Releases | Open Source Science

What's Changed

Features

Feature/imd anova model selection by @clabornd in https://github.com/pmartR/pmartR/pull/338: Users can now specify imd_anova to use only the full or reduced model in 2-way ANOVA via the model_selection argument.
add sum rollup by @rarichardson92 in https://github.com/pmartR/pmartR/pull/346: protein_rollup has a new 'sum' option for the combination function.
Expand combine_lipidData by @rarichardson92 in https://github.com/pmartR/pmartR/pull/348: combinelipidData is now `combineomicsDataand can handle bothlipidDataandmetabData` objects.
Update to SPANS results plot to include percentage of biomolecules by @rarichardson92 in https://github.com/pmartR/pmartR/pull/350

Bugfixes/Tidying

check.names = F on all data.frame calls by @rarichardson92 in https://github.com/pmartR/pmartR/pull/335
Bugfix/dimres and docs by @clabornd in https://github.com/pmartR/pmartR/pull/337
V2.5.0 by @clabornd in https://github.com/pmartR/pmartR/pull/339
Bugfix/volcano join by @clabornd in https://github.com/pmartR/pmartR/pull/342
Update vignette by @rarichardson92 in https://github.com/pmartR/pmartR/pull/344
Fix breaking plots with checkable sample names by adding check.names … by @clabornd in https://github.com/pmartR/pmartR/pull/347

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.6...v2.5.0

- R
Published by clabornd 11 months ago

What's Changed

Features

Feature/imd anova model selection by @clabornd in https://github.com/pmartR/pmartR/pull/338: Users can now specify imd_anova to use only the full or reduced model in 2-way ANOVA via the model_selection argument.
add sum rollup by @rarichardson92 in https://github.com/pmartR/pmartR/pull/346: protein_rollup has a new 'sum' option for the combination function.
Expand combine_lipidData by @rarichardson92 in https://github.com/pmartR/pmartR/pull/348: combinelipidData is now `combineomicsDataand can handle bothlipidDataandmetabData` objects.

Bugfixes/Tidying

check.names = F on all data.frame calls by @rarichardson92 in https://github.com/pmartR/pmartR/pull/335
Bugfix/dimres and docs by @clabornd in https://github.com/pmartR/pmartR/pull/337
V2.5.0 by @clabornd in https://github.com/pmartR/pmartR/pull/339
Bugfix/volcano join by @clabornd in https://github.com/pmartR/pmartR/pull/342
Update vignette by @rarichardson92 in https://github.com/pmartR/pmartR/pull/344
Fix breaking plots with checkable sample names by adding check.names … by @clabornd in https://github.com/pmartR/pmartR/pull/347

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.6...v2.5.0

- R
Published by clabornd 11 months ago

pmartr - v2.5.0

Main change is in #338. Users can now specify imd_anova to use only the full or reduced model in 2-way ANOVA via the model_selection argument.

What's Changed

check.names = F on all data.frame calls by @rarichardson92 in https://github.com/pmartR/pmartR/pull/335
Bugfix/dimres and docs by @clabornd in https://github.com/pmartR/pmartR/pull/337
Feature/imd anova model selection by @clabornd in https://github.com/pmartR/pmartR/pull/338

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.6...v2.5.0

- R
Published by clabornd about 1 year ago

What's Changed

Bugfixes

fix hard-coded column in cv_filter by @clabornd in https://github.com/pmartR/pmartR/pull/324
Bugfix/arm64 fp by @clabornd in https://github.com/pmartR/pmartR/pull/325
protein_quant error on biomolecules with no observations by @clabornd in https://github.com/pmartR/pmartR/pull/323
Catch main_effects named vector bug by @rarichardson92 in https://github.com/pmartR/pmartR/pull/329
Update applyFilt.R by @rarichardson92 in https://github.com/pmartR/pmartR/pull/330
Fix bad key reference in development version of Bioconductor/edgeR by @clabornd in https://github.com/pmartR/pmartR/pull/331

Documentation

add CONTRIBUTING.md [skip ci] by @clabornd in https://github.com/pmartR/pmartR/pull/320

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.5...v2.4.6

- R
Published by clabornd over 1 year ago

pmartr - Version 2.4.5

Miscellaneous bugfixes plus a new [0-1] normalization option (see PRs).
Fixes to noSuggests errors on CRAN
add rhub workflow file

