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Changelog

Source: NEWS.md

usefulfunctions 0.3.0

A quality release: correctness fixes found by a much larger test suite, original replacements for code that was derived from another package, and a documentation site.

Breaking or behaviour-changing

  • tcga_survival() now splits patients at the true upper and lower quartiles of expression. Previously the quartiles were rounded with floor() / ceiling(), which classified nearly every patient as “high” for genes with low expression (TPM below 1). Results for such genes will change.
  • sc_correlation() returns genes sorted by decreasing correlation (it was alphabetical), drops genes with undefined correlation, always keeps the gene of interest when filtering by expression, and writes the CSV without an extra row-name column. output.tables = NULL skips writing. debug.mode is ignored.
  • The plotting helpers (umap_optimise(), correlation_heatmaps(), plot_correlation(), dendrogram_samples()) no longer rely on dev.copy() of the active graphics device. They return their plots (or paths) and write PDFs to output.dir; NULL skips writing.
  • The dot.case names (makeTransparent(), GO.function(), TCGA.OS(), …) now warn once per session before forwarding to the snake_case function; see ?legacy_aliases.

New

  • volcano_plot(): an original, compact volcano plot (ggplot2, optional ggrepel) that takes the per-point colour, alpha and size helpers. custom_enhanced_volcano() is now a deprecated wrapper.
  • stratify_by_expression(): high / low sample strata for a gene or a multi-gene signature (mean z-score). Multi-gene signatures were previously not implemented in tcga_survival().
  • tcga_survival() returns the annotated clinical table invisibly.
  • A getting-started vignette and a pkgdown site.
  • jax.table argument to the ortholog converters for offline use.

Fixes

  • convert_human_to_mouse(use.jax = TRUE) converted in the wrong direction (mouse to human).
  • dendrogram_samples() failed with current factoextra (k must be at least 2); it now clusters with hclust() directly.
  • umap_optimise() plotted through Seurat::UMAPPlot(), which fails unless Seurat is attached.
  • moving_average() failed when the window was longer than the vector.
  • Deprecated tidyselect usage (.data$col inside select()) in clean_volcano_data().
  • Barcode matching in the TCGA helpers no longer depends on stringr, and patients with samples in both strata are left unlabelled instead of silently assigned to “Low”.

Removed

  • The vendored copy of the EnhancedVolcano plotting code (GPL-3) and the optional ggalt dependency.
  • Build artefacts (usefulfunctions.Rcheck/) and internal migration notes from the repository.

usefulfunctions 0.2.0

Ground-up rebuild: heavy Bioconductor dependencies moved to Suggests and checked at call time, snake_case names with dot.case aliases, unit tests and continuous integration.