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Allowed labeling plots with ability to filter labels by p-value
antonvsdata
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Jul 12, 2022
Co-authored-by: Anton Klåvus <anton.klavus@iki.fi>
antonvsdata
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Jul 14, 2022
attlih
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Aug 29, 2022
* bug fix: impute_simple succeeds when only one feature satifies NA limit * Updated logging (#6) * Add factor check to pairwise t-test (#11) * Update logging (#8) * Update logging Updated stats.R logging. * Updated logging Removed unnecessary comments * Updated logging Removed more unnecessary comments * Update logging Error messages are now logged in the log file * Update logging Fixed mentioned issues * Update to mz/rt plot and data reading (#7) * Updated mz/rt plot Added feature to filter plot by p-values and to drop low quality features from the plot for MetaboSet object. Added feature to set title and subtitle to the plot. * Updated data reading Function now checks for unique feature IDs and that mz/rt values make sense. Added feature to specify ID column from the excel file. * Fixed commented things Asked changes made, all seem reasonable. * Minor fix to scatter.R Fixed plotter function to always having data frame as input. * Check QC column for missing values * Create dummy injection order When merging, dummy injection order is created if injection orders differ between modes * Warn if QC contains NAs Checks that QC column doesn't contain NAs * Skip mz/rt limit check when validating MetaboSet * Added tests for changing feature/sample names * Approved suggestion * Update volcano plot (#10) * Update volcano plot Allowed labeling plots with ability to filter labels by p-value * Approve suggestion Code follows notame syntax * Update volcano plot labeling (#16) * Update volcano plot Allowed labeling plots with ability to filter labels by p-value * Approve suggestion Co-authored-by: Anton Klåvus <anton.klavus@iki.fi> * Update volcano plot Label visualization is now clean Co-authored-by: Anton Klåvus <anton.klavus@iki.fi> * Fix correlation test argument (#15) ... arguments will now be passed to cor.test() * Update .Rd files (#13) I noticed these won't update automatically * Enabled pairwise paired t-tests * Add stats cleaning function (#12) * Stats cleaning function * Enabled column renaming * Fix dummy injection error (#19) dummy_injection was not found during merging if x was already merged * Fixed bug in pairwise t-tests * Add PERMANOVA (#9) * Add PERMANOVA Basic wrapper for package called PERMANOVA. * Minor fixes Fixed one argument name and documentation * Fix test_logging (#18) * Fix test_logging expect_null didn't work * Add tests for logging * Update Cohen's D (#14) * Update Cohen's D Cohen's D can now be counted to all groups and time points at once * Minor fixes * Fixed tests to match new commits Fixed hardcoded values in tests, known warnings in testing and group order in log messages when calculating Cohen's D * Changed column names in tests Changed column names in tests to match new style * Changed column names Changed column names to match new uniform style * Changed column names in functions Changed column names in t-tests, Cohen's D and fold change to match new uniform style. Linear models do not follow that style. * Cleaned code * Updated dependencies * Fixed bugs (#20) * Fixed tests to match new commits Fixed hardcoded values in tests, known warnings in testing and group order in log messages when calculating Cohen's D * Changed column names in tests Changed column names in tests to match new style * Changed column names in functions Changed column names in t-tests, Cohen's D and fold change to match new uniform style. Linear models do not follow that style. * Cleaned code * Updated dependencies * Updated manuals and examples * Removed BatchCorrMetabolomics dependency As it's not updated regularly * Enabled pairwise paired t-tests (#17) * Enabled pairwise paired t-tests * Changed column names Changed column names to match new uniform style * Updated warning handling when testing * Updated Cohen's d error handling * Updated volcano plot example * Updated Cohen's D error handling and other minor changes (#23) * Updated warning handling when testing * Updated Cohen's d error handling * Updated volcano plot example * Version 0.1.0 Co-authored-by: Anton Klåvus <anton.klavus@iki.fi>
antonvsdata
added a commit
that referenced
this pull request
Jan 21, 2023
