ENH: added citations

q2_diversity/citations.bib

@@ -0,0 +1,164 @@
+@article{lozupone2005unifrac,
+  title={UniFrac: a new phylogenetic method for comparing microbial communities},
+  author={Lozupone, Catherine and Knight, Rob},
+  journal={Applied and environmental microbiology},
+  volume={71},
+  number={12},
+  pages={8228--8235},
+  year={2005},
+  publisher={Am Soc Microbiol},
+  doi={10.1128/AEM.71.12.8228-8235.2005}
+}
+
+@article{lozupone2007quantitative,
+  title={Quantitative and qualitative $\beta$ diversity measures lead to different insights into factors that structure microbial communities},
+  author={Lozupone, Catherine A and Hamady, Micah and Kelley, Scott T and Knight, Rob},
+  journal={Applied and environmental microbiology},
+  volume={73},
+  number={5},
+  pages={1576--1585},
+  year={2007},
+  publisher={Am Soc Microbiol},
+  doi={10.1128/AEM.01996-06}
+}
+
+@article{chang2011variance,
+  title={Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny},
+  author={Chang, Qin and Luan, Yihui and Sun, Fengzhu},
+  journal={BMC bioinformatics},
+  volume={12},
+  number={1},
+  pages={118},
+  year={2011},
+  publisher={BioMed Central},
+  doi={https://doi.org/10.1186/1471-2105-12-118}
+}
+
+@article{chen2012associating,
+  title={Associating microbiome composition with environmental covariates using generalized UniFrac distances},
+  author={Chen, Jun and Bittinger, Kyle and Charlson, Emily S and Hoffmann, Christian and Lewis, James and Wu, Gary D and Collman, Ronald G and Bushman, Frederic D and Li, Hongzhe},
+  journal={Bioinformatics},
+  volume={28},
+  number={16},
+  pages={2106--2113},
+  year={2012},
+  publisher={Oxford University Press},
+  doi={10.1093/bioinformatics/bts342}
+}
+
+@article{faith1992conservation,
+  title={Conservation evaluation and phylogenetic diversity},
+  author={Faith, Daniel P},
+  journal={Biological conservation},
+  volume={61},
+  number={1},
+  pages={1--10},
+  year={1992},
+  publisher={Elsevier},
+  doi={https://doi.org/10.1016/0006-3207(92)91201-3}
+}
+
+@article{vazquez2013emperor,
+  title={EMPeror: a tool for visualizing high-throughput microbial community data},
+  author={V{\'a}zquez-Baeza, Yoshiki and Pirrung, Meg and Gonzalez, Antonio and Knight, Rob},
+  journal={Gigascience},
+  volume={2},
+  number={1},
+  pages={16},
+  year={2013},
+  publisher={BioMed Central},
+  doi={10.1186/2047-217X-2-16}
+}
+
+@article{sorensen1948method,
+  title={A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons},
+  author={S{\o}rensen, Thorvald},
+  journal={Biol. Skr.},
+  volume={5},
+  pages={1--34},
+  year={1948}
+}
+
+@article{jaccard1908nouvelles,
+  title={Nouvelles recherches sur la distribution floral},
+  author={Jaccard, P},
+  journal={Bull. Soc. Vard. Sci. Nat},
+  volume={44},
+  pages={223--270},
+  year={1908}
+}
+
+@article{pielou1966measurement,
+  title={The measurement of diversity in different types of biological collections},
+  author={Pielou, Evelyn C},
+  journal={Journal of theoretical biology},
+  volume={13},
+  pages={131--144},
+  year={1966},
+  publisher={Elsevier},
+  doi={https://doi.org/10.1016/0022-5193(66)90013-0}
+}
+
+@article{clarke1993method,
+  title={A method of linking multivariate community structure to environmental variables},
+  author={Clarke, KR and Ainsworth, M},
+  journal={Marine ecology progress series},
+  pages={205--219},
+  year={1993},
+  publisher={JSTOR}
+}
+
+@article{kruskal1952use,
+  title={Use of ranks in one-criterion variance analysis},
+  author={Kruskal, William H and Wallis, W Allen},
+  journal={Journal of the American statistical Association},
+  volume={47},
+  number={260},
+  pages={583--621},
+  year={1952},
+  publisher={Taylor \& Francis}
+}
+
+@article{anderson2001new,
+  title={A new method for non-parametric multivariate analysis of variance},
+  author={Anderson, Marti J},
+  journal={Austral ecology},
+  volume={26},
+  number={1},
+  pages={32--46},
+  year={2001},
+  publisher={Wiley Online Library},
+  doi={https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x}
+}
+
+@article{mantel1967detection,
+  title={The detection of disease clustering and a generalized regression approach},
+  author={Mantel, Nathan},
+  journal={Cancer research},
+  volume={27},
+  number={2 Part 1},
+  pages={209--220},
+  year={1967},
+  publisher={AACR}
+}
+
+@article{pearson1895note,
+  title={Note on regression and inheritance in the case of two parents},
+  author={Pearson, Karl},
+  journal={Proceedings of the Royal Society of London},
+  volume={58},
+  pages={240--242},
+  year={1895},
+  publisher={JSTOR}
+}
+
+@article{spearman1904proof,
+  title={The proof and measurement of association between two things},
+  author={Spearman, Charles},
+  journal={The American journal of psychology},
+  volume={15},
+  number={1},
+  pages={72--101},
+  year={1904},
+  publisher={JSTOR}
+}

