Changelog

Source: NEWS.md

HPOExplorer 1.0.5

New features

  • Store HPO ontology in default KGExplorer cache dir to reduce disk storage.

Bug fixes

  • add_death: Fix incorrect column checking.

HPOExplorer 1.0.4

Bug fixes

  • Fix tests expecting fixed number of phenotypes.
  • Vignette
    • HPOExplorer: Fix rendering of final plot.

HPOExplorer 1.0.3

New features

  • Upgrade add_disease to use cached definitions.

Bug fixes

HPOExplorer 1.0.1

New features

  • Add Issues templates

Bug fixes

  • Fix tests:
    • gpt_annot_check
    • add_hpo_id
  • Fix functions: gpt_annot_plot

HPOExplorer 1.0.0

New features

  • MAJOR CHANGES: Switched from ontologyIndex to simona, which seems to be better written and has extensive analysis functions.
  • MAJOR CHANGES: Moved most non-HPO data annotation to KnowledgeNets
  • New exported functions:
    • Helper functions:
      • convert_hpo
    • Functions to map IDs across ontologies:
      • add_medgen
      • add_omop
      • add_prevalence
      • add_prevalence_report
  • New internal functions:
    • dt_to_matrix

Bug fixes

HPOExplorer 0.99.12

New features

  • get_hpo
    • Updated to latest release: 2023-08-01
  • gpt_annot_*
    • Ensure consistent use of updated column names.
  • Add version attribute data within HPO objects
    • get_hpo: already built in to ontologyIndex objects.
    • load_phenotypes_to_genes: new attribute.
    • New exported helper function: get_version
    • New exported helper function: clear_cache
  • Add make_ontology internal function.
  • Ensure consistent function naming:
    • create_node_data –> make_node_data
  • get_gencc
    • Export
    • Add version info
  • Increase code coverage throughout

HPOExplorer 0.99.11

New features

  • New GPT annotation functions
    • gpt_annot_read
    • gpt_annot_check
    • gpt_annot_codify
    • gpt_annot_plot
  • get_hpo

Bug fixes

HPOExplorer 0.99.10

New features

  • load_phenotype_to_genes
    • Update to use new annotation files.
  • Switch terms:
    • “HPO_ID” –> “hpo_id”
    • “Phenotype” –> “hpo_name”
    • “FREQUENCY” –> “gene_freq”
    • “Onset” –> “onset”
    • “Modifier” –> “modifier”
    • “Aspect” –> “aspect”
    • “Gene” –> “gene_symbol”
    • “LinkID” –> “disease_id”
  • Update all “data” objects.
  • Update hpo object to “2023-06-17” release.

Bug fixes

  • allow.cartesion –> allow.cartesian
  • Document all args.
  • add_onset
    • Circumvent Inf warnings.

HPOExplorer 0.99.9

New features

  • load_phenotype_to_genes
    • Temporary fix while the HPO annotations are being fixed (they accidentally uploaded a version without the LinkIDs): use old files which I’ve uploaded copies of to GitHub Releases.
  • get_gene_lengths
    • Turn off seqnames filter when keep_seqnames=NULL.
  • New function: add_genes
    • Extracted from phenos_to_granges code.

Bug fixes

  • phenos_to_granges
    • Make sure phenotype_to_genes is unique before.
    • Make sure there is only one gene length per gene symbol.
  • add_disease
    • Make sure annot <- load_phenotype_to_genes(3) only has one entry per hpo_id/disease_id combination.

HPOExplorer 0.99.8

New features

  • HPO data
    • Update from Bioportal: 2023-04-05
    • Recreate HPO with extract_tags = "everything".
    • Now includes useful tags like xref to get HPO ID mappings with other databases (MESH, SNOMED, UMLS).
    • store in Releases via piggyback to reduce package size.
  • MONDO data
    • Create updated ontology_index obj and store in Releases.
    • New func: get_mondo
    • Now includes useful tags like xref to get HPO ID mappings with other databases (DOID, MESH, ICD9, GARD, EFO, SCTID, NCIT UMLS, Orphanet).
  • get_data
    • New internal support func to get piggyback data.
  • hpo_meta
    • Remove as this information is now stored within new hpo tags: hpo$def, hpo$xref, etc.

