NEWS
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
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:
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.
- 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_dataaggregate_mapped_genes(method='stat')sparsityinfer_species
orthogene 1.1.4
Bug fixes
- Remove
source_all as it included a library call.
orthogene 1.1.3
New features
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
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.