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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.

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).