Changelog

Source: NEWS.md

MSTExplorer 1.0.6

Bug fixes

• get_color_map
  • Fix color_vector assignment.

MSTExplorer 1.0.5

Bug fixes

• Tests
  • Use force_new=TRUE where some tests occasionally fail with cached files.
  • test-load_example_results: Update test files.
  • test-prioritise_targets: Remove unused arguments and change input size.
  • test-prioritise_targets_network: Process top_targets to include effect
  • test-plot_differential_outcomes: Use non-specific plot name in patchwork::wrap_plots.
  • test-plot_differential_outcomes: Wrap p3 in expect_error to prevent test failure even if error was handled.
  • test-report_plot: Fix detection for ggplot object. variable.
• Vignettes
  • MSTExplorer: Update effect variable to fold_change.
• add_logfc
  • Return results with new column rather than directly modifying the original input.
  • Update references (add_logfc(results) -> results <- add_logfc(results)).
• ttd_check, plot_differential_outcomes, prioritise_targets_grid
  • Add check for disease_name column before executing HPOExplorer::add_disease on input.
• plot_ttd
  • Remove fill aesthetic for geom_text (doesn’t exist anymore).
• extract_help
  • [DEVELOPEMENT ONLY] Look for help docs only in legitimate pkg installation paths.
• subset_results
  • Add new effect_var argument.
  • Adjust default effect_threshold to 0.1.
• add_symptom_results
  • Only merge results and phenotypes_to_genes if required (prevents column duplicates with altered names).
• map_tissue
  • Rewrite merge logic to fix error: attempt to replicate non-vector.
• test_target_celltypes
  • Uncomment add_ancestors(results) to ensure required ancestor columns are present.
• Add missing import: simona

MSTExplorer 1.0.4

New features

• run_phenomix: can now take multiple annotLevels at once (will iterate).

MSTExplorer 1.0.3

New features

• add function run_congenital_enrichment
• add function plot_celltype_severity

MSTExplorer 1.0.2

New features

• add function prioritise_targets_grid

MSTExplorer 1.0.1

Bug fixes

• plot_bar_dendro_facets
  • Add hpo arg to pass HPO directly.
  • Fix data_summary so that denominator is the number of on-target cell types only.

MSTExplorer 1.0.0

New features

• Rename MSTExplorer.
• Revamp to work with KGExplorer.