Remove prime fix (#117)

* added camera/tests

* added tests

* checkpoint

* naive implementation of bp tree

* added travis

* removed travis

* added preorder

* added basic drawer

* added space

* addressed PR comments

* addressed PR comment

* added hello-world test

* moved package.json

* changed travis

* added dep

* update

* added yarn

* added dev

* npm

* npm

* nodeJS 10

* removed node_modules

* fixed tests

* fixed travis test

* added cache for open-close

* first attempt to color sample

* generalized coloring

* Finished the sample coloring UI

* removed Travis tests

* Added python byte code folder

* modularized sample coloring

* fixed biom.getSampleObs

* removed travis

* fixed biom-table getSampleObs

* addressed pull request comments

* addressed remaining comments

* added python tests

* addressed pr requests

* added nose to travis

* applied fix to travis

* fixed pep8 issues

* Allowed for more than 4 sample categories

* now more that four categories can be colored

* merged #121

* address pr comments

* removed old empress scripts

* added underscore.js

.gitignore

@@ -3,6 +3,7 @@ data/
 *.qza
 *.qzv
 *.tsv
+empress-biom.py
 
 # NodeJS file used for chrome headless QUnit tests
 node_modules/

empress/_plot.py

@@ -51,21 +51,24 @@ def plot(output_dir: str,
     empress_tree.coords(4020, 4020)
 
     tree_data = {}
-    pre_to_name = {}
-    for i, node in enumerate(empress_tree.preorder(include_self=True)):
-        tree_data[i+1] = {
+    names_to_keys = {}
+    for i, node in enumerate(empress_tree.postorder(include_self=True), 1):
+        tree_data[i] = {
             'name': node.name,
             'x': node.x2,
             'y': node.y2,
             'color': [0.75, 0.75, 0.75],
             'sampVal': 1,
             'visible': True,
             'single_samp': False}
-        pre_to_name[node.name] = i
+        if node.name in names_to_keys:
+            names_to_keys[node.name].append(i)
+        else:
+            names_to_keys[node.name] = [i]
 
     names = []
-    for i, node in enumerate(empress_tree.preorder(include_self=True)):
-        names.append(i+1)
+    for node in empress_tree.preorder(include_self=True):
+        names.append(node.name)
 
     env = Environment(loader=FileSystemLoader(TEMPLATES))
     temp = env.get_template('empress-template.html')
@@ -86,10 +89,10 @@ def plot(output_dir: str,
         'base_url': './support_files',
         'tree': bp_tree,
         'tree_data': tree_data,
+        'names_to_keys': names_to_keys,
         'sample_data': sample_data,
         'obs_data': obs_data,
         'names': names,
-        'p_to_n': pre_to_name
         })
 
     copytree(SUPPORT_FILES, os.path.join(output_dir, 'support_files'))