NEWS.md

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

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).

neurogenomics/MultiEWCE documentation built on Aug. 24, 2024, 1:41 a.m.