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author eschen42
date Sun, 04 Mar 2018 14:51:42 -0500
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1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.6"> 1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.7">
2 2
3 <description>OPLS-DA Contrasts of Univariate Results</description> 3 <description>OPLS-DA Contrasts of Univariate Results</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package">r-batch</requirement> 6 <requirement type="package">r-batch</requirement>
324 324
325 325
326 Motivation 326 Motivation
327 ---------- 327 ----------
328 328
329 OPLS-DA\ :superscript:`®` and the SIMCA\ :superscript:`®` S-PLOT\ :superscript:`®` (Wiklund *et al.*, 2008) may be employed to draw attention to metabolomic features that are potential biomarkers, i.e. features that are potentially useful to discriminate to which class a sample should be assigned (e.g. Sun *et al.*, 2016). Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014, Guitton *et al.*, 2017) provides a suite of tools for preprocessing and statistical analysis of LC-MS, GC-MS, and NMR metabolomics data; however, it does not (as of release 3.0) include a tool for making the equivalent of an S-PLOT. 329 OPLS-DA and the SIMCA S-PLOT (Wiklund *et al.*, 2008) may be employed to draw attention to metabolomic features that are potential biomarkers, i.e. features that are potentially useful to discriminate to which class a sample should be assigned (e.g. Sun *et al.*, 2016). Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014, Guitton *et al.*, 2017) provides a suite of tools for preprocessing and statistical analysis of LC-MS, GC-MS, and NMR metabolomics data; however, it does not (as of release 3.0) include a tool for making the equivalent of an S-PLOT.
330 330
331 The S-PLOT is computed from mean-centered, pareto-scaled data. This plot presents the correlation of the first score vector from an OPLS-DA model with the sample-variables used to produce that model versus the covariance of the scores with the sample-variables. For OPLS-DA, the first score vector represents the variation among the sample-variables that is related to the predictor (i.e., the contrasting factor). 331 The S-PLOT is computed from mean-centered, pareto-scaled data. This plot presents the correlation of the first score vector from an OPLS-DA model with the sample-variables used to produce that model versus the covariance of the scores with the sample-variables. For OPLS-DA, the first score vector represents the variation among the sample-variables that is related to the predictor (i.e., the contrasting factor).
332 332
333 The primary aims of this tool are: 333 The primary aims of this tool are:
334 334
340 Description 340 Description
341 ----------- 341 -----------
342 342
343 The purpose of the 'PLS-DA Contrasts' tool is to visualize GC-MS or LC-MS features that are possible biomarkers. 343 The purpose of the 'PLS-DA Contrasts' tool is to visualize GC-MS or LC-MS features that are possible biomarkers.
344 344
345 The W4M 'Univariate' tool (Thévenot *et al.*, 2015) adds the results of family-wise corrected pairwise significance-tests as columns of the **variableMetadata** dataset. 345 The W4M 'Univariate' tool (Th]]>&#233;<![CDATA[venot *et al.*, 2015) adds the results of family-wise corrected pairwise significance-tests as columns of the **variableMetadata** dataset.
346 For instance, suppose that you ran Kruskal-Wallis testing for a column named 'cluster' in sampleMetadata that has values 'k1' and 'k2' and at least one other value. 346 For instance, suppose that you ran Kruskal-Wallis testing for a column named 'cluster' in sampleMetadata that has values 'k1' and 'k2' and at least one other value.
347 347
348 - A column of variableMetadata would be labelled 'cluster_kruskal_sig' and would have values '1' and '0'; when the samples are grouped by 'cluster', '1' means that there is strong evidence against the hypothesis that there is no difference among the intensities for the feature across all sample-groups. 348 - A column of variableMetadata would be labelled 'cluster_kruskal_sig' and would have values '1' and '0'; when the samples are grouped by 'cluster', '1' means that there is strong evidence against the hypothesis that there is no difference among the intensities for the feature across all sample-groups.
349 - A column of variableMetadata would be labelled 'cluster_kruskal_k1.k2_sig' and would have values '1' and '0', where '1' means that there is significant evidence against the hypothesis that samples from sampleMetadata whose 'cluster' column contains 'k1' or 'k2' have the same intensity for that feature. 349 - A column of variableMetadata would be labelled 'cluster_kruskal_k1.k2_sig' and would have values '1' and '0', where '1' means that there is significant evidence against the hypothesis that samples from sampleMetadata whose 'cluster' column contains 'k1' or 'k2' have the same intensity for that feature.
350 350
351 The 'PLS-DA Contrasts' tool produces graphics and data for OPLS-DA contrasts of feature-intensities between significantly different pairs of factor-levels. For each factor-level, the tool performs a contrast with all other factor-levels combined and then separately with each other factor-level. 351 The 'PLS-DA Contrasts' tool produces graphics and data for OPLS-DA contrasts of feature-intensities between significantly different pairs of factor-levels. For each factor-level, the tool performs a contrast with all other factor-levels combined and then separately with each other factor-level.