q2_diversity/plugin_setup.py

@@ -8,7 +8,7 @@
 
 from qiime2.plugin import (Plugin, Str, Properties, Choices, Int, Bool, Range,
                            Float, Set, Visualization, Metadata, MetadataColumn,
-                           Categorical)
+                           Categorical, Citations)
 
 import q2_diversity
 from q2_diversity import _alpha as alpha
@@ -20,6 +20,8 @@
 from q2_types.ordination import PCoAResults
 
 
+citations = Citations.load('citations.bib', package='q2_diversity')
+
 sklearn_n_jobs_description = (
     'The number of jobs to use for the computation. This works by breaking '
     'down the pairwise matrix into n_jobs even slices and computing them in '
@@ -40,18 +42,6 @@
                  'statistics and visualizations in the context of sample '
                  'metadata.'),
     short_description='Plugin for exploring community diversity.',
-    citation_text=('Unweighted UniFrac: '
-                   'Lozupone and Knight 2005 Appl Environ Microbiol; DOI: '
-                   '10.1128/AEM.71.12.8228-8235.2005.\n'
-                   'Weighted UniFrac: '
-                   'Lozupone et al. 2007 Appl Environ Microbiol; DOI: '
-                   '10.1128/AEM.01996-06.\n'
-                   'Variance adjusted UniFrac: '
-                   'Chang et al. BMC Bioinformatics 2011 '
-                   'https://doi.org/10.1186/1471-2105-12-118.\n'
-                   'Generalized UniFrac: '
-                   'Chen et al. 2012 Bioinformatics; DOI: '
-                   '10.1093/bioinformatics/bts342')
 )
 
 plugin.methods.register_function(
@@ -78,7 +68,10 @@
     output_descriptions={'distance_matrix': 'The resulting distance matrix.'},
     name='Beta diversity (phylogenetic)',
     description=("Computes a user-specified phylogenetic beta diversity metric"
-                 " for all pairs of samples in a feature table.")
+                 " for all pairs of samples in a feature table."),
+    citations=[
+        citations['lozupone2005unifrac'],
+        citations['lozupone2007quantitative']]
 )
 
