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... to be passed to
pairwise_adonis and pairwise_anosim (.e.g.
parallel = 10 can be called now).tryCatch and better error handling in
omics$sample_subset, omics$feature_subset and
omics$samplepair_subset.R/dependencies.R file as placeholder to prevent
NAMESPACE declaration issue by R6 class (reducing namespace
imports).is.color internal util function to check for
valid color input.pairwise_test as an util that uses
matrixTests functions, and implements t.test,
t.equalvar and wilcox with paired option.roxygen2 code, documentation
style and error handling.jsonlite by yyjsonr
functionality, much faster and cleaner code.tests/testthat/input/metagenomics/biom_with_taxonomy_json.biom
with one from BIOM v2 example.foldchange into omics and option
to use different fold-change computations via argument
method and aggregate_method.ggpubr by ggplot2 functions in
diversity_plot.rstatix by inbuilt
pairwise_wilcox_test, added also tests for the util."groups" to
actual col_name in omics$ordinationcountData to handle data.tables with
both feature and sample columns.omics$validate() from public to private, since it
is only used as an internal function in $new()omics$feature_merge is optional in
omics$foldchangeomics$removeNAs uses stats::complete.cases
instead of na.omitmetagenomics when
biomData is used.feature_names in metagenomics that do not
match supplied taxonomies are automatically removed.
FEATURE_ID is fixed as first column.diversity_plot is replaced by
stats_boxplot. The original diversity_plot is
scheduled for deprecation.col_name to be replaced by groups in
composition_plot, colormap,
boxjitter_test, omics$alpha_diversitycol_name to be replaced by add_cols in
omics$compositiongroup_by to be replaced by split_by in
omics$foldchange, omics$alpha_diversity and
boxjitter_test.method for labelling is removed in
boxjitter_plot, instead an argument test can
be specified to perform a pairwise statistcal tests on the
groups.group_by in foldchange.omics$scale(), added
euclidean method and aitchison. Improved all dissimilarity metrics
(except for UniFrac) by 2x speed & 7x less memory, UniFrac is 4x
faster.foldchange method in omics abstract
class and in metagenomics subclassautoFlow with new changesfoldchange from namespace to
omics$foldchange and
metagenomics$foldchangeSAMPLE_IDs are matching
during private$synccolormap doesn’t return any NAs.FEATURE_ID as first column.position_nudge with
position_jittersync.featureData is now always created as placeholder.removeZeros() function is now private.initialize and field tags.denseMatrix as sparseMatrix are converted
to CsparseMatrix, compatible to
omics$normalize, omics$feature_merge,
diversity, hill_taxa and
C-functions.tmp_link and tmp_restore with
inline code. Seems like private$.countData doesn’t work
with a private function.cli formatting and visualisation of
different arguments.print() inherited for each sub-class from
omics and uses cli::cli_inform instead of
catdiversity_plot, now
also added group_by to perform grouped statistical
tests.read_rarefraction_qiime by
check_table from private function of class
omics.autoFlow compatible to denseMatrix formats, applies fdr
correction in other omics layers, report can be set to False, removed
nmds.initialize function.tmp_restore and tmp_linkread_rarefraction_qiimegeom_boxplot global function note for CRANrankstat has now an unique option.private$check_matrix checks if any zero’s are present
before creating a sparseMatrix.omics$compositon Doesn’t show Others when
there are none.volcano_plot only sizes the points if there are significant
features found.gghalves in diversity_plotunifrac for both weighted/unweighted and normalized
options.bray for both weighted/unweighted options.jaccard for both weighted/unweighted options.jsd for both weighted/unweighted options.cosine for both weighted/unweighted options.canberra for both weighted/unweighted options.manhattan for both weighted/unweighted options.omics$distance as wrapper for all new dissimilarity
metrics.pairwise_adonis2 and pairwise_anosim now allow
custom permutation designs from permute R package.metagenomics and proteomics classes now
align the countData (rows) and featureData by the treeData
tip.labels.omics$ordination uses now omics$distance
to compute dissimilarity metrics (previously computed via
rbiom).inst/extdata instead of
re-using mock.rds object.pak from github instead of CRAN.viridis dependency, purrr:map is
replaced by lapplyrbiom and it’s dependency
slam.testthat removed autoflow testtestthat now uses seed & tempdir() to
meet CRAN policyreport.md now also displays volcano plotsomics$autoFlow() saves report html in correct current
pathautoflow #10autoFlow and report.md now contain
downloadable data #11feature_glom to feature_merge@returns documentation in manualscitations.mdreadme.mdrmarkdown::render (compatible in docker/bioconda etc.)covr code coverage
and R CMD build check.inst/extdata with test datawrite_biom and
autoFlow files.on.exit now solves issue during error occurance that
class items are changed, issue #3.exec folder with autoFlow.R
function to be called from the command line #8.private functions check_matrix and
check_table for loading of files or existing data
structures, issue #6.autoFlow.R now has option to select sub-class from the
command line.inst folder with report.Rmd and
css.stylesautoFlow now automatically loads
report.Rmd from inst folder #3.autoflow, handles now both paired and
unpaired data #3.combine_conditions automatically check if comparison is
significant and updates the list with new conditions.foldchange.R now handles zero’s and doesn’t return Inf
valuesvolcano_plot now offers option to visualize only
abundant bacteria@examples in documentation #4.citation.md for all used R packages in bibtex
formatcolumn_exist for efficient error handling of
missing/empty columns in tableswrite_biom is now functional and tested compared to
python API biom-format.feature_filter is not compatible with newer version of
feature_glomfeatureData now replaces empty strings with NA,
compatible with metaData.write_biom is now functional and tested compared to
python API biom-formatsamplepair_subset finds automatically pairs and subsets
class.validate.metataxonomics is now called metagenomics
sub-class, supports both hdf5, json formats.metagenomics class first loads omics class
and then fills up any additional information.find_pairsunpaired_fold and paired_fold are now
combined into a single function foldchange.doParallel and foreach from
foldchange computation.feature_glom now handles multiple columns or single
ones.metataxonomics sub-class now automatically renames the
last taxonomy columns.read_sparseTable now efficiently reads in tsv, txt,
csv, url or compressed files cleans it before creating a
sparseMatrixtools class is now called omics
class.diversity_plot now only shows significant pvalues,
supports p.adjust methodsfeature_glom can now be repeated multiple times without
throwing an error.ggpubr::compare_means by
rstatix::pairwise_wilcox_test, makes it more flexible.preoteomics-class.Rcli error-handling in abstract classfeature_glom. More
robust and equal fast method.autoFlow.R, placed it on
docker hub.roxygen2
requirements.write_biom function in sub-class
metataxonomicsdifferential_feature_expression now uses
sparseMatrixtools classtools classhill_taxa.R that implements
sparseMatrix.differential_feature_expression now uses
sparseMatrixdiversity function that uses
sparseMatrix and uses 5x less memory.vegan::diversitysparseMatrix instead of
data.tabletestthat R scripts for metataxonomics-class.RremoveZeros for efficiency.ggpubr R packagedifferential_feature_expressionfetch_colors function to get setNames from
RColorBrewer.alpha_diversity, more options for
shannon metricsautoFlow-class.Rforeach parallel in foldchange computationoriginal_data, tmp_link and
tmp_restore. Prevents modifications of tools
components.differential_feature_expression within
tools classtools-class.Rdata.table for efficiency.removeZeros within class
tools.feature_subset within class
tools.sample_subset within class
tools.feature_glom within class
tools.transform within class
tools.composition within class
tools.shannon within class
tools.rankstat within class
tools.ordination within class
tools.fold_plot.Rmetataxonomics sub-class for 16S
metagenomics dataprint() similar to Phyloseqreset() to undo changesgenerate_matrix from a biom
file.composition_plot, ordination_plot,
paired_fold, stats_plot,
unpaired_foldThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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