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?rworkflows
for GHA.orthogene
data resources on Zenodo:
dplyr::%>%
usage with |>
prepare_tree
:map_species
:trimws
step to remove flanking " " or "'".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
. test-map_orthologs_babelgene
less stringent with the
number of genes expected.create_background
:bg
gets used:
https://github.com/neurogenomics/orthogene/issues/22 devtools::document
doesn't expect them to be exported objects. plot_orthotree
: Pass up tree_source
arg. 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_genes
: Fix report at completion. gene_df
isn't a matrix.DelayedMatrixStats
Import (no longer needed). check_agg_args
. test-map_orthologs_babelgene
less stringent
with the number of expected genes.map_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)
). 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
source_all
as it included a library
call. 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. orthogene
now supports DelayedArray
objects as gene_df
input. create_background
now uses all_genes
when all 3 species are the same. 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". report_orthologs
no longer throws error due to not finding tar_genes
.report_orthologs
. convert_orthologs
.GenomeInfoDbData
now required.orthogene
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