What's Changed

Update seqData_wrappers.R by @rarichardson92 in https://github.com/pmartR/pmartR/pull/316
Fix gtest heatmap incorrectly showing no significance, other issues by @clabornd in https://github.com/pmartR/pmartR/pull/314
Feature/range scaling norm by @rarichardson92 in https://github.com/pmartR/pmartR/pull/311
proteinquant: combine different emetacols values mapping to a protein by @evanglass in https://github.com/pmartR/pmartR/pull/308
dont apply imdanovafilter to check for filtered molecules in imdanova by @clabornd in https://github.com/pmartR/pmartR/pull/319

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.4...v2.4.5

- R
Published by clabornd almost 2 years ago

pmartr - Version 2.4.5

Miscellaneous bugfixes plus a new [0-1] normalization option (see PRs).
Fixes to noSuggests errors on CRAN
add rhub workflow file

What's Changed

Update seqData_wrappers.R by @rarichardson92 in https://github.com/pmartR/pmartR/pull/316
Fix gtest heatmap incorrectly showing no significance, other issues by @clabornd in https://github.com/pmartR/pmartR/pull/314
Feature/range scaling norm by @rarichardson92 in https://github.com/pmartR/pmartR/pull/311
proteinquant: combine different emetacols values mapping to a protein by @evanglass in https://github.com/pmartR/pmartR/pull/308
dont apply imdanovafilter to check for filtered molecules in imdanova by @clabornd in https://github.com/pmartR/pmartR/pull/319

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.4...v2.4.5

- R
Published by clabornd almost 2 years ago

Pending merge of #318 which adds rhub workflows and fixes noSuggests failures/NOTE's related to #314

What's Changed

Update seqData_wrappers.R by @rarichardson92 in https://github.com/pmartR/pmartR/pull/316
Fix gtest heatmap incorrectly showing no significance, other issues by @clabornd in https://github.com/pmartR/pmartR/pull/314
Feature/range scaling norm by @rarichardson92 in https://github.com/pmartR/pmartR/pull/311

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.4...v2.4.5

- R
Published by clabornd almost 2 years ago

pmartr - Version 2.4.4

NOTE: Skipped 2.4.3 due to problems with CRAN submission.

New Features

Add transcriptomics plots to trelliscope plots by @David-Degnan in https://github.com/pmartR/pmartR/pull/295
add threshold argument to edata_replace by @clabornd in https://github.com/pmartR/pmartR/pull/306

Bugfixes and Package Misc.

Fix bad corRes plot when sample names have dashes by @evanglass in https://github.com/pmartR/pmartR/pull/300
Fix problems with rmd_filter on object with only singletons by @evanglass in https://github.com/pmartR/pmartR/pull/301
Fix wrong gsub in volcano plot causing duplicated points and bad labels by @clabornd in https://github.com/pmartR/pmartR/pull/305
fix na-res scatterplot for singleton group datasets [skip ci] by @clabornd in https://github.com/pmartR/pmartR/pull/307
Move plotly to suggests by @evanglass in https://github.com/pmartR/pmartR/pull/299
add CRAN badge, add disclaimer about BioConductor repos to README by @clabornd in https://github.com/pmartR/pmartR/pull/303

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.2...v2.4.4

- R
Published by clabornd about 2 years ago

What's Changed

Fix bad corRes plot when sample names have dashes by @evanglass in https://github.com/pmartR/pmartR/pull/300
Fix problems with rmd_filter on object with only singletons by @evanglass in https://github.com/pmartR/pmartR/pull/301
Move plotly to suggests by @evanglass in https://github.com/pmartR/pmartR/pull/299
add CRAN badge, add disclaimer about BioConductor repos to README by @clabornd in https://github.com/pmartR/pmartR/pull/303
Add transcriptomics plots to trelliscope plots by @David-Degnan in https://github.com/pmartR/pmartR/pull/295
Fix wrong gsub in volcano plot causing duplicated points and bad labels by @clabornd in https://github.com/pmartR/pmartR/pull/305
add threshold argument to edata_replace by @clabornd in https://github.com/pmartR/pmartR/pull/306
fix na-res scatterplot for singleton group datasets [skip ci] by @clabornd in https://github.com/pmartR/pmartR/pull/307