352 352
353 **Along the left-to-right axis, the plots show the supervised projection of the variation explained by the predictor** (i.e., the factor specified when invoking the tool); **the top-to-bottom axis displays the variation that is orthogonal to the predictor level** (i.e., independent of it). 353 **Along the left-to-right axis, the plots show the supervised projection of the variation explained by the predictor** (i.e., the factor specified when invoking the tool); **the top-to-bottom axis displays the variation that is orthogonal to the predictor level** (i.e., independent of it).
354 354
355 Although this tool can be used in a purely exploratory manner by supplying the variableMetadata file without the columns added by the W4M 'Univariate' tool, **the preferred workflow is to use univariate testing to exclude features that are not significantly different and use OPLS-DA to visualize the differences identified in univariate testing** (Thévenot *et al.*, 2015); an appropriate exception would be to visualize contrasts of a specific list of metabolites. 355 Although this tool can be used in a purely exploratory manner by supplying the variableMetadata file without the columns added by the W4M 'Univariate' tool, **the preferred workflow is to use univariate testing to exclude features that are not significantly different and use OPLS-DA to visualize the differences identified in univariate testing** (Th]]>&#233;<![CDATA[venot *et al.*, 2015); an appropriate exception would be to visualize contrasts of a specific list of metabolites.
356 356
357 It must be stressed that there may be no *single* definitive computational approach to select features that are reliable biomarkers, especially from a small number of samples or experiments. A few possible choices are: 357 It must be stressed that there may be no *single* definitive computational approach to select features that are reliable biomarkers, especially from a small number of samples or experiments. A few possible choices are:
358 358
359 - picking features with maximum loadings along the projection parallel to the predictor (loadp), 359 - picking features with maximum loadings along the projection parallel to the predictor (loadp),
360 - examining extreme values on S-PLOTs (for which covariance is linearly related to loadp), 360 - examining extreme values on S-PLOTs (for which covariance is linearly related to loadp),
448 448
449 [OUT] Contrast-detail output PDF 449 [OUT] Contrast-detail output PDF
450 | Several plots for each two-projection OPLS-DA analysis: 450 | Several plots for each two-projection OPLS-DA analysis:
451 451
452 - (top-left) **correlation-versus-covariance plot** of OPLS-DA results (a work-alike for the S-PLOT, computed using formula in Supplement to Wiklund, *op. cit.*); point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto *et al.* 2014) ranges from 0.83 and 1.21 (Mehmood *et al.* 2012) 452 - (top-left) **correlation-versus-covariance plot** of OPLS-DA results (a work-alike for the S-PLOT, computed using formula in Supplement to Wiklund, *op. cit.*); point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto *et al.* 2014) ranges from 0.83 and 1.21 (Mehmood *et al.* 2012)
453 - (bottom-left) **model-overview plot** for the two projections; grey bars are the correlation coefficient for the fitted data; black bars indicate performance in cross-validation tests (Thévenot, 2017) 453 - (bottom-left) **model-overview plot** for the two projections; grey bars are the correlation coefficient for the fitted data; black bars indicate performance in cross-validation tests (Th]]>&#233;<![CDATA[venot, 2017)
454 - (top-right) OPLS-DA **scores-plot** for the two projections (Thévenot *et al.*, 2015) 454 - (top-right) OPLS-DA **scores-plot** for the two projections (Th]]>&#233;<![CDATA[venot *et al.*, 2015)
455 - (bottom-right) OPLS-DA **loadings-plot** for the two projections (*ibid.*) 455 - (bottom-right) OPLS-DA **loadings-plot** for the two projections (*ibid.*)
456 456
457 [OUT] Contrast Correlation-Covarinace data TABULAR 457 [OUT] Contrast Correlation-Covarinace data TABULAR
458 | A tab-separated values file of metadata for each feature for each contrast in which it was included. 458 | A tab-separated values file of metadata for each feature for each contrast in which it was included.
459 | Thus, a given feature may appear many times, but *the combination of featureID, factorLevel1, and factorLevel2 will be unique.* 459 | Thus, a given feature may appear many times, but *the combination of featureID, factorLevel1, and factorLevel2 will be unique.*
533 Working examples 533 Working examples
534 ---------------- 534 ----------------
535 535
536 **Input files** 536 **Input files**
537 537
538 +-------------------+-------------------------------------------------------------------------------------------------------------------+ 538 +-------------------------------------------------------------------------------------------------------------------+
539 | Input File | Download from URL | 539 | Download from URL |
540 +===================+===================================================================================================================+ 540 +===================================================================================================================+
541 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_dataMatrix.tsv | 541 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_dataMatrix.tsv |
542 +-------------------+-------------------------------------------------------------------------------------------------------------------+ 542 +-------------------------------------------------------------------------------------------------------------------+
543 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv | 543 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv |
544 +-------------------+-------------------------------------------------------------------------------------------------------------------+ 544 +-------------------------------------------------------------------------------------------------------------------+
545 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_variableMetadata.tsv | 545 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_variableMetadata.tsv |
546 +-------------------+-------------------------------------------------------------------------------------------------------------------+ 546 +-------------------------------------------------------------------------------------------------------------------+
547 547
548 **Example 1:** Include in the analysis only features identified as pair-wise significant in the Univariate test. 548 **Example 1:** Include in the analysis only features identified as pair-wise significant in the Univariate test.
