Changes in version 1.13.1
Bug fixes
- Making ewce_plot functionality more clear - will no fail if
make_dendro=TRUE and ggdendro is not installed or CTD is not
provided rather than issuing a warning.
Changes in version 1.11.5
Bug fixes
- check_bootstrap_args:
- annotation level for checking cell type names was previous
hardcoded to level 1, now updated to match user input for
annotation level.
Changes in version 1.11.4
Bug fixes
- drop_uninformative_genes:
- Will now catch cases where expression matrix is a dataframe and
convert to a matrix
- This was causing weird errors, see issue 92:
https://github.com/NathanSkene/EWCE/issues/92
- Fix made in check_sce() function.
Changes in version 1.11.2
New features
- bootstrap_enrichment_test:
- New args: standardise_sct_data=, standardise_hits=: let users
have more control over data standardisation steps.
- check_ewce_genelist_inputs: updated accordingly.
- New arg: store_gene_data to avoid hitting memory limits.
- Modify test-bootstrap_enrichment_test_2.R to use test new args.
Changes in version 1.11.1
Bug fixes
- ewce_plot() - Dendrogram not reordering cell types in plot
- see issue
- Occurs when ctd does not contain the plotting info
- Fixed now and unit test added.
- Note that cell type order on the x-axis is based on hierarchical
clustering for both plots if make_dendro = TRUE for ewce_plot().
Changes in version 1.9.3
Bug fixes
- generate_bootstrap_plots
- Use stored gene_data object whenever possible.
- Only show filtered celltypes.
Changes in version 1.9.2
Bug fixes
- generate_bootstrap_plots
- Missing available parameters for check_ewce_genelist_inputs()
call.
Changes in version 1.9.1
Bug fixes
- drop_uninformative_genes
- Hash out DGE options. Somehow these got re-exposed to users in
Bioc>=3.16.
Changes in version 1.7.4
New features
- check_species:
- Added new arg sctSpecies_origin_default
- standardise_ctd:
- Can now specify sctSpecies_origin, which will be added to the
metadata.
Bug fixes
- standardise_ctd:
- When "annot" slot is not provided in the original CTD, a new one
will be created from matrix columns names instead of assigning
NULL.
Changes in version 1.7.3
New features
- check_ewce_genelist_inputs/bootstrap_enrichment_test
- New arg: sctSpecies_origin lets users clarify that their data
originally came from mouse even when it is currently formatted
as human orthologs. This is necessary for creating the
appropriate background gene lists.
- Remove grDevices as dep entirely.
- fix_celltype_names
- Add new arg make_unique to make this function easily usable for
vectors where the same celltype appears multiple times.
- bootstrap_enrichment_test
- Return gene-level scores based on adaptation of code from
generate_bootstrap_plots. now stored as a list element named
gene_data in data.table format.
- generate_bootstrap_plots
- Revamp wrap code into reusable subfunctions.
- Avoid resampling random genes when the gene data is stored in
the bootstrap results as gene_data. It will also tell you which
of these options it's using.
- Save with ggsave instead if grDevices.
- Facet by celltype instead of generating tons of separate plots.
- Let users decide cutoff threshold with new arg adj_pval_thresh
- Now returns a named list with the plots themselves ("plot") and
the paths to where they're saved ("paths") rather than just a
higher-level directory path in which users had to search for the
right files (and didn't ever have access to the ggplot2
objects).
- Show significance with barplot fill/color instead of asterices.
Much easier to see now.
- Change savePath arg to the more accurate save_dir. Expose
appending BootstrapPlots to the user within the argument.
- generate_bootstrap_plots_for_transcriptome
- Change savePath arg to the more accurate save_dir. Expose
appending BootstrapPlots to the user within the argument.
- Save with ggsave instead if grDevices.
- Standardise hits + hitGenes arg all to hits.
- Update hex:
- Off load large source image from DALLE to Releases instead of
including it within the package.
Bug fixes
- drop_uninformative_genes / generate_celltype_data
- Pass verbose arg to matrix formatting functions.
- generate_controlled_bootstrap_geneset
- Removed combinedGenes arg as it was not being used anywhere
within.
- check_args_for_bootstrap_plot_generation
- Removed unused args: ttSpecies, sctSpecies
- test-bootstrap_enrichment_test_2.R
- "monkey_ctd" tests seems to be running more smoothly than before
(not just getting NAs). This might have to with orthogene
databases improving.