Bug fixes

  • Update/simplify HPOExplorer vignette.

HPOExplorer 0.99.7

New features

  • prioritise_targets
    • Move filtering steps and arg docs inside respective HPOExplorer::add_* functions.
  • New funcs:
    • add_ndisease
    • add_disease_definition

Bug fixes

  • De-aggregate add_* functions so that everything occurs at the level of “disease_id” + “hpo_id”.
  • Remove Roxygen links to MultiEWCE

HPOExplorer 0.99.6

New features

  • New function for creating gene x phenotype matrix
    • hpo_to_matrix

Bug fixes

  • Add R.utils as Suggest.

HPOExplorer 0.99.5

New features

  • New functions:
    • make_igraph_network
    • network_3d
    • kde_surface
  • make_network_object: Now takes additional arguments to control the network layout.

HPOExplorer 0.99.4

New features

  • example_phenos:
    • Simplified and fast
    • Used in all applicable examples.
  • Create new hpo object:
    • This updates the HPO from 2016 (distributed by ontologyIndex) with an updated one from 2023.
    • Updated all data objects in HPOExplorer that may have relied on hpo to be generated.
  • fix_hpo_ids
  • New function for fixing issues with missing HPO IDs.

Bug fixes

  • hpo_tiers:
    • Found lots of typos, outdated phenotype names, and mismatched HPO IDs. We through and manually re-curated all of these and checked that they match up with the map_phenotypes output.
    • Add original hpo_tiers csv to inst/extdata.
  • Delete get_hpo_id function in favor of get_hpo_id_direct which is more reliable and comprehensive.

HPOExplorer 0.99.3

Bug fixes

  • get_ont_lvls:
    • Worked w Bobby to clarify the role of each ontology level function.
    • Added new internal function to get the max ontology level: get_max_ont_lvl
    • Rewrote function description to make the differences between absolute/relative level more clear.
  • make_network_object:
    • Use list_columns so that ontLvl_relative gets added to network obj.
  • list_columns
  • Add new arg extra_cols

HPOExplorer 0.99.2

New features

  • Automatically load hpo with new func: get_hpo()
  • Remove wesanderson from deps.
  • Add remaining functions from rare_disease_celltyping_apps.
  • Remove unused functions:
    • make_hoverbox
    • get_disease_description_dataframe
  • Add hpo_tiers data from Momoko’s thesis.
  • Make make_phenos_dataframe far more efficient.
  • adjacency_matrix:
    • Simply turn into a shallow wrapper for nearly identical function: ontologyIndex::get_term_descendancy_matrix
  • load_phenotype_to_genes:
    • Can now downlaod either phenotypes_to_genes or genes_to_phenotypes.
  • New functions supporting gene target prioritisation:
    • phenos_to_granges
    • add_onset
    • add_tier
    • map_phenotypes
    • get_gene_lists
    • get_gene_lengths
    • list_onsets

Bug fixes

  • Remove globals.R.
  • Avoid redundancy with:
    • get_relative_ont_level ~= find_parent ~= get_ont_level –> get_ont_lvl
    • get_relative_ont_level_multiple ~= get_hierarchy –> get_ont_lvls

HPOExplorer 0.99.2

New features

  • Added a NEWS.md file to track changes to the package.
  • Implemented rworkflows
  • make_network_plot: make interactive with plotly
  • Add simplifying wrapper functions:
    • make_hoverboxes
    • make_phenos_dataframe
  • Add verbose arg throughout.
  • Cache file from load_phenotype_to_genes
  • Add hpo_meta data to speed everything up.
    • Add helper func to preprocess data: as_ascii

Bug fixes

  • Make examples runnable.
  • Fix Imports
  • Update and streamline Get started vignette.
  • Remove unused functions:
    • download_phenotype_to_genes
    • hpo_term_definition_list