- #34 Extra argument
group_byinfoldchange.
- #33 Combined two methods into a single
omics$scale(), added euclidean method and aitchison. Improved all dissimilarity metrics (except for UniFrac) by 2x speed & 7x less memory, UniFrac is 4x faster. - #36 Created
foldchangemethod inomicsabstract class and inmetagenomicssubclass - Adapted & tested
autoFlowwith new changes
- #36 Moved
foldchangefrom namespace toomics$foldchangeandmetagenomics$foldchange
- Extended unit-tests to uncovered code sections.
- Added error handling when none
SAMPLE_IDs are matching duringprivate$sync
- #31
colormapdoesn't return any NAs. - #30 Placed
FEATURE_IDas first column. - #29 replaced
position_nudgewithposition_jitter - foldchange was matching sub-strings, fixed by changing it to exact matching.
- #23 active bindings on data types, in place modification and automatic synchronisation between other data types by default via private function
sync. - #23
featureDatais now always created as placeholder.
- #23 omics classes are now cloneable.
- #23
removeZeros()function is now private. - #26 clarified
initializeand field tags. - #27 Both
denseMatrixassparseMatrixare converted toCsparseMatrix, compatible toomics$normalize,omics$feature_merge,diversity,hill_taxaandC-functions. - Replaced
tmp_linkandtmp_restorewith inline code. Seems likeprivate$.countDatadoesn't work with a private function. - Improved the
cliformatting and visualisation of different arguments. print()inherited for each sub-class fromomicsand usescli::cli_informinstead ofcat- #21 introduced custom half boxplot/point in
diversity_plot, now also addedgroup_byto perform grouped statistical tests. - Replaced
read_rarefraction_qiimebycheck_tablefrom private function of classomics. autoFlowcompatible to denseMatrix formats, applies fdr correction in other omics layers, report can be set to False, removednmds.
- #25 changed default value of
initializefunction.
- Removed
tmp_restoreandtmp_link - Utils function
read_rarefraction_qiime
geom_boxplotglobal function note for CRAN
- #20
rankstathas now anuniqueoption.
- #22
private$check_matrixchecks if any zero's are present before creating asparseMatrix. - #20
omics$compositonDoesn't showOtherswhen there are none. - #24
volcano_plotonly sizes the points if there are significant features found.
- #21 Removed
gghalvesindiversity_plot
- #14
unifracfor both weighted/unweighted and normalized options. - #14
brayfor both weighted/unweighted options. - #14
jaccardfor both weighted/unweighted options. - #14
jsdfor both weighted/unweighted options. - #14
cosinefor both weighted/unweighted options. - #14
canberrafor both weighted/unweighted options. - #14
manhattanfor both weighted/unweighted options. omics$distanceas wrapper for all new dissimilarity metrics.- #18
pairwise_adonis2andpairwise_anosimnow allow custom permutation designs frompermuteR package. - Unit tests for dissimilarity metrics
metagenomicsandproteomicsclasses now align the countData (rows) and featureData by the treeData tip.labels.omics$ordinationuses nowomics$distanceto compute dissimilarity metrics (previously computed viarbiom).- Example data loaded from
inst/extdatainstead of re-usingmock.rdsobject.
- #15 Fixed flipped log2 values when condition A or B is zero.
- #17 Docker is built via
pakfrom github instead of CRAN.
- #13 Removed
viridisdependency,purrr:mapis replaced bylapply - Removed
rbiomand it's dependencyslam.
testthatremoved autoflow test
- rhub yaml to check for additional platforms
testthatnow uses seed &tempdir()to meet CRAN policyreport.mdnow also displays volcano plotsomics$autoFlow()saves report html in correct current path
- Docker support for R package
autoflow#10
autoFlowandreport.mdnow contain downloadable data #11- Renamed
feature_glomtofeature_merge - Added
@returnsdocumentation in manuals - Updated
citations.md - Finalized
readme.md
- working directory is set to current working directory in
rmarkdown::render(compatible in docker/bioconda etc.)
- Included github actions workflow for
covrcode coverage and R CMD build check. - github MIT license
- created folder
inst/extdatawith test data
- testthat now only checks presence of
write_biomandautoFlowfiles. - All other testthat functions are replaced by snapshot testing, issues #2 and #3
on.exitnow solves issue during error occurance that class items are changed, issue #3.
- included
execfolder withautoFlow.Rfunction to be called from the command line #8. - New
privatefunctionscheck_matrixandcheck_tablefor loading of files or existing data structures, issue #6.
autoFlow.Rnow has option to select sub-class from the command line.
- included
instfolder withreport.Rmdandcss.styles autoFlownow automatically loadsreport.Rmdfrominstfolder #3.- Test displayed on plots changes based on boolean paired value.
