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.