- Reassuringly, "godzilla" tests still fail as expected :)
- Add tess/testthat/Rplots.pdf to .gitignore.
Changes in version 1.7.1
New features
- Use rworkflows GHA.
- Add rworkflows::use_badges to README.Rmd.
- Remove Dockerfile (no longer necessary).
- Make all 3 platforms (Linux, Mac, Windows) use Bioc dev, as
ewceData (>=1.7.1) is now required, due to a fix made only in
the development version of rtracklayer.
- Remove cowplot dependency.
- Replace all %>% with |>
Bug fixes
- calc_quantiles:
- This function was only used in filter_variance_quantiles
- Compare stats::ecdf vs. dplyr::ntile methods.
- Remove from EWCE as it's not longer used anywhere.
- bin_columns_into_quantiles:
- Rename arg matrixIn --> vec to reflect what the function
actually does.
- filter_variance_quantiles:
- Change to use bin_columns_into_quantiles instead of
calc_quantiles to be consistent with how quantiles are handled
in the rest of EWCE.
- Updated tests in test-get_celltype_table.r to reflect that the
number of genes filtered is unaffected by the normalization
procedure (when quantiles are computed with stats::quantile).
- ewce_plot:
- Celltypes were producing NAs because the names in the results
were not always standardized in the same way as the CTD. Now
this is done internally.
- Celltypes were not ordered factors, meaning the dendrogram
didn't line up correctly.
- Switched from gridArrange/cowplot to patchwork.
- Added dedicated unit tests file: test-ewce_plot.r
New features
- Offline runs enabled with functions using reference datasets (from
ewceData). These functions have the parameter localhub added to
control this.
Changes in version 1.5.8
Bug fixes
- GHA fix.
Changes in version 1.5.7
Bug fixes
- orthogene dependency has been replacing user entered background gene
list with one generated from all known genes when species across
gene lists and reference dataset are the same. This has now been
fixed.
Changes in version 1.5.5
Bug fixes
- standardise_ctd:
- Always force "specificity_quantiles" to be one of the matrices
in each level.
Changes in version 1.5.4
New features
- filter_ctd_genes
- Now exported.
- Can handle standardized CTD format.
- get_ctd_matrix_names: New function to get a list of all data
matrices in CTD.
Bug fixes
- check_ewce_genelist_inputs:
- User reported potential bug in
code:https://github.com/NathanSkene/EWCE/issues/71
- Fixed by removing conditional and instead always filtering out
genes not present in CTD/SCT.
- standardise_ctd:
- Add check_species()
- Ensure all matrices become sparse when as_sparse=TRUE.
- Generalize to matrices of any name.
- fix_celltype_names:
- Ensure all celltype names are unique after standardization.
Changes in version 1.5.3
New features
- genelistSpecies now passed to prepare_genesize_control_network in
bootstrap_enrichment_test meaning gene list species will be inferred
from user input.
Changes in version 1.5.2
New features
- drop_uninformative_genes:
- Expose new args: dge_method, dge_test, min_variance_decile
- merged_ctd: Actually merge the CTDs into one when as_SCE=FALSE.
Bug fixes
- Remove hard-coded file path separators (e.g.
sprintf("%s/MRK_List2.rpt", tempdir())) to be more compatible with
Windows.
Changes in version 1.5.1
New features
- Made substantial updates to orthogene, so going through and making
sure everything still works / is able to take advantage of new
features (e.g. separation of non121_strategy and agg_func args,
many:many mapping):
- filter_nonorthologs: Pass up args from
orthogene::convert_orthologs.
- generate_celltype_data: @inheritDotParams
- Update GHA.
- Bump to R (>= 4.2) now that we're developing on Bioc 3.16.
Bug fixes
- Avoid downloading large "MRK_List2.rpt" file any more than is
necessary for testing.
Changes in version 1.3.3
New features
- method argument from orthogene::create_background and
orthogene::convert_orthologs is now passed up as an argument to EWCE
functions to give users more control. "homologene" chosen as default
for all functions. "homologene" has fewer species than "orthogene"
but doesnt need to import data from the web. It also has more 1:1
mouse:human orthologs.
- Include notes on mismatches between GitHub documentation and current
Bioc release version.
- Allow bin_specificity_into_quantiles to set specificity matrix name
produced.
