NEWS.md

In neurogenomics/orthogene: Interspecies gene mapping

orthogene 1.9.1

New features

• Bump version for Bioc 3.19.
• Use GHCR instead of Dockerhub, update vignette accordingly.
• Increase code coverage.

Bug fixes

• Catch case where no genes are found in the species in map_genes() & test case added.

orthogene 1.7.3

New features

• Added yeast (Saccharomyces cerevisiae) as a valid taxonomy choice.

orthogene 1.7.2

Bug fixes

orthogene 1.7.1

New features

• remove_all_nas
  • Can handle multiple cols.
• plot_orthotree
  • New arg clades_rotate
  • New func: rotate_clades

Bug fixes

• add_columns
  • Handle both vectors and columns.
• sort_rows_func
  • Handle both vectors and columns.
• filter_gene_df
  • Avoid coercing single-col dataframe into vector.
  • Flagged in #34
• Fix test-report_orthologs
  • Recognize either Gene.symbol or input_gene cols depending on when ortholog conversion was done.
• Fix test-convert_orthologs
  • Line 99 test had wrong number of cols.
• map_genes_planosphere
  • Add backup download strategy.

orthogene 1.7.0

New features

• Bump version.

orthogene 1.5.3

New features

• convert_orthologs
  • Can now take a user-supplied gene_map to use instead of gprofiler/homologene/babelgene.
  • Lets user take advantage of all of the many:many ortholog mapping functions for organisms not covered in any of the databases (eg. earthworm).
• New helper function: set_gprofiler (to use beta version)
• map_genes
  • Can now translate planarian gene synonyms using subfunction: map_genes_planosphere.

Bug fixes

• convert_orthologs
  • Now returns original data when input_species==output species (after performing method-specific species mapping) AND standardise_genes==FALSE.
• add_synonyms
  • When syn_map is NULL, will use the gene_map instead.
• map_orthologs_custom
  • Remove if(input_species==output_species) return(NULL)
• drop_non121
  • Don't run grouped slicing when "input_gene","ortholog_gene" are the only cols.

orthogene 1.5.2

New features

• Remove unnecessary Suggests
• map_species
  • get_all_orgs: When species=NULL, now returns an extra columns called "scientific_name_formatted".
  • format_species_name: New args remove_parentheses, remove_subspecies, remove_subspecies_exceptions
• report_orthologs
  • Make much more efficient by only querying ref_genes once.
  • Added new internal func report_orthologs_i instead of recursion to make this easier.
  • Ensure that map and report get rbound separately and returned according to the return_report arg.
• format_species
  • Export function that was previously named format_species_name.
• all_species:
  • New exported function
  • Originally implemented a version of this in EWCE::list_species, but decided to extend it and export it here.
• get_silhouettes
  • Previously was internal func: gather_images.
  • Now an exported function.
• plot_orthotree
  • Add "Invertebrates" to default clades
• Update README to showcase more functions.

Bug fixes

• drop_non121
  • New arg symbol_only to ONLY consider gene symbols (not ensemble IDs) when identifying non-121 orthologs.
  • This make a drastic difference in the number of 1:1 orthologs that get dropped!
• gather_images
  • Update to use newly released rphylopic 1.0.0 which uses the new phylopic API.
  • Add another tryCatch for when the SVG is available but not the png.
• is_human
  • Add "9606" and "homo sapiens sapiens" species ID to list of options.
• all_genes_babelgene
  • Don't filter by support when speices is human, because this column will always be NA since it's irrelevant for humans.
• Fix unit tests:
  • report_orthologs
• dMcast
  • Fix stats::pass --> stats::na.pass. Weirdly, only a problem on Linux. Did base R change a fundamental function name?

orthogene 1.5.1

New features

• Bumped to 1.5.1 for Bioc devel 3.17
• Merged upstream devel.
• Now using rworkflows for GHA.
  • Removed Dockerfile
• Host orthogene data resources on Zenodo:
  • https://doi.org/10.5281/zenodo.7315418
• Upgrade TimeTree phylogeny to v5 (2022):
  • 50k+ species --> 137k+ species!
• Replace dplyr::%>% usage with |>
• Add CITATION file

Bug fixes

• prepare_tree:
  • Ignore species name case and trim "'" when filtering tree.
• map_species:
  • Add trimws step to remove flanking " " or "'".

orthogene 1.3.4

Bug fixes

• Remove Matrix.utils since it's now deprecated.
  • Reimplement the dMcast function as a new internal function within orthogene, since that's the only function I use from Matrix.utils.
• Fix GHA workflow now that r-lib/actions@master has been removed.

orthogene 1.3.3

Bug fixes

• Make test-map_orthologs_babelgene less stringent with the number of genes expected.

orthogene 1.3.2

New features

• Add inst/grofiler_namespace.csv.gz for documentation purposes.

