Changelog

Source: NEWS.md

MSTExplorer 1.0.9

New features

  • Copy all core phenomix functions used in MSTExplorer into new package phenomix.core to reduce dependencies and issues installing phenomix (which requires scKirby and echoconda).
  • validate_associations_correlate_ctd: Drastically reduce figure size by aggregating
    data to ancestral phenotype groups first.

MSTExplorer 1.0.8

Bug fixes

  • plot_celltype_severity: Ensure cell types are ordered by composite severity.
  • get_ggstatsplot_stats: Return all stats, not just specific labels.
  • ttd_check  ttd_plot
    • Make % prioritised targets a percentage of the total number of rows.
    • Fix mistake where I was including non-gene therapies too (due to how grepping collapsed listed works in data.tables).
    • Account for situations when there’s no failed targets to check.
  • plot_bar_dendro: Pass “top_ancestor_name” to get_color_map= arg instead of “ancestor_name”.

New features

  • validate_associations_correlate_ctd: Add downsample arg to reduce plot size.

MSTExplorer 1.0.7

New features

  • get_cl: new wrapper for getting the exact version of the Cell Ontology used in our original study.
  • Update README to better reflect the package’s current state.

Bug fixes

  • Use BiocMananger to install in README.
  • plot_bar_dendro: Fix https://github.com/neurogenomics/MSTExplorer/issues/22
  • plot_tissues: Don’t try to facet plot types that aren’t requested.
  • prioritise_targets_network: Fix examples and tests.
  • plot_celltype_severity: Fix tests.

MSTExplorer 1.0.6

Bug fixes

  • get_color_map
    • Fix color_vector assignment.

MSTExplorer 1.0.5

Bug fixes

  • ttd_hypergeo via ttd_check: Missing column (NULL) made overlap always 0, and thus hypergeo p-value always equal 1.

  • 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

  • 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.