sovacool)
Fix ggplot2 size deprecation warning in plot_volcano_summary(). (#228, @kelly-sovacool)
docs: show how to set output_dir in render_report(). (#235, @kelly-sovacool)

Support ggplot2 v4.0.0 for correlation heatmap plots in filter_counts(), normalize_counts(), and batch_correct_counts(). (#205, @copilot, @kelly-sovacool)

Fix recursion error in plot_venn_diagram(). (#188, @kelly-sovacool)
Fix S7 dispatch argument mismatch in plot_read_depth() and plot_histogram(). (#200, @copilot, @kelly-sovacool)
Fix bug in remove_low_count_genes() when use_group_based_filtering = TRUE. (#200, @copilot, @kelly-sovacool)
Fix color palette selection to fall back to random colors with a message when the number of categories exceeds the palette maximum. (#204, @copilot, @kelly-sovacool)
Update S7 class, generic, and method documentation to use roxygen2 v8.0.0. (#206, #212, @copilot, @kelly-sovacool)
A docker container with only MOSuite's dependencies, not MOSuite itself, is now available: https://hub.docker.com/r/nciccbr/mosuite-minimal. (#209, @kelly-sovacool)
Minor bug fixes in calc_cpm_df(), create_multiOmicDataSet_from_dataframes(), and diff_counts() docstring. (#214, @kelly-sovacool)

New function write_multiOmicDataSet_properties(). (#173, @kelly-sovacool)
- Extracts all the properties from a multiOmicDataSet and writes any data frames as csv files, other objects are written as rds files.
New utility functions to reduce code duplication across Code Ocean capsules: (#185, @kelly-sovacool) setup_capsule_environment(), load_moo_from_data_dir(), parse_optional_vector(), parse_vector_with_default(), and parse_samples_to_rename().

Fixed bug in clean_raw_counts() where duplicate gene rows were not being aggregated correctly. (#162, @TJoshMeyer)
Fixed batch_correct_counts() to gracefully skip batch correction when only a single batch level exists; the function now warns without erroring. (#158, @TJoshMeyer)
Fixed multiOmicDataSet validator to return character vector instead of using stop() per S7 documentation. (#177, @copilot, @kelly-sovacool)
Fixed duplicate PCA figure files in filter_counts(), normalize_counts(), and batch_correct_counts(). (#180, @kelly-sovacool)
Bug fixes: (#174, @kelly-sovacool)
- Fixed bugs in plot_volcano_summary(), plot_volcano_enhanced(), and plot_pca_3d() when used with multiOmicDataSet objects.
- Fixed bug in filter_diff() when filtering_mode = "all" that was causing plot rendering errors.
- Fixed plot_pca_2d() to save plots to disk correctly.
Replaced deprecated arrange_() with arrange() in plot_expr_heatmap(). (#182, @kelly-sovacool)
Improvements for use with Galaxy. (#168, #170, #171, #174, @kelly-sovacool)

A docker image is now available. (#134)
- https://hub.docker.com/r/nciccbr/mosuite
Minor documentation improvements. (#135)
Improvements for use with Galaxy. (#149)
Fixed bug where 3D PCA plots were not being saved. (#149)

Any user-facing function can now be called from the unix command line to support Galaxy. (#126, #127) Usage: mosuite [function] --json=path/to/args
- It is not recommended for most users to run MOSuite via the CLI; this is only intended for the Galaxy workflow.
MOSuite is now archived in Zenodo with a DOI: 10.5281/zenodo.16371580

This is the first release of MOSuite 🎉

Note: at the start of development, this package was called reneeTools. Later it was renamed to MOSuite. (#76)

multiOmicDataSet (#16, #28)
- create_multiOmicDataSet_from_files()
- create_multiOmicDataSet_from_dataframes()
run_deseq2()
calc_cpm() (#38)
filter_counts() (#38)
clean_raw_counts() (#79)
normalize_counts() (#82)
batch_correct_counts() (#87)
diff_counts() (#102)
filter_diff() (#110)