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.2...v2.4.3

- R
Published by clabornd about 2 years ago

What's Changed

Fix bad corRes plot when sample names have dashes by @evanglass in https://github.com/pmartR/pmartR/pull/300
Fix problems with rmd_filter on object with only singletons by @evanglass in https://github.com/pmartR/pmartR/pull/301
Move plotly to suggests by @evanglass in https://github.com/pmartR/pmartR/pull/299
add CRAN badge, add disclaimer about BioConductor repos to README by @clabornd in https://github.com/pmartR/pmartR/pull/303
Add transcriptomics plots to trelliscope plots by @David-Degnan in https://github.com/pmartR/pmartR/pull/295
Fix wrong gsub in volcano plot causing duplicated points and bad labels by @clabornd in https://github.com/pmartR/pmartR/pull/305
add threshold argument to edata_replace by @clabornd in https://github.com/pmartR/pmartR/pull/306
fix na-res scatterplot for singleton group datasets [skip ci] by @clabornd in https://github.com/pmartR/pmartR/pull/307

Full Changelog: https://github.com/pmartR/pmartR/compare/v2.4.2...v2.4.3

- R
Published by clabornd about 2 years ago

This is the first stable version on CRAN (resubmit of 2.4.1 to fix some errors in automated checks), go ahead and install.packages("pmartR"). Binaries are also available for certain R versions and operating systems: https://cran.r-project.org/web/packages/pmartR/index.html

Features

imd_anova now reports the least squares means (aka the estimated marginal means, see the emmeans package) #290 . See the updated "Statistical Analysis with the pmartR Package" article.

Bugfixes

Fixed imd_anova not handling imbalanced covariates correctly #290
The proteomics filter now has an order to it: First the degenerate peptides are removed, then proteins without min_num_peps peptides mapping to them are removed. This matters since the removal of degenerate peptides may affect which proteins pass the min_num_peps threshold. #291
Fixed G-test heatmap plot (option plot_type = 'gheatmap' in plot.statRes) incorrectly ordering axes. #289
Fixed problem with volcano plots #285
Various fixes to trelliscope functionality #284
Fix sample id issue with plot.dimRes #280

- R
Published by clabornd about 2 years ago

pmartr - Version 2.4.0

Features

More options for plot.naRes and plot.dimRes
- Each can color by the grouping factor as well as any columns in f_data
- plot.naRes can plot count or proportion missing (or non-missing)
- color_by and shape_by options for plot.dimRes
Trelliscope plots:
- Option to filter panels by p-value, see ?trelli_pvalue_filter
- Small changes to some plots and summary functions

Bugfixes

Zeros in the data all shared rows with an NA caused pre-flight filtering to remove too many rows #243
Removed version dependent purrr:: call in pre_flight #246
Applying two sample filters that removed the same sample erased object #245
Error in g-test heatmap when there were no significant biomolecules #271
Make legend order alphabetical on boxplots and other orderable plots #274
Incorrect titles in some plots, suggesting data was reference or global normalized when it was not #277

- R
Published by clabornd over 2 years ago

pmartr - Version 2.3.0

Added RNA-seq data as an omicsData type:
- Has associated analysis methods DESeq2, limma-VOOM, and edgeR
- Diagnostic tests and associated plots
- RNA-seq specific filters totalcountFilt and RNAFilt
API for trelliscope displays. Create trelliscope displays directly from omicsData objects with a wide choice of plot types. See the vignette on Trelliscope for details.
Added pvalue adjustment for biomolecules "FDR adjustment". In imd_anova, the arguments pval_adjust_a_multcomp and pval_adjust_g_multcomp now adjust p-values for multiple comparisons within each biomolecule for the anova and g-test. pval_adjust_a_fdr/pval_adjust_g_fdr perform p-value adjustment across all biomolecules.

- R
Published by clabornd over 2 years ago

pmartr - Version 1.0.0

Incrementing version number to 1.0.0 from 0.10.0

- R
Published by lmbramer almost 4 years ago

Recent Releases of pmartr

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Features

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Pending merge of #318 which adds rhub workflows and fixes noSuggests failures/NOTE's related to #314

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