- refactoring of
autoflow, handles now both paired and unpaired data #3. combine_conditionsautomatically check if comparison is significant and updates the list with new conditions.- updated manuals
foldchange.Rnow handles zero's and doesn't return Inf values
volcano_plotnow offers option to visualize only abundant bacteria
- Wrong order of normalization and feature aggregation #7
- Improved regex pattern in json file, now checks and doesnt allow for spaces.
- removed personal files, cleaned up directory.
- Included
@examplesin documentation #4.
- Created a
citation.mdfor all used R packages in bibtex format - Added more error handling and documentation to functions/methods #2.
- Updated documentation, manual #2
- Removed non-used functions
- created
column_existfor efficient error handling of missing/empty columns in tables
write_biomis now functional and tested compared to python APIbiom-format.feature_filteris not compatible with newer version offeature_glomfeatureDatanow replaces empty strings with NA, compatible withmetaData.
write_biomis now functional and tested compared to python APIbiom-format
samplepair_subsetfinds automatically pairs and subsets class.- created metadata validation based on json schema, function
validate. - additional error handling is added with cli R package.
metataxonomicsis now calledmetagenomicssub-class, supports both hdf5, json formats.metagenomicsclass first loadsomicsclass and then fills up any additional information.- ordination plot now only shows ecclipses on T distribution.
- Removed
find_pairs
unpaired_foldandpaired_foldare now combined into a single functionfoldchange.
- Removed
doParallelandforeachfrom foldchange computation.
feature_glomnow handles multiple columns or single ones.metataxonomicssub-class now automatically renames the last taxonomy columns.
read_sparseTablenow efficiently reads in tsv, txt, csv, url or compressed files cleans it before creating asparseMatrix
- error-handling for treeData
- Extra check for metadata & countdata alignment based of sample-ids
- Improved visualizations of triplot, using ggplot functions
toolsclass is now calledomicsclass.diversity_plotnow only shows significant pvalues, supports p.adjust methods
feature_glomcan now be repeated multiple times without throwing an error.- Replaced
ggpubr::compare_meansbyrstatix::pairwise_wilcox_test, makes it more flexible.
- Created new
preoteomics-class.R - Added basic
clierror-handling in abstract class
- Labelling issue of features in
feature_glom. More robust and equal fast method.
- Finalized docker image for
autoFlow.R, placed it on docker hub.
- autoflow now takes optionally pre-computed alpha or beta diversity in table format.
- Added documentation to all functions based on
roxygen2requirements. - Created
write_biomfunction in sub-classmetataxonomics
- Finalised autoFlow.R standalone function, with docker image
differential_feature_expressionnow usessparseMatrix- Updated manuals
- Error handling in
toolsclass - autoFlow now handles missing data, including all other methods of
toolsclass
- Created
hill_taxa.Rthat implementssparseMatrix.
- Finalised autoFlow.R standalone function, with docker image
differential_feature_expressionnow usessparseMatrix
- Created new
diversityfunction that usessparseMatrixand uses 5x less memory.
- Removed
vegan::diversity
- countData class item now uses
sparseMatrixinstead ofdata.table
testthatR scripts for metataxonomics-class.R
- improved
removeZerosfor efficiency.
- Test data
- included documentation, focused on creating an R package
- alpha_diversity uses
ggpubrR package - Improved visualizations in
differential_feature_expression
- created a
fetch_colorsfunction to get setNames fromRColorBrewer.
- renamed shannon to
alpha_diversity, more options for shannon metrics
- added dockerfile to use autoFlow
- Replaced single R scripts for
autoFlow-class.R - Applied
foreachparallel in foldchange computation
- Removed single R scripts for automated analysis
- Added private functions within tools class;
original_data,tmp_linkandtmp_restore. Prevents modifications of tools components.
- Created a new foldchange plot that replaces DFE_plot
- Created
differential_feature_expressionwithintoolsclass - Created a volcano_plot
- Created
tools-class.R
- Removed deprecated phyloseq functions
- Removed DFE_plot
- Created a tools abstract class based on R6 OOP method, which uses
data.tablefor efficiency. - Created function
removeZeroswithin classtools. - Created function
feature_subsetwithin classtools. - Created function
sample_subsetwithin classtools. - Created function
feature_glomwithin classtools. - Created function
transformwithin classtools. - Created function
compositionwithin classtools. - Created function
shannonwithin classtools. - Created function
rankstatwithin classtools. - Created function
ordinationwithin classtools. - Differential Feature Analysis plot;
fold_plot.R - Started with
metataxonomicssub-class for 16S metagenomics data - Created
print()similar to Phyloseq - Created a
reset()to undo changes - Created a private
generate_matrixfrom a biom file. - Created an utils folder of new graph functions for
composition_plot,ordination_plot,paired_fold,stats_plot,unpaired_fold