- add function
run_congenital_enrichment
- add function
plot_celltype_severity
- add function
prioritise_targets_grid
plot_bar_dendro_facets
- Add
hpo
arg to pass HPO directly. - Fix
data_summary
so that denominator is the number of on-target cell types only.
- Add
- Rename
MSTExplorer
. - Revamp to work with
KGExplorer
.
gene_results
- Return merged versions of
$results
as well as$gene_data
(when available).
- Return merged versions of
- New function:
get_bg
:- Creates and caches background made with
gprofiler
.
- Creates and caches background made with
- New function:
standardise_genes
- May move this to
orthogene
package as it's quite generally useful.
- May move this to
- Allow users to set min number of genes:
min_genes
arg ingen_results
/ewce_para
.
gen_results
/ewce_para
bg
was incorrectly set to use only genes ingene_data
.- Now uses
get_bg
to create background using gprofiler.
get_valid_gene_lists
- Throw error when 0 valid gene lists found.
get_unfinished_list_names
- Fix example
- Use rworkflows@dev to avoid API limit.
MultiEWCE
finally gets a hex sticker!gen_results
/gen_overlap
- Check for existing results and import if already there.
- Name all results "gen_results.rds" or "gen_overlap.rds" to avoid rerunning duplicate analyses on HPC.
- Update rworkflows.yml
- Fix unit tests and examples to use "hpo_id" instead of "hpo_name".
load_hpo_graph
:- export
- Regenerate and update "hpo_graph.rds" file.
- Drastically reduce time to run examples.
ontology_plot
- Fix function and add test.
- DESCRIPTION
Depends: R (>= 2.10)
-->Depends: R (>= 4.1)
, to ensure|>
function available.- Rewrite
Description
field to reflectMultiEWCE
's current purpose.
- Update to coordinate with
HPOExplorer
updates. - New funcs:
plot_ontology_levels
ttd_check
ttd_plot
ttd_import
- Require
HPOExplorer (>= 0.99.10)
- Switch terms:
- "HPO_ID" --> "hpo_id"
- "Phenotype" --> "hpo_name"
- "FREQUENCY" --> "gene_freq"
- "Onset" --> "onset"
- "Modifier" --> "modifier"
- "Aspect" --> "aspect"
- "Gene" --> "gene_symbol"
- "DatabaseID" --> "disease_id"
- "LinkID" --> "disease_id"
- Update all "data" objects.
get_data
- Add
tag
arg.
- Add
load_example_results
- Change
tag
to "latest". - Update colnames dynamically.
- Change
load_example_ctd
- Change
tag
to "latest".
- Change
load_hpo_graph
- Change
tag
to "latest".
- Change
map_tissues
- Fix docs.
agg_results
- Add "hpo_id" column before aggregation.
correlation_heatmap
- Ensure row annot order is correct.
add_ctd
- Fix example.
prioritise_targets
- New arg
evidence_score_threshold
to utilise GenCC evidence scores provided viaHPOExplorer
. - Merge symptom-level driver genes after unlisting the "intersection" column instead of using indirect approach that on nested "intersection" column.
- New arg
prioritise_targets_network
- Add feature to resize plot after double-click.
- New function:
add_tissues
- Add tissues that each cell type is found in, using a celltype-tissue mapping file.
- Regenerate "DescartesHuman_celltype_mapping.csv" file as the one previously generated wrong (had every celltype in every tissue)
prioritise_targets_network
- Fill screen better in saved plots with new default args:
width = "100%", height = "90vh"
- Fill screen better in saved plots with new default args:
prioritise_targets
- Move filtering steps and arg docs inside respective
HPOExplorer::add_*
functions.
- Move filtering steps and arg docs inside respective
gen_results
- New arg
parallel_boot
lets users choose which level to parallelise over.
- New arg
- New exported func:
gen_overlap
- Compute simple overlap enrichment results.
- Overcomes requirement of >=4 genes.
- Faster than EWCE (but less robust)
- New internal func:
save_results
load_example_results
- New arg
force_new
- New arg
get_valid_gene_lists
- Can now handle any
list_name_column
- Can now handle any
-
ggnetwork_plot_full
:- Handles multiple celltypes by aggregation.
-
New internal function:
agg_results
. -
New functions for generating/visualizing prioritised targets:
prioritise_targets
prioritise_targets_heatmap
prioritise_targets_network
plot_report
correlation_heatmap
frequency_bar
plot_frequency_histogram
-
Added
example_targets
data:- Speeds up run time of examples/tests.
- Remove unused function:
count_results
- Make
get_unfinished_list_names
much more efficient. - Add leeway to
gen_results
test, as the number of sig results varies from run to run.
- New functions:
load_example_results
ontology_plot
terminal_celltypes
- various support functions
- Add
ontologyPlot
as new Import. - Was able to replicate Momoko's results!!!
load_example_ctd
- Pass
file
topiggyback::pb_download
- Pass
- Remove redundant
get_gene_list
function (now handled byHPOExplorer::get_gene_lists
). - Make
get_valid_gene_lists
much more efficient and consider the intersect between ctd/gene_data genes. merge_results
:- Handle
NULL
results in list.
- Handle
- Added a
NEWS.md
file to track changes to the package. - Added
rworkflows
ewce_para
- Harmonize arguments with
EWCE
- Set default
list_names
arg - Output named list of saved files instead of
TRUE
. - Add messages that appear in parallel. Make EWCE message silent.
- Harmonize arguments with
ewce_plot
:- Simply make this a shallow wrapper for
EWCE::ewce_plot
as the latter function has since been fixed.
- Simply make this a shallow wrapper for
- Speed up with
lapply
throughout. gen_results
:- Allow speedup by skipping writing to RDS and returning merged results directly instead.
- Use
@inheritParams
throughout. - Use
\link
throughout. load_example_ctd
:- Cache file
merge_results
:- Now handles lists of file path AND list of results lists.
- Remove
RDA_assign_load
- Not used and supplanted by
EWCE::load_rdata()
anyway.
- Not used and supplanted by
- Remove unnecessary parameter descriptions in MultiEWCE vignette.
- Change
results_dir
-->save_dir
throughout. load_example_CTD
-->load_example_ctd
for function naming consistency.- Add README.Rmd.
- Update to use
EWCE
>1.0.0 - Make more functions internal:
is_not_analysed
get_valid_gene_lists
- Make paths with
file.path
instead of hard-coded "/" - Write files to
tempdir()
instead of current working directory. - Remove unused packages:
cowplot
ewceData
- Fix all unit tests (not set up in correct format originally).