 
@@ -132,7 +125,12 @@
                  "2012), Variance Adjusted UniFrac (Chang et al. 2011), "
                  "as well as Weighted normalized and unnormalized UniFrac "
                  "(Lozupone et al. 2007) and unweighted UniFrac "
-                 "(Lozupone et al. 2005)")
+                 "(Lozupone et al. 2005)"),
+    citations=[
+        citations['lozupone2005unifrac'],
+        citations['lozupone2007quantitative'],
+        citations['chang2011variance'],
+        citations['chen2012associating']]
 )
 
 
@@ -180,7 +178,9 @@
     },
     name='Alpha diversity (phylogenetic)',
     description=("Computes a user-specified phylogenetic alpha diversity "
-                 "metric for all samples in a feature table.")
+                 "metric for all samples in a feature table."),
+    citations=[
+        citations['faith1992conservation']]
 )
 
 plugin.methods.register_function(
@@ -302,7 +302,7 @@
     },
     name='Core diversity metrics (phylogenetic and non-phylogenetic)',
     description="Applies a collection of diversity metrics (both "
-                "phylogenetic and non-phylogenetic) to a feature table.",
+                "phylogenetic and non-phylogenetic) to a feature table."
 )
 
 plugin.pipelines.register_function(
@@ -357,7 +357,7 @@
     },
     name='Core diversity metrics (non-phylogenetic)',
     description=("Applies a collection of diversity metrics "
-                 "(non-phylogenetic) to a feature table."),
+                 "(non-phylogenetic) to a feature table.")
 )
 
 plugin.methods.register_function(
@@ -413,7 +413,8 @@
     },
     name='Alpha diversity comparisons',
     description=("Visually and statistically compare groups of alpha diversity"
-                 " values.")
+                 " values."),
+    citations=[citations['kruskal1952use']]
 )
 
 plugin.visualizers.register_function(
@@ -433,7 +434,8 @@
                  "considered, and samples which are missing data will be "
                  "dropped. The output visualization will indicate how many "
                  "samples were dropped due to missing data, if any were "
-                 "dropped.")
+                 "dropped."),
+    citations=[citations['clarke1993method']]
 )
 
 beta_group_significance_methods = \
@@ -462,7 +464,8 @@
     name='Beta diversity group significance',
     description=('Determine whether groups of samples are significantly '
                  'different from one another using a permutation-based '
-                 'statistical test.')
+                 'statistical test.'),
+    citations=[citations['anderson2001new']]
 )
 
 plugin.visualizers.register_function(
@@ -504,6 +507,10 @@
         'label1': 'Label for `dm1` in the output visualization.',
         'label2': 'Label for `dm2` in the output visualization.'
     },
+    citations=[
+        citations['mantel1967detection'],
+        citations['pearson1895note'],
+        citations['spearman1904proof']]
 )
 
 
@@ -524,7 +531,8 @@
     },
     name='Alpha diversity correlation',
     description=('Determine whether numeric sample metadata columns are '
-                 'correlated with alpha diversity.')
+                 'correlated with alpha diversity.'),
+    citations=[citations['pearson1895note'], citations['spearman1904proof']]
 )
 
 _metric_set = Set[Str % Choices(alpha.alpha_rarefaction_supported_metrics)]
@@ -622,5 +630,9 @@
                 'provide: an Emperor jackknifed PCoA plot, samples clustered '
                 'by UPGMA or neighbor joining with support calculation, and '
                 'a heatmap showing the correlation between rarefaction trials '
-                'of that beta diversity metric.'
+                'of that beta diversity metric.',
+    citations=[
+        citations['mantel1967detection'],
+        citations['pearson1895note'],
+        citations['spearman1904proof']]
 )

setup.py

@@ -23,6 +23,7 @@
                       'alpha_rarefaction_assets/index.html',
                       'alpha_rarefaction_assets/dist/*',
                   ],
+                  'q2_diversity': ['citations.bib'],
                   'q2_diversity._beta': [
                       'beta_group_significance_assets/index.html',
                       'mantel_assets/index.html',