- Merge GHA workflow yamls into one.
Bug fixes
- Add try({}) and error=TRUE to avoid "polygon edge not found" error
in vignettes.
Changes in version 1.3.1
New features
- Major changes: Pull Request from bschilder_dev branch.
- All functions can now use lists and CellTypeDatasets (CTD) from any
species and convert them to a common species (human by default) via
orthogene.
- Automated CTD standardisation via standardise_ctd.
- Can handle (sparse) matrices.
- Can create CTD from very large datasets using DelayedArray object
class.
- All functions automatically create appropriate gene backgrounds
given species.
- More modular, simplified vignettes.
- Additional gene pre-filtering options (DESeq2, MAST, variance
quantiles).
- New/improved plotting functions (e.g. plot_ctd).
- Added example bootstrapping enrichment results as extdata to speed
up examples (documented in data.R). Accessed via
EWCE::example_bootstrap_results().
- Replaced GHA workflow with check-bioc to automatically: run R-CMD
checks, run BiocCheck, and rebuild/deploy pkgdown site.
- Parallelised functions:
- drop_uninformative_genes
- generate_celltype-data
- bootstrap_enrichment_test
- Added tests (multiple functions tests per file to reduce number of
times ewceData files have to be downloaded):
- test-DelayedArray
- test-merge_sce
- test-get_celltype_table
- test-list_species
- test-run_DGE
- test-check_percent_hits
- Added function is_32bit() to all tests to ensure they don't get run
twice on Windows OS.
- Added GitHub Actions workflows:
- check-bioc-docker.yml: Runs CRAN/Bioc checks, rebuilds and
pushes pkgdown website, runs and uploads test coverage report,
- dockerhub.yml: Builds Bioconductor Docker container with EWCE
installed, runs CRAN checks and (if checks are successful)
pushes container to neurogenomicslab DockerHub.
- Removed docs folder, as the documentation website comes from the
gh-pages branch now, and is automatically built by GHA workflow
after each push to main branch.
- Added new exported function fix_celltype_names to help with
standardising celltype names in alignment with standardise_ctd.
- generate_bootstrap_plots_for_transcriptome: Now supports any species
(not just mouse or human).
- Converts CTD and DGE table (tt) into output_species gene
symbols.
- Automatically generates appropriate gene background.
- Faster due to now having the option to only generate certain
plot types.
- Provide precomputed results from ewce_expression_data via new
example_transcriptome_results function.
- Reduced build runtime and oversized vignettes by not evaluating
certain code chunks.
- Prevent extended vignette from running entirely.
- @return documentation for internal functions.
- Added more installation checks to GHA.
- Fixed inconsistent naming of unit test files: test_ ==> test-
- Removed DGE args in drop_uninformative_genes for now until we run
benchmarking to see how each affects the EWCE results.
- Make bootstrap_plots function internal.
- Add report on how orthogene improve within- and across-species gene
mappings in extended vignette.
- Record extra info in standardise_ctd output:
- "species": both input_species and output_species
- "versions": of EWCE, orthogene, and homologene
Changes in version 1.0.0
New features
- EWCE v1.0 on Bioconductor replaces the defunct EWCE v1.3.0 available
on Bioconductor v3.5.
- EWCE has been rendered scalable to the analysis of large datasets
- drop_uninformative_genes() has been expanded to allow the
utilisation of differential expression approaches
- EWCE can now handle SingleCellExperiment (SCE) objects or other
Ranged SummarizedExperiment (SE) data types and as input as well as
the original format, described as a single cell transcriptome (SCT)
object.
Deprecated & Defunct
- The following functions have been renamed to use underscore in
compliance with Bioconductor nomenclature:
- check.ewce.genelist.inputs
- cell.list.dist
- bootstrap.enrichment.test
- bin.specificity.into.quantiles
- bin.columns.into.quantiles
- add.res.to.merging.list
- prepare.genesize.control.network
- prep.dendro
- get.celltype.table
- calculate.specificity.for.level
- calculate.meanexp.for.level
- generate.celltype.data
- generate.bootstrap.plots
- generate.bootstrap.plots.for.transcriptome
- fix.bad.mgi.symbols
- fix.bad.hgnc.symbols
- filter.genes.without.1to1.homolog
- ewce.plot
- cells.in.ctd
- drop.uninformative.genes