NEWS.md

MSTExplorer 1.0.11

Bug fixes

• plot_ttd: Add fill=TRUE when binding dts

MSTExplorer 1.0.10

New features

• run_permutation_test_cor: New function to run permutation tests.
• plot_ontology_levels: Add more args. Make "info_content_binned" a separate col from raw "info_content".

Bug fixes

• Update all calls to facet_grid to not use deprecated facets arg.

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 #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

  • 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.

MultiEWCE 0.1.10

New features

• gene_results
  • Return merged versions of $results as well as $gene_data (when available).

MultiEWCE 0.1.9

New features

• New function: get_bg:
  • Creates and caches background made with gprofiler.
• New function: standardise_genes
  • May move this to orthogene package as it's quite generally useful.
• Allow users to set min number of genes:
  • min_genes arg in gen_results / ewce_para.

Bug fixes

• gen_results / ewce_para
  • bg was incorrectly set to use only genes in gene_data.
  • Now uses get_bg to create background using gprofiler.
• get_valid_gene_lists
  • Throw error when 0 valid gene lists found.
• get_unfinished_list_names
  • Fix example
• Use rworkflows@dev to avoid API limit.

MultiEWCE 0.1.8

New features

• MultiEWCE finally gets a hex sticker!
• gen_results / gen_overlap
  • Check for existing results and import if already there.
  • Name all results "gen_results.rds" or "gen_overlap.rds" to avoid rerunning duplicate analyses on HPC.
• Update rworkflows.yml

Bug fixes

• Fix unit tests and examples to use "hpo_id" instead of "hpo_name".
• load_hpo_graph:
  • export
  • Regenerate and update "hpo_graph.rds" file.
• Drastically reduce time to run examples.
• ontology_plot
  • Fix function and add test.
• DESCRIPTION
  • Depends: R (>= 2.10) --> Depends: R (>= 4.1), to ensure |> function available.
  • Rewrite Description field to reflect MultiEWCE's current purpose.

MultiEWCE 0.1.7

New features

• Update to coordinate with HPOExplorer updates.
• New funcs:
  • plot_ontology_levels
  • ttd_check
  • ttd_plot
  • ttd_import

MultiEWCE 0.1.6

New features

• Require HPOExplorer (>= 0.99.10)
• Switch terms:
  • "HPO_ID" --> "hpo_id"
  • "Phenotype" --> "hpo_name"
  • "FREQUENCY" --> "gene_freq"
  • "Onset" --> "onset"
  • "Modifier" --> "modifier"
  • "Aspect" --> "aspect"
  • "Gene" --> "gene_symbol"
  • "DatabaseID" --> "disease_id"
  • "LinkID" --> "disease_id"
• Update all "data" objects.
• get_data
  • Add tag arg.

Bug fixes

• load_example_results
  • Change tag to "latest".
  • Update colnames dynamically.
• load_example_ctd
  • Change tag to "latest".
• load_hpo_graph
  • Change tag to "latest".
• map_tissues
  • Fix docs.
• agg_results
  • Add "hpo_id" column before aggregation.
• correlation_heatmap
  • Ensure row annot order is correct.
• add_ctd
  • Fix example.

MultiEWCE 0.1.5

New features

• prioritise_targets
  • New arg evidence_score_threshold to utilise GenCC evidence scores provided via HPOExplorer.
  • Merge symptom-level driver genes after unlisting the "intersection" column instead of using indirect approach that on nested "intersection" column.
• prioritise_targets_network
  • Add feature to resize plot after double-click.
• New function: add_tissues
  • Add tissues that each cell type is found in, using a celltype-tissue mapping file.
  • Regenerate "DescartesHuman_celltype_mapping.csv" file as the one previously generated wrong (had every celltype in every tissue)

Bug fixes

• prioritise_targets_network
  • Fill screen better in saved plots with new default args: width = "100%", height = "90vh"

MultiEWCE 0.1.4

New features

• prioritise_targets
  • Move filtering steps and arg docs inside respective HPOExplorer::add_* functions.
• gen_results
  • New arg parallel_boot lets users choose which level to parallelise over.
• New exported func: gen_overlap
  • Compute simple overlap enrichment results.
  • Overcomes requirement of >=4 genes.
  • Faster than EWCE (but less robust)
• New internal func: save_results
• load_example_results
  • New arg force_new

Bug fixes

• get_valid_gene_lists
  • Can now handle any list_name_column

MultiEWCE 0.1.3

New features

• ggnetwork_plot_full:

  • Handles multiple celltypes by aggregation.

• New internal function: agg_results.

• New functions for generating/visualizing prioritised targets:

  • prioritise_targets
  • prioritise_targets_heatmap
  • prioritise_targets_network
  • plot_report
  • correlation_heatmap
  • frequency_bar
  • plot_frequency_histogram

• Added example_targets data:

  • Speeds up run time of examples/tests.

Bug fixes

• Remove unused function: count_results
• Make get_unfinished_list_names much more efficient.
• Add leeway to gen_results test, as the number of sig results varies from run to run.

MultiEWCE 0.1.2

New features

• New functions:
  • load_example_results
  • ontology_plot
  • terminal_celltypes
  • various support functions
• Add ontologyPlot as new Import.
• Was able to replicate Momoko's results!!!

Bug fixes

• load_example_ctd
  • Pass file to piggyback::pb_download
• Remove redundant get_gene_list function (now handled by HPOExplorer::get_gene_lists).
• Make get_valid_gene_lists much more efficient and consider the intersect between ctd/gene_data genes.
• merge_results:
  • Handle NULL results in list.

MultiEWCE 0.1.1

New features

• Added a NEWS.md file to track changes to the package.
• Added rworkflows
• ewce_para
  • Harmonize arguments with EWCE
  • Set default list_names arg
  • Output named list of saved files instead of TRUE.
  • Add messages that appear in parallel. Make EWCE message silent.
• ewce_plot:
  • Simply make this a shallow wrapper for EWCE::ewce_plot as the latter function has since been fixed.
• Speed up with lapply throughout.
• gen_results:
  • Allow speedup by skipping writing to RDS and returning merged results directly instead.
• Use @inheritParams throughout.
• Use \link throughout.
• load_example_ctd:
  • Cache file
• merge_results:
  • Now handles lists of file path AND list of results lists.
• Remove RDA_assign_load
  • Not used and supplanted by EWCE::load_rdata() anyway.
• Remove unnecessary parameter descriptions in MultiEWCE vignette.
• Change results_dir --> save_dir throughout.
• load_example_CTD --> load_example_ctd for function naming consistency.
• Add README.Rmd.

Bug fixes

• Update to use EWCE>1.0.0
• Make more functions internal:
  • is_not_analysed
  • get_valid_gene_lists
• Make paths with file.path instead of hard-coded "/"
• Write files to tempdir() instead of current working directory.
• Remove unused packages:
  • cowplot
  • ewceData
• Fix all unit tests (not set up in correct format originally).