Merge pull request #38 from sbslee/1.13.0-dev

1.13.0 dev

Author: sbslee

CHANGELOG.rst

@@ -1,6 +1,11 @@
 Changelog
 *********
 
+1.13.0 (2022-04-02)
+-------------------
+
+* :issue:`37`: Add new methods :meth:`cross_association_table`, :meth:`cross_association_heatmap`, and :meth:`cross_association_regplot`.
+
 1.12.0 (2022-02-11)
 -------------------
 

data/miscellaneous/lipids.csv

@@ -44,7 +44,8 @@
     'scipy',
     'matplotlib',
     'seaborn',
-    'skbio'
+    'skbio',
+    'statsmodels',
 ]
 
 issues_github_path = 'sbslee/dokdo'

data/miscellaneous/otu.csv

@@ -329,6 +329,13 @@ As expected, above gives the same result as using the Visualization file created
 General Methods
 ===============
 
+cross_association_table
+-----------------------
+
+.. currentmodule:: dokdo.api.cross_association
+
+.. autofunction:: cross_association_table
+
 get_mf
 ------
 
@@ -479,6 +486,20 @@ clustermap
 
 .. autofunction:: clustermap
 
+cross_association_heatmap
+-------------------------
+
+.. currentmodule:: dokdo.api.cross_association
+
+.. autofunction:: cross_association_heatmap
+
+cross_association_regplot
+-------------------------
+
+.. currentmodule:: dokdo.api.cross_association
+
+.. autofunction:: cross_association_regplot
+
 regplot
 -------
 

docs/conf.py

@@ -15,6 +15,7 @@
 from .distance_matrix_plot import distance_matrix_plot
 from .taxa_abundance import taxa_abundance_bar_plot, taxa_abundance_box_plot
 from .ancom_volcano_plot import ancom_volcano_plot
+from .cross_association import cross_association_table, cross_association_heatmap, cross_association_regplot
 
 from .addsig import addsig
 from .addpairs import addpairs
@@ -28,5 +29,6 @@
            'alpha_rarefaction_plot', 'beta_2d_plot', 'beta_3d_plot',
            'beta_scree_plot', 'beta_parallel_plot', 'distance_matrix_plot',
            'taxa_abundance_bar_plot', 'taxa_abundance_box_plot',
-           'ancom_volcano_plot', 'addsig', 'regplot', 'addbiplot',
-           'ordinate', 'pname', 'get_mf']
+           'ancom_volcano_plot', 'cross_association_table',
+           'cross_association_heatmap', 'cross_association_regplot',
+           'addsig', 'regplot', 'addbiplot', 'ordinate', 'pname', 'get_mf']

docs/dokdo_api.rst

@@ -116,7 +116,7 @@ def pname(name, levels=None):
     .. code:: python3
 
         import dokdo
-        
+
         dokdo.pname('d__Bacteria;p__Actinobacteriota;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces;s__Schaalia_radingae')
         # Will print: 's__Schaalia_radingae'
 
@@ -139,7 +139,7 @@ def pname(name, levels=None):
                 return rank
             if rank == '__':
                 continue
-            if rank.split('__')[1] is '':
+            if not rank.split('__')[1]:
                 return ranks[i+1] + ';' + rank
             return rank
     else: