Changes in version 1.7.2
Bug fixes
-
Changes in version 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.
Changes in version 1.7.0
New features
- Bump version.
Changes in version 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.
Changes in version 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?
Changes in version 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 "'".
Changes in version 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.
Changes in version 1.3.3
Bug fixes
- Make test-map_orthologs_babelgene less stringent with the number of
genes expected.
Changes in version 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.
Changes in version 1.3.1
New features
- plot_orthotree: Pass up tree_source arg.
Changes in version 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.
Changes in version 1.2.1
Bug fixes
- Make test-map_orthologs_babelgene less stringent with the number of
expected genes.
Changes in version 1.2.0
Bug fixes
- Increment to v2.0 now that Bioc 3.15 is the RELEASE.
Changes in version 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
Changes in version 1.1.4
Bug fixes
- Remove source_all as it included a library call.
Changes in version 1.1.3
New features
- Update GHA
Bug fixes
- Fix failing benchmarking tests.
Changes in version 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.
Changes in version 1.1.1
Bug fixes
- Made GHA less dependent on hard-coded R/bioc versions.
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 0.99.6
Bug fixes
- Allow all messages to be suppressed in report_orthologs.
Changes in version 0.99.3
New features
- License switched to GPL-3 (to be compliant with Bioc).
- New method "babelgene" added to convert_orthologs.
Changes in version 0.99.2
New features
- License switched to GPL3 (>=3).
Bug fixes
- GenomeInfoDbData now required.
Changes in version 0.1.0
New features
- orthogene released to Bioconductor.