Bug fixes

• create_background:
  • Ensure user-supplied bg gets used: https://github.com/neurogenomics/orthogene/issues/22
• Properly document internal data so that devtools::document doesn't expect them to be exported objects.

orthogene 1.3.1

New features

• plot_orthotree: Pass up tree_source arg.

orthogene 1.3.0

New features

• aggregate_mapped_genes:
  • Pass up additional args from map_genes.
  • Add map_orthologs as a way to create gene_map automatically, when gene_map=NULL and input_species!=output_species.
  • Split species into input_species and output_species args.
  • Change method --> agg_method, and use method to pass to map_orthologs instead.
  • Pass up additional args from map_orthologs.
  • Add link to detailed explanation of matrix aggregation/expansion in many2many_rows docs.
  • Automatically pick best method for many:1 or many:many mapping.
  • as_integers: new arg that uses floor.
  • Rename FUN to agg_fun.
• Add new data gprofiler_namespace. Used to validate target= arg in gprofiler2 functions.
• Upgraded aggregate_mapped_genes:
  • Can now used gene_map made by map_orthologs or map_genes.
  • Can now handle many:many relationships.
  • Will automatically pick the best method to perform aggregation and/or expansion.
• Removed internal function aggregate_mapped_genes_twice
• Extracted aggregation args from non121_strategy and placed them in their own new own (agg_fun) since these options are no longer mutually exclusive due to many:many expansion/aggregation.
• Pass up as_DelayedArray
• Bump to v1.3.0 and R >=4.2 now that we're developing on Bioc 3.16.
• Add ISSUE_TEMPLATE.
• prepare_tree:
  • Add tree_source options: path / URL / OmaDB / UCSC / timetree

Bug fixes

• map_genes: Fix report at completion.
• Add safeguards against using aggregation when gene_df isn't a matrix.
• Removed DelayedMatrixStats Import (no longer needed).
• Fix all unit tests and examples after making all updates.
• Recognize sparse/dense matrix or delayedarray in check_agg_args.

orthogene 1.2.1

Bug fixes

• Make test-map_orthologs_babelgene less stringent with the number of expected genes.

orthogene 1.2.0

Bug fixes

• Increment to v2.0 now that Bioc 3.15 is the RELEASE.

orthogene 1.1.5

Bug fixes

• map_orthologs_babelgene
  • Add "Bad credentials" check for piggyback.
  • Add use_old as an optional arg so I can switch to more recent versions of babelgene::orthologs_df if need be.
  • Use updated built-in babelgene::orthologs_df by default.
  • Throw error if trying to map between two non-human species.
  • Filter support==NA mappings by default, not but support>=2 like babelgene does by default (even when babelgene::orthologs(min_support = 1)).
  • See here for discussion of discrepancies with babelgene maintainer: https://github.com/igordot/babelgene/issues/2

New features

• Removed aggregate_rows_delayedarray as it wasn't being used and was far less efficient than the other methods anyway (which are also compatible with DelayedArray matrices anyway). * New unit tests:
  • load_data
  • aggregate_mapped_genes(method='stat')
  • sparsity
  • infer_species

orthogene 1.1.4

Bug fixes

• Remove source_all as it included a library call.

orthogene 1.1.3

New features

• Update GHA

Bug fixes

• Fix failing benchmarking tests.

orthogene 1.1.2

Bug fixes

• convert_orthologs(method="babelgene") now gets gene mappings from all_genes_babelgene instead babelgene::orthologs (which doesn't seem to work very well, despite being dedicated for this purpose).
• map_species:
  • Avoid running this function redundantly when nested in multiple layers of other functions.
  • common_species_names_dict now return "scientific_name" by default, instead of "taxonomy_id"
  • Match map_species method to whatever method is being used in the function it's wrapped within, to avoid dropping species due to naming differences.
  • Add "id" column (e.g. "celegans") to all org databases to enhance their searchability.
  • Add map_species_check_args.
• Ensure proper method-specific output_format when passing species to other functions.

New features

• plot_orthotree: Automated plotting of phylogenetic trees with 1:1 ortholog report annotations. Includes several subfunctions:
  • prepare_tree (exported): Read, prune and standardise a phylogenetic tree.
  • gather_images (internal): More robust way to find and import valid phylopic silhouettes. Will make PR requests to rphylopic and ggimage/ggtree to include this functionality.
• Added unit tests for report_orthologs, especially when method="babelgene".
• GitHub Actions:
  • Merge both GHA workflows into one, as implemented in templateR.
• Added citation info to README.
• Save all_genes_babelgene ortholog data to orthogene-specific cache instead of tempdir to avoid re-downloading every R session.

orthogene 1.1.1

Bug fixes

• Made GHA less dependent on hard-coded R/bioc versions.

orthogene 1.1.0

New features

• Now on Bioconductor release 3.14.
• Docker containers automatically built and pushed to DockerHub via GitHub Actions.
• Dockerfile provided to build and check any R package efficiently with AnVil.
• CRAN checks and Bioc checks run via GitHub Actions.
• Added documentation on using Docker container to README.
• Documentation website now automatically built via GitHub Actions.
• Code coverage tests now automatically run and uploaded via GitHub Actions.

orthogene 0.99.9

New features

• Replaced R-CMD GHA with bioc-check GHA.
• Added new badges.

Bug fixes

• Adjusted vignette yamls to make resulting htmls smaller.

orthogene 0.99.8

New features

• orthogene now supports DelayedArray objects as gene_df input.
• create_background now uses all_genes when all 3 species are the same.

orthogene 0.99.7

New features

• Added new function create_background.
• Added new function infer_species.
• report_orthologs and convert_orthologs can now handle cases where input_species is the same as output_species.
• Add internal function get_all_orgs to easily list all organisms from different packages.
• Added all_genes method "babelgene".

Bug fixes

• report_orthologs no longer throws error due to not finding tar_genes.

orthogene 0.99.6

Bug fixes

• Allow all messages to be suppressed in report_orthologs.

orthogene 0.99.3

New features

• License switched to GPL-3 (to be compliant with Bioc).
• New method "babelgene" added to convert_orthologs.

orthogene 0.99.2

New features

• License switched to GPL3 (>=3).

Bug fixes

• GenomeInfoDbData now required.

orthogene 0.1.0

New features

• orthogene released to Bioconductor.

neurogenomics/orthogene documentation built on Jan. 30, 2024, 4:44 a.m.