NEWS
LIPIDIFy 0.99.0
New features
- Added
normalize_mean() and full pipeline builder supporting TIC, PQN,
Quantile, VSN, Median, Mean, Log2, Log10, Sqrt, None
- Added
get_normalization_descriptions() for UI help text
- Shiny app: Select All / Deselect All buttons on every checkbox group
- Shiny app: group-coloured normalization comparison plots
- Shiny app: full plot history tracked across the session for complete reports
- Shiny app: samples sorted by group in Lipid Expression plots
- Shiny app: descriptive, timestamped download filenames for all plots
Bug fixes
create_pca_plot_with_ellipses(): fixed duplicate legend keys when ellipses
are drawn (fill + color legends now merged into one)
create_lipid_expression_barplot(): samples now sorted by group, not by
sample name
- Excel export: worksheet names truncated to Excel's 31-character limit
- Normalization help text modal and ellipse help modal now display correctly
perform_plsda(): replaced cat() with message() (Bioconductor requirement)
perform_enrichment_analysis(): replaced cat() with message()
Notes
- Quantile normalization producing near-identical boxplots is expected and
correct behaviour; inline documentation and UI now make this explicit
- Median and Mean normalization can look similar on symmetric (log-normal)
lipidomics data; on skewed data they differ — this is also expected