NEWS

orthogene 1.19.3

Test coverage

Lifted overall test coverage from ~84% to ~92% by adding ~370 new assertions across 7 new test files and 4 expanded ones. New tests cover:
- check_species_babelgene, check_agg_args, check_keep_popular, check_sparseMatrix, check_gene_map, check_gene_df_type, check_gene_output, check_bool_args, check_agg_opts (helper validation functions);
- map_orthologs_gprofiler non-chunked, chunked-serial, and chunked-parallel paths plus null/empty-input and same-source/target early returns and chunk_size validation;
- prepare_tree local-newick else-branch and age_max calibration paths;
- aggregate_mapped_genes transpose=TRUE, within-species, sort_rows, as_integers, and the early-exit "rename only" branch;
- infer_species test_species=NULL defaults and method-as-test_species expansion plus make_plot=FALSE;
- create_background use_intersect=FALSE (union), user-supplied bg, and within-species fast path;
- run_benchmark_once cache-hit, run_convert_orthologs=FALSE, and within-species (is_human) branches;
- aggregate_rows_monocle3 mean and count aggregation;
- rotate_clades, is_gha, load_rda, cache_dir, gconvert_target_opts, non121_strategy_opts, is_human, is_matrix/is_sparse_matrix, is_converted, add_rowcol_names, messager, format_species, methods_opts, gene_input_opts/gene_output_opts, invert_dictionary, and get_orgdb_gprofiler (use-local + use-remote) paths;
- Error/skip paths in filter_gene_df, aggregate_rows, map_orthologs, all_genes, and many2many_rows (aggregate_orthologs=FALSE).

orthogene 1.19.2

Bug fixes

test-map_genes: replace message(e) with message(conditionMessage(e)) in the planarian (Schmidtea mediterranea) tryCatch error handler. Same pattern as the 1.17.4 fix to run_benchmark_once(): passing a condition object to message() re-signals it, and under testthat's calling handlers an error condition signaled this way escapes the tryCatch and is reported as a test failure. This caused test-map_genes to fail on the GitHub Actions Windows runner whenever the planosphere mapping file failed to download. Same fix has been backported to RELEASE_3_23 as 1.18.1.

orthogene 1.19.1

Bug fixes

Revert the g:Profiler workarounds shipped in 1.17.3. Upstream (g:Profiler) confirmed and fixed the API regression that was returning literal NaN in JSON responses; unmatched genes are once again returned as "N/A". Examples and tests that test the default ortholog-mapping path now exercise g:Profiler honestly again — no method = "homologene" workarounds, no skip-on-error wrappers around explicit g:Profiler tests. The point of these tests is to catch an API regression, not to mask it.
Kept from 1.17.4: run_benchmark_once()'s message(conditionMessage(e)) fix — message(e) re-signals condition objects, which under testthat's calling handlers escapes tryCatch as a test failure. Unrelated to the g:Profiler API issue and remains a real bug.
Kept from 1.17.3: test-infer_species tolerates ties in top_match. When two species (e.g. human and monkey via babelgene) tie at the top percent_match, infer_species() returns both; the test now passes as long as the expected species is among them.

orthogene 1.17.4

Bug fixes

run_benchmark_once(): replace message(e) with message(conditionMessage(e)) inside the tryCatch error handlers. Passing a condition object to message() re-signals it, and under testthat's calling handlers an error condition signaled this way escapes the tryCatch and is reported as a test failure — even though tryCatch did catch it. This caused test-run_benchmark to fail on GitHub Actions whenever the g:Profiler API returned malformed JSON, even though run_benchmark_once() was supposed to record NA and move on.

orthogene 1.17.3

Bug fixes

Make examples of convert_orthologs(), map_orthologs(), and all_genes() use method = "homologene" so they don't depend on the g:Profiler API. The remote g:Profiler service has been intermittently returning JSON with literal NaN tokens, which jsonlite cannot parse, causing the Bioconductor R CMD check for examples to fail.
Tests that incidentally exercised the default g:Profiler path (test-aggregate_mapped_genes, test-convert_orthologs, test-infer_species) now request method = "homologene" explicitly.
Tests that intentionally cover the g:Profiler backend (test-all_genes_gprofiler, the method = "gprofiler" block in test-convert_orthologs) now skip gracefully with a clear message when the API is unavailable, rather than halting the whole suite.
test-run_benchmark: aggregate mean() checks now use na.rm = TRUE so a transient g:Profiler failure doesn't NA-poison the benchmark assertions.
test-infer_species: tolerate ties in top_match so that when two species are equally well-matched (e.g. human and monkey via babelgene), the test passes as long as the expected species is among them.

orthogene 1.17.2

New features

all_genes: enable method/species-specific caching.
run_benchmark_once: enable caching
cache_dir(): new function for consistency
map_orthologs_gprofiler: BIG upgrade! Can now rapidly query large gene lists via batching and parallelzation without server-side timeout errors.
Improve test coverage.

orthogene 1.16.1

Bug fixes

Remove grr dep as it's now deprecated #47
Add usage/returns sections to gprofiler_orgs and gprofiler_namespace to avoid "WARNING: Empty or missing \value sections found in man page(s)"
Error: invalid version specification ‘1.17.1 ’: Remove extra space in description to avoid rworkflows::use_badges error.

orthogene 1.15.02

Bug fixes

Fix #46

New features

Disable blank Issues
Update inst/orthogene manual

orthogene 1.15.01

Bug fixes

Update ggplot2 facet calls to avoid deprecation errors.
Fix all roxygen note warnings.

orthogene 1.14.01

Bug fixes

Update ggplot2 facet calls to avoid deprecation errors.
Fix all roxygen note warnings.

orthogene 1.13.0

New features

check_bool_args: Add check that boolean args are boolean, to avoid issues like https://github.com/neurogenomics/orthogene/issues/41
Warn instead of Error when not all Suggests are installed: https://github.com/neurogenomics/orthogene/issues/40
Bump Docker container in rworkflows to RELEASE_3_20

Bug fixes

format_gene_df: Fix report so that the minimum number of dropped genes is 0 (not negative number), and the percentage of retained genes is <=100.

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".