NEWS.md
map_genes() & test case added.remove_all_nas
plot_orthotree
clades_rotate
rotate_clades
add_columns
sort_rows_func
filter_gene_df
test-report_orthologs
test-convert_orthologs
map_genes_planosphere
convert_orthologs
set_gprofiler (to use beta version)map_genes
map_genes_planosphere.convert_orthologs
input_species==output species (after performing method-specific species mapping) AND standardise_genes==FALSE.add_synonyms
syn_map is NULL, will use the gene_map instead.map_orthologs_custom
if(input_species==output_species) return(NULL)
drop_non121
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
ref_genes once.report_orthologs_i instead of recursion to make this easier.map and report get rbound separately and returned according to the return_report arg.format_species
format_species_name.all_species:
EWCE::list_species, but decided to extend it and export it here.get_silhouettes
gather_images.plot_orthotree
clades
drop_non121
symbol_only to ONLY consider gene symbols (not ensemble IDs) when identifying non-121 orthologs.gather_images
rphylopic 1.0.0 which uses the new phylopic API.tryCatch for when the SVG is available but not the png.is_human
all_genes_babelgene
NA since it’s irrelevant for humans.dMcast
stats::pass –> stats::na.pass. Weirdly, only a problem on Linux. Did base R change a fundamental function name?Matrix.utils since it’s now deprecated.
dMcast function as a new internal function within orthogene, since that’s the only function I use from Matrix.utils.create_background:
bg gets used: https://github.com/neurogenomics/orthogene/issues/22
devtools::document doesn’t expect them to be exported objects.aggregate_mapped_genes:
map_genes.map_orthologs as a way to create gene_map automatically, when gene_map=NULL and input_species!=output_species.species into input_species and output_species args.method –> agg_method, and use method to pass to map_orthologs instead.map_orthologs.many2many_rows docs.as_integers: new arg that uses floor.FUN to agg_fun.gprofiler_namespace. Used to validate target= arg in gprofiler2 functions.aggregate_mapped_genes:
gene_map made by map_orthologs or map_genes.aggregate_mapped_genes_twice
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.as_DelayedArray
prepare_tree:
tree_source options: path / URL / OmaDB / UCSC / timetreemap_orthologs_babelgene
piggyback.use_old as an optional arg so I can switch to more recent versions of babelgene::orthologs_df if need be.babelgene::orthologs_df by default.babelgene does by default (even when babelgene::orthologs(min_support = 1)).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:
common_species_names_dict now return “scientific_name” by default, instead of “taxonomy_id”map_species method to whatever method is being used in the function it’s wrapped within, to avoid dropping species due to naming differences.map_species_check_args.output_format when passing species to other functions.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.report_orthologs, especially when method="babelgene".templateR.all_genes_babelgene ortholog data to orthogene-specific cache instead of tempdir to avoid re-downloading every R session.create_background.infer_species.report_orthologs and convert_orthologs can now handle cases where input_species is the same as output_species.get_all_orgs to easily list all organisms from different packages.all_genes method “babelgene”.