549 549
550 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 550 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
551 | Input Parameter or Result | Value | 551 | Input Parameter or Result | Value |
560 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 560 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
561 | Level-name matching | use regular expressions for matching level-names | 561 | Level-name matching | use regular expressions for matching level-names |
562 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 562 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
563 | Number of features having extreme loadings | ALL | 563 | Number of features having extreme loadings | ALL |
564 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 564 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
565 | Label feat. having extreme orth. loadings | Yes |
566 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
565 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov.tsv | 567 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov.tsv |
566 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 568 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
567 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience.tsv | 569 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience.tsv |
568 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 570 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
569 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail.pdf | 571 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail.pdf |
584 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 586 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
585 | Level-name matching | use wild cards for matching level-names | 587 | Level-name matching | use wild cards for matching level-names |
586 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 588 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
587 | Number of features having extreme loadings | 5 | 589 | Number of features having extreme loadings | 5 |
588 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 590 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
591 | Label feat. having extreme orth. loadings | No |
592 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
589 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_all.tsv | 593 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_all.tsv |
590 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 594 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
591 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_all.tsv | 595 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_all.tsv |
592 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 596 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
593 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_all.pdf | 597 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_all.pdf |
608 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 612 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
609 | Level-name matching | use regular expressions for matching level-names | 613 | Level-name matching | use regular expressions for matching level-names |
610 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 614 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
611 | Number of features having extreme loadings | 0 | 615 | Number of features having extreme loadings | 0 |
612 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 616 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
617 | Label feat. having extreme orth. loadings | Yes |
618 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
613 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_global.tsv | 619 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_global.tsv |
614 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 620 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
615 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_global.tsv | 621 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_global.tsv |
616 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 622 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
617 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_global.pdf | 623 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_global.pdf |
632 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 638 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
633 | Level-name matching | use regular expressions for matching level-names | 639 | Level-name matching | use regular expressions for matching level-names |
634 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 640 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
635 | Number of features having extreme loadings | 3 | 641 | Number of features having extreme loadings | 3 |
636 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 642 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
643 | Label feat. having extreme orth. loadings | Yes |
644 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
637 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_lohi.tsv | 645 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_lohi.tsv |
638 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 646 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
639 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_lohi.tsv | 647 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_lohi.tsv |
640 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ 648 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
641 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_lohi.pdf | 649 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_lohi.pdf |
643 651
644 652
645 Trademarks 653 Trademarks
646 ---------- 654 ----------
647 655
648 OPLS-DA\ :superscript:`®`, SIMCA\ :superscript:`®`, and S-PLOT\ :superscript:`®` are registered trademarks of the Umetrics company. http://umetrics.com/about-us/trademarks 656 OPLS-DA, SIMCA, and S-PLOT are registered trademarks of the Umetrics company. http://umetrics.com/about-us/trademarks
649 657
650 658
651 Release notes 659 Release notes
652 ------------- 660 -------------
661
662 0.98.7
663
664 - bug fix: handle case of a treatment level with only one sample.
653 665
654 0.98.6 666 0.98.6
655 667
656 - bug fix: set 'crossvalI' param (of R function 'ropls::opls') to the number of samples when the there are fewer than seven samples. 668 - bug fix: set 'crossvalI' param (of R function 'ropls::opls') to the number of samples when the there are fewer than seven samples.
657 669
687 <citation type="doi">10.1016/j.chemolab.2008.08.004</citation> 699 <citation type="doi">10.1016/j.chemolab.2008.08.004</citation>
688 <!-- Rinuardo 2016 --> 700 <!-- Rinuardo 2016 -->
689 <citation type="doi">10.3389/fmolb.2016.00026</citation> 701 <citation type="doi">10.3389/fmolb.2016.00026</citation>
690 <!-- Sun_2016 Urinary Biomarkers for adolescent idiopathic scoliosis --> 702 <!-- Sun_2016 Urinary Biomarkers for adolescent idiopathic scoliosis -->
691 <citation type="doi">10.1038/srep22274</citation> 703 <citation type="doi">10.1038/srep22274</citation>
692 <!-- Th_venot_2015 Urinary metabolome statistics --> 704 <!-- Thevenot_2015 Urinary metabolome statistics -->
693 <citation type="doi">10.1021/acs.jproteome.5b00354</citation> 705 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
694 <!-- ropls package --> 706 <!-- ropls package -->
695 <citation type="bibtex"><![CDATA[ 707 <citation type="bibtex"><![CDATA[
696 @incollection{Thevenot_ropls_2017, 708 @incollection{Thevenot_ropls_2017,
697 author = {Th{\'{e}}venot, Etienne A.}, 709 author = {Th{\'{e}}venot, Etienne A.},