* bug fix: impute_simple succeeds when only one feature satifies NA limit * Updated logging (#6) * Add factor check to pairwise t-test (#11) * Update logging (#8) * Update logging Updated stats.R logging. * Updated logging Removed unnecessary comments * Updated logging Removed more unnecessary comments * Update logging Error messages are now logged in the log file * Update logging Fixed mentioned issues * Update to mz/rt plot and data reading (#7) * Updated mz/rt plot Added feature to filter plot by p-values and to drop low quality features from the plot for MetaboSet object. Added feature to set title and subtitle to the plot. * Updated data reading Function now checks for unique feature IDs and that mz/rt values make sense. Added feature to specify ID column from the excel file. * Fixed commented things Asked changes made, all seem reasonable. * Minor fix to scatter.R Fixed plotter function to always having data frame as input. * Check QC column for missing values * Create dummy injection order When merging, dummy injection order is created if injection orders differ between modes * Warn if QC contains NAs Checks that QC column doesn't contain NAs * Skip mz/rt limit check when validating MetaboSet * Added tests for changing feature/sample names * Approved suggestion * Update volcano plot (#10) * Update volcano plot Allowed labeling plots with ability to filter labels by p-value * Approve suggestion Code follows notame syntax * Update volcano plot labeling (#16) * Update volcano plot Allowed labeling plots with ability to filter labels by p-value * Approve suggestion Co-authored-by: Anton Klåvus <anton.klavus@iki.fi> * Update volcano plot Label visualization is now clean Co-authored-by: Anton Klåvus <anton.klavus@iki.fi> * Fix correlation test argument (#15) ... arguments will now be passed to cor.test() * Update .Rd files (#13) I noticed these won't update automatically * Enabled pairwise paired t-tests * Add stats cleaning function (#12) * Stats cleaning function * Enabled column renaming * Fix dummy injection error (#19) dummy_injection was not found during merging if x was already merged * Fixed bug in pairwise t-tests * Add PERMANOVA (#9) * Add PERMANOVA Basic wrapper for package called PERMANOVA. * Minor fixes Fixed one argument name and documentation * Fix test_logging (#18) * Fix test_logging expect_null didn't work * Add tests for logging * Update Cohen's D (#14) * Update Cohen's D Cohen's D can now be counted to all groups and time points at once * Minor fixes * Fixed tests to match new commits Fixed hardcoded values in tests, known warnings in testing and group order in log messages when calculating Cohen's D * Changed column names in tests Changed column names in tests to match new style * Changed column names Changed column names to match new uniform style * Changed column names in functions Changed column names in t-tests, Cohen's D and fold change to match new uniform style. Linear models do not follow that style. * Cleaned code * Updated dependencies * Fixed bugs (#20) * Fixed tests to match new commits Fixed hardcoded values in tests, known warnings in testing and group order in log messages when calculating Cohen's D * Changed column names in tests Changed column names in tests to match new style * Changed column names in functions Changed column names in t-tests, Cohen's D and fold change to match new uniform style. Linear models do not follow that style. * Cleaned code * Updated dependencies * Updated manuals and examples * Removed BatchCorrMetabolomics dependency As it's not updated regularly * Enabled pairwise paired t-tests (#17) * Enabled pairwise paired t-tests * Changed column names Changed column names to match new uniform style * Updated warning handling when testing * Updated Cohen's d error handling * Updated volcano plot example * Updated Cohen's D error handling and other minor changes (#23) * Updated warning handling when testing * Updated Cohen's d error handling * Updated volcano plot example * Version 0.1.0 * Added summary for statistics Cleaning stats results can now also count significant p-values and keep track of the smallest one. * Added Mann-Whiney u test * Added Wilcoxon signed rank test * Added pairwise non-parametric tests * Change QC finding logic * Change QC colum generator warning message * Change QC generator log message * add plot saving function * add possibility to save effect plots to different formats * Remove deprecated function dependencies * combine save_plot_helper with save_plot * update documentation * remove plot saving from this function * minor changes * minor changes * update documentation * Add tests for plot saving * remove deprecated dependencies * update docs * Changes to visualization documentation * Non-parametric tests and tests for the functions * Unified column names of statistics, removed unworking options to edit CI level from linear models * Updated documentation of linear models * Version 0.2.0 Co-authored-by: attlih <98050742+attlih@users.noreply.github.com> Co-authored-by: attlih <atte.lihtamo@gmail.com>
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Allowed labeling plots with ability to filter labels by p-value