Merge pull request #46 from KrishnaswamyLab/dev

v0.2.8.5: bugfix graph reset and plotting tools

Author: scottgigante

.travis.yml

@@ -6,17 +6,10 @@
 
   sudo: required
 
-  before_install:
-    - pip install nose2
-
   install:
-    - cd Python
-    - python setup.py install
-    - cd ..
+    - cd Python; python setup.py install; cd ..
 
   script:
-    - cd Python
+    - cd Python; pip install -U .[test,doc]
     - python setup.py test
-    - cd doc
-    - pip install -r source/requirements.txt
-    - make html
+    - cd doc; make html; cd ../..

Python/doc/source/requirements.txt

@@ -4,6 +4,6 @@ pandas>=0.21.0
 scipy>=1.1.0
 matplotlib
 future
-graphtools>=0.1.7
+graphtools>=0.1.8.1
 sphinx
 sphinxcontrib-napoleon

Python/phate/phate.py

@@ -281,6 +281,17 @@ def _set_graph_params(self, **params):
             # graph not defined
             pass
 
+    def _reset_graph(self):
+        self.graph = None
+        self._reset_potential()
+
+    def _reset_potential(self):
+        self.diff_potential = None
+        self._reset_embedding()
+
+    def _reset_embedding(self):
+        self.embedding = None
+
     def set_params(self, **params):
         """Set the parameters on this estimator.
 
@@ -443,7 +454,7 @@ def set_params(self, **params):
         if 'n_landmark' in params and params['n_landmark'] != self.n_landmark:
             if self.n_landmark is None or params['n_landmark'] is None:
                 # need a different type of graph, reset entirely
-                self.graph = None
+                self._reset_graph()
             else:
                 self._set_graph_params(n_landmark=params['n_landmark'])
             self.n_landmark = params['n_landmark']
@@ -466,13 +477,11 @@ def set_params(self, **params):
 
         if reset_kernel:
             # can't reset the graph kernel without making a new graph
-            self.graph = None
-            reset_potential = True
+            self._reset_graph()
         if reset_potential:
-            reset_embedding = True
-            self.diff_potential = None
+            self._reset_potential()
         if reset_embedding:
-            self.embedding = None
+            self._reset_embedding()
 
         self._check_params()
         return self
@@ -583,7 +592,7 @@ def fit(self, X):
                 If the same data is used, we can reuse existing kernel and
                 diffusion matrices. Otherwise we have to recompute.
                 """
-                self.graph = None
+                self._reset_graph()
             else:
                 try:
                     self.graph.set_params(
@@ -596,7 +605,7 @@ def fit(self, X):
                 except ValueError as e:
                     # something changed that should have invalidated the graph
                     log_debug("Reset graph due to {}".format(str(e)))
-                    self.graph = None
+                    self._reset_graph()
 
         self.X = X
 

Python/phate/plot.py

@@ -58,12 +58,19 @@ def _get_plot_data(data, ndim=None):
 def _auto_params(data, c, discrete, cmap, legend):
     """Automatically select nice parameters for a scatter plot
     """
+    for d in data[1:]:
+        if d.shape[0] != data[0].shape[0]:
+            raise ValueError("Expected all axis of data to have the same length"
+                             ". Got {}".format([d.shape[0] for d in data]))
     if c is not None and not mpl.colors.is_color_like(c):
         try:
             c = c.values
         except AttributeError:
             # not a pandas Series
             pass
+        if not len(c) == data[0].shape[0]:
+            raise ValueError("Expected c of length {} or 1. Got {}".format(
+                len(c), data.shape[0]))
         if discrete is None:
             # guess
             if isinstance(cmap, dict) or \
@@ -124,7 +131,7 @@ def scatter(data,
             xlabel="PHATE1",
             ylabel="PHATE2",
             zlabel="PHATE3",
-            legend_title=None,
+            legend_title="",
             **plot_kwargs):
     """Create a scatter plot
 
@@ -184,7 +191,7 @@ def scatter(data,
         Label for the y axis. If None, no label is set.
     zlabel : str or None (default : "PHATE3")
         Label for the z axis. If None, no label is set. Only used for 3D plots
-    legend_title : str or None (default: None)
+    legend_title : str (default: "")
         title for the colorbar of legend
     **plot_kwargs : keyword arguments
         Extra arguments passed to `matplotlib.pyplot.scatter`.
@@ -208,10 +215,12 @@ def scatter(data,
     else:
         show = False
     if legend and not discrete:
-        im = ax.imshow(np.arange(10).reshape(-1, 1),
+        im = ax.imshow(np.linspace(np.min(data[1]), np.max(data[1]), 10).reshape(-1, 1),
                        vmin=np.min(c), vmax=np.max(c), cmap=cmap,
-                       aspect='auto')
+                       aspect='auto', origin='lower')
         im.remove()
+        ax.relim()
+        ax.autoscale()
     try:
         if c is not None and not mpl.colors.is_color_like(c):
             c = c[plot_idx]

Python/phate/version.py

@@ -1 +1 @@
-__version__ = "0.2.8.4"
+__version__ = "0.2.8.5"

Python/requirements.txt

@@ -4,4 +4,4 @@ scipy>=1.1.0
 matplotlib>=2.0.1
 scikit-learn>=0.19.1
 future
-graphtools>=0.1.7
+graphtools>=0.1.8.1

Python/setup.py

@@ -2,6 +2,22 @@
 import sys
 from setuptools import setup
 
+install_requires = [
+    'numpy>=1.14.0',
+    'pandas>=0.21.0',
+    'scipy>=1.1.0',
+    'matplotlib>=2.0.1',
+    'scikit-learn>=0.19.1',
+    'future',
+    'graphtools>=0.1.8.1']
+
+test_requires = [
+    'nose2']
+
+doc_requires = [
+    'sphinx',
+    'sphinxcontrib-napoleon']
+
 version_py = os.path.join(os.path.dirname(__file__), 'phate', 'version.py')
 version = open(version_py).read().strip().split(
     '=')[-1].replace('"', '').strip()
@@ -18,30 +34,10 @@
       author_email='daniel.burkhardt@yale.edu',
       packages=['phate', ],
       license='GNU General Public License Version 2',
-      install_requires=['numpy>=1.14.0',
-                        'pandas>=0.21.0',
-                        'scipy>=1.1.0',
-                        'matplotlib>=2.0.1',
-                        'scikit-learn>=0.19.1',
-                        'future',
-                        'graphtools>=0.1.7'],
+      install_requires=install_requires,
       extras_require={
-          'tests': [
-              'doctest',
-              'nose2',
-          ],
-          'docs': [
-              'sphinx>=1.6.5',
-              'sphinx-rtd-theme<0.3',
-              'readthedocs-sphinx-ext<0.6',
-              'recommonmark>=0.4.0',
-              'commonmark>=0.5.4',
-              'alabaster!=0.7.5,<0.8,>=0.7',
-              'pillow==2.6.1',
-              'mock==1.0.1',
-              'docutils==0.13.1',
-              'Pygments==2.2.0',
-          ]},
+          'test': test_requires,
+          'doc': doc_requires},
       test_suite='nose2.collector.collector',
       long_description=readme,
       url='https://github.com/KrishnaswamyLab/PHATE',