Updating heatmaps in notebook (#201)

* DOC: Fixing linear mixed effects summary plots.
Also separating out qiime2 tutorials

* ENH: Adding in multiple hypothesis correction

* forgot import

* TST: Fixing file creation issues

* pep8

* FIX: Fixing orientation of pvalues for lme

* Updating qiime2 tutorials for 88 soils and cf

* TST: Fixing summary test

* Adding in all of the updated IPython notebooks

* Updating bokeh tests

* pep8

* DOC: Adding much more documentation

* Updating docs for principal balances

* DOC: Fixing references

* Updating taxonomies to meet qiime2 format

* DOC: Addressing #199.

* DOC: Updating notebooks to reflect on changes in heatmap orientation

* DOC: Removing warning

* ENH: Changing types over to Hierarchy instead of Phylogeny[Rooted]

* FIX: fixing typos in assign-ids
Fixing types in regression

* FIX: Fixing types with plotting and clustering functions

* Updating notebooks

gneiss/plot/_plot.py

@@ -17,7 +17,7 @@
 from gneiss.plot._decompose import balance_barplots, balance_boxplot
 from gneiss.util import (match, NUMERATOR, DENOMINATOR)
 
-from q2_types.tree import Phylogeny, Rooted
+from q2_types.tree import Hierarchy
 from q2_composition.plugin_setup import Composition, Balance
 from q2_types.feature_table import FeatureTable
 from q2_types.feature_data import FeatureData, Taxonomy
@@ -111,7 +111,7 @@ def f(x):
 
 plugin.visualizers.register_function(
     function=balance_taxonomy,
-    inputs={'balances': FeatureTable[Balance], 'tree': Phylogeny[Rooted],
+    inputs={'balances': FeatureTable[Balance], 'tree': Hierarchy,
             'taxonomy': FeatureData[Taxonomy]},
     parameters={'balance_name': Str,
                 'taxa_level': Int,
@@ -188,7 +188,7 @@ def dendrogram_heatmap(output_dir: str, table: pd.DataFrame,
 plugin.visualizers.register_function(
     function=dendrogram_heatmap,
     inputs={'table': FeatureTable[Composition],
-            'tree': Phylogeny[Rooted]},
+            'tree': Hierarchy},
     parameters={'metadata': MetadataCategory, 'ndim': Int,
                 'method': Str % Choices(_transform_methods),
                 'color_map': Str % Choices(_mpl_colormaps)},

gneiss/regression/_regression.py

@@ -12,7 +12,7 @@
 
 from q2_composition.plugin_setup import Balance
 from q2_types.feature_table import FeatureTable
-from q2_types.tree import Phylogeny, Rooted
+from q2_types.tree import Hierarchy
 from qiime2.plugin import Str, Metadata
 from gneiss.plugin_setup import plugin
 from gneiss.plot._regression_plot import ols_summary, lme_summary
@@ -31,7 +31,7 @@ def ols_regression(output_dir: str,
 plugin.visualizers.register_function(
     function=ols_regression,
     inputs={'table': FeatureTable[Balance],
-            'tree': Phylogeny[Rooted]},
+            'tree': Hierarchy},
     parameters={'formula': Str, 'metadata': Metadata},
     name='Simplicial Ordinary Least Squares Regression',
     input_descriptions={
@@ -65,7 +65,7 @@ def lme_regression(output_dir: str,
 plugin.visualizers.register_function(
     function=lme_regression,
     inputs={'table': FeatureTable[Balance],
-            'tree': Phylogeny[Rooted]},
+            'tree': Hierarchy},
     parameters={'metadata': Metadata, 'formula': Str, 'groups': Str},
     name='Simplicial Linear mixed effects regression',
     input_descriptions={

ipynb/88soils/88soils-qiime2-tutorial.ipynb

@@ -86,7 +86,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[32mSaved Phylogeny[Rooted] to: ph_tree.nwk.qza\u001b[0m\r\n"
+      "\u001b[32mSaved Hierarchy to: ph_tree.nwk.qza\u001b[0m\r\n"
      ]
     }
    ],

ipynb/cfs/cfs-qiime2-tutorial.ipynb

@@ -12,7 +12,9 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "!qiime tools import --input-path final.withtax.biom \\\n",
@@ -98,7 +100,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[32mSaved Phylogeny[Rooted] to: correlated_hierarchy.nwk.qza\u001b[0m\r\n"
+      "\u001b[32mSaved Hierarchy to: correlated_hierarchy.nwk.qza\u001b[0m\r\n"
      ]
     }
    ],

ipynb/cfstudy/cfstudy-qiime2-tutorial.ipynb

@@ -28,26 +28,6 @@
     "    --type FeatureData[Taxonomy]"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[32mSaved FeatureTable[Frequency] to: cfstudy_common.biom.qza\u001b[0m\r\n"
-     ]
-    }
-   ],
-   "source": [
-    "!qiime feature-table filter-samples \\\n",
-    "    --i-table cfstudy.biom.qza \\\n",
-    "    --m-sample-metadata-file cfstudy_modified_metadata.txt \\\n",
-    "    --o-filtered-table cfstudy_common.biom.qza"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -57,7 +37,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -84,14 +64,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "\u001b[32mSaved Phylogeny[Rooted] to: ph_tree.nwk.qza\u001b[0m\r\n"
+      "\u001b[32mSaved Hierarchy to: ph_tree.nwk.qza\u001b[0m\r\n"
      ]
     }
    ],
@@ -113,7 +93,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -133,7 +113,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -160,7 +140,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -192,7 +172,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {