Merge pull request #29 from KrishnaswamyLab/dev

graphtools v0.2.0

.travis.yml

@@ -6,6 +6,8 @@
 
   sudo: required
 
+  cache: pip
+
   addons:
     apt:
       packages:

README.rst

@@ -5,6 +5,9 @@ graphtools
 .. image:: https://img.shields.io/pypi/v/graphtools.svg
     :target: https://pypi.org/project/graphtools/
     :alt: Latest PyPi version
+.. image:: https://anaconda.org/conda-forge/tasklogger/badges/version.svg
+    :target: https://anaconda.org/conda-forge/tasklogger/
+    :alt: Latest Conda version
 .. image:: https://api.travis-ci.com/KrishnaswamyLab/graphtools.svg?branch=master
     :target: https://travis-ci.com/KrishnaswamyLab/graphtools
     :alt: Travis CI Build
@@ -28,7 +31,11 @@ Installation
 
 graphtools is available on `pip`. Install by running the following in a terminal::
 
-        pip install --user graphtools
+    pip install --user graphtools
+
+Alternatively, graphtools can be installed using `Conda <https://conda.io/docs/>`_ (most easily obtained via the `Miniconda Python distribution <https://conda.io/miniconda.html>`_)::
+
+    conda install -c conda-forge graphtools
 
 Or, to install the latest version from github::
 
@@ -45,14 +52,14 @@ The `graphtools.Graph` class provides an all-in-one interface for k-nearest neig
 
 Use it as follows::
 
-        from sklearn import datasets
-        import graphtools
-        digits = datasets.load_digits()
-        G = graphtools.Graph(digits['data'])
-        K = G.kernel
-        P = G.diff_op
-        G = graphtools.Graph(digits['data'], n_landmark=300)
-        L = G.landmark_op
+    from sklearn import datasets
+    import graphtools
+    digits = datasets.load_digits()
+    G = graphtools.Graph(digits['data'])
+    K = G.kernel
+    P = G.diff_op
+    G = graphtools.Graph(digits['data'], n_landmark=300)
+    L = G.landmark_op
 
 Help
 ----

graphtools/__init__.py

@@ -1,2 +1,2 @@
-from .api import Graph
+from .api import Graph, from_igraph
 from .version import __version__

graphtools/api.py

@@ -1,6 +1,7 @@
 import numpy as np
 import warnings
 import tasklogger
+from scipy import sparse
 
 from . import base
 from . import graphs
@@ -9,14 +10,15 @@
 def Graph(data,
           n_pca=None,
           sample_idx=None,
-          adaptive_k='sqrt',
+          adaptive_k=None,
           precomputed=None,
           knn=5,
           decay=10,
+          bandwidth=None,
           distance='euclidean',
           thresh=1e-4,
           kernel_symm='+',
-          gamma=None,
+          theta=None,
           n_landmark=None,
           n_svd=100,
           beta=1,
@@ -61,6 +63,11 @@ def Graph(data,
     decay : `int` or `None`, optional (default: 10)
         Rate of alpha decay to use. If `None`, alpha decay is not used.
 
+    bandwidth : `float`, list-like or `None`, optional (default: `None`)
+        Fixed bandwidth to use. If given, overrides `knn`. Can be a single
+        bandwidth or a list-like (shape=[n_samples]) of bandwidths for each
+        sample.
+
     distance : `str`, optional (default: `'euclidean'`)
         Any metric from `scipy.spatial.distance` can be used
         distance metric for building kNN graph.
@@ -75,25 +82,25 @@ def Graph(data,
         Defines method of MNN symmetrization.
         '+'  : additive
         '*'  : multiplicative
-        'gamma' : min-max
+        'theta' : min-max
         'none' : no symmetrization
 
-    gamma: float (default: None)
-        Min-max symmetrization constant or matrix. Only used if kernel_symm='gamma'.
-        K = `gamma * min(K, K.T) + (1 - gamma) * max(K, K.T)`
+    theta: float (default: None)
+        Min-max symmetrization constant or matrix. Only used if kernel_symm='theta'.
+        K = `theta * min(K, K.T) + (1 - theta) * max(K, K.T)`
 
     precomputed : {'distance', 'affinity', 'adjacency', `None`}, optional (default: `None`)
         If the graph is precomputed, this variable denotes which graph
         matrix is provided as `data`.
         Only one of `precomputed` and `n_pca` can be set.
 
     beta: float, optional(default: 1)
-        Multiply within - batch connections by(1 - beta)
+        Multiply between - batch connections by beta
 
     sample_idx: array-like
         Batch index for MNN kernel
 
-    adaptive_k : `{'min', 'mean', 'sqrt', 'none'}` (default: 'sqrt')
+    adaptive_k : `{'min', 'mean', 'sqrt', 'none'}` (default: None)
         Weights MNN kernel adaptively using the number of cells in
         each sample according to the selected method.
 
@@ -221,3 +228,31 @@ def Graph(data,
                    for key, value in params.items()
                    if key != "data"])))
     return Graph(**params)
+
+
+def from_igraph(G, **kwargs):
+    """Convert an igraph.Graph to a graphtools.Graph
+
+    Creates a graphtools.graphs.TraditionalGraph with a
+    precomputed adjacency matrix
+
+    Parameters
+    ----------
+    G : igraph.Graph
+        Graph to be converted
+    kwargs
+        keyword arguments for graphtools.Graph
+
+    Returns
+    -------
+    G : graphtools.graphs.TraditionalGraph
+    """
+    if 'precomputed' in kwargs:
+        if kwargs['precomputed'] != 'adjacency':
+            warnings.warn(
+                "Cannot build graph from igraph with precomputed={}. "
+                "Use 'adjacency' instead.".format(kwargs['precomputed']),
+                UserWarning)
+        del kwargs['precomputed']
+    return Graph(sparse.coo_matrix(G.get_adjacency().data),
+                 precomputed='adjacency', **kwargs)

graphtools/base.py

@@ -311,12 +311,12 @@ class BaseGraph(with_metaclass(abc.ABCMeta, Base)):
         Defines method of MNN symmetrization.
         '+'  : additive
         '*'  : multiplicative
-        'gamma' : min-max
+        'theta' : min-max
         'none' : no symmetrization
 
-    gamma: float (default: 0.5)
+    theta: float (default: 0.5)
         Min-max symmetrization constant.
-        K = `gamma * min(K, K.T) + (1 - gamma) * max(K, K.T)`
+        K = `theta * min(K, K.T) + (1 - theta) * max(K, K.T)`
 
     initialize : `bool`, optional (default : `True`)
         if false, don't create the kernel matrix.
@@ -337,11 +337,20 @@ class BaseGraph(with_metaclass(abc.ABCMeta, Base)):
     """
 
     def __init__(self, kernel_symm='+',
+                 theta=None,
                  gamma=None,
                  initialize=True, **kwargs):
+        if gamma is not None:
+            warnings.warn("gamma is deprecated. "
+                          "Setting theta={}".format(gamma), FutureWarning)
+            theta = gamma
+        if kernel_symm == 'gamma':
+            warnings.warn("kernel_symm='gamma' is deprecated. "
+                          "Setting kernel_symm='theta'", FutureWarning)
+            kernel_symm = 'theta'
         self.kernel_symm = kernel_symm
-        self.gamma = gamma
-        self._check_symmetrization(kernel_symm, gamma)
+        self.theta = theta
+        self._check_symmetrization(kernel_symm, theta)
 
         if initialize:
             tasklogger.log_debug("Initializing kernel...")
@@ -350,25 +359,25 @@ def __init__(self, kernel_symm='+',
             tasklogger.log_debug("Not initializing kernel.")
         super().__init__(**kwargs)
 
-    def _check_symmetrization(self, kernel_symm, gamma):
-        if kernel_symm not in ['+', '*', 'gamma', None]:
+    def _check_symmetrization(self, kernel_symm, theta):
+        if kernel_symm not in ['+', '*', 'theta', None]:
             raise ValueError(
                 "kernel_symm '{}' not recognized. Choose from "
-                "'+', '*', 'gamma', or 'none'.".format(kernel_symm))
-        elif kernel_symm != 'gamma' and gamma is not None:
-            warnings.warn("kernel_symm='{}' but gamma is not None. "
-                          "Setting kernel_symm='gamma'.".format(kernel_symm))
-            self.kernel_symm = kernel_symm = 'gamma'
-
-        if kernel_symm == 'gamma':
-            if gamma is None:
-                warnings.warn("kernel_symm='gamma' but gamma not given. "
-                              "Defaulting to gamma=0.5.")
-                self.gamma = gamma = 0.5
-            elif not isinstance(gamma, numbers.Number) or \
-                    gamma < 0 or gamma > 1:
-                raise ValueError("gamma {} not recognized. Expected "
-                                 "a float between 0 and 1".format(gamma))
+                "'+', '*', 'theta', or 'none'.".format(kernel_symm))
+        elif kernel_symm != 'theta' and theta is not None:
+            warnings.warn("kernel_symm='{}' but theta is not None. "
+                          "Setting kernel_symm='theta'.".format(kernel_symm))
+            self.kernel_symm = kernel_symm = 'theta'
+
+        if kernel_symm == 'theta':
+            if theta is None:
+                warnings.warn("kernel_symm='theta' but theta not given. "
+                              "Defaulting to theta=0.5.")
+                self.theta = theta = 0.5
+            elif not isinstance(theta, numbers.Number) or \
+                    theta < 0 or theta > 1:
+                raise ValueError("theta {} not recognized. Expected "
+                                 "a float between 0 and 1".format(theta))
 
     def _build_kernel(self):
         """Private method to build kernel matrix
@@ -400,26 +409,26 @@ def symmetrize_kernel(self, K):
         elif self.kernel_symm == "*":
             tasklogger.log_debug("Using multiplication symmetrization.")
             K = K.multiply(K.T)
-        elif self.kernel_symm == 'gamma':
+        elif self.kernel_symm == 'theta':
             tasklogger.log_debug(
-                "Using gamma symmetrization (gamma = {}).".format(self.gamma))
-            K = self.gamma * elementwise_minimum(K, K.T) + \
-                (1 - self.gamma) * elementwise_maximum(K, K.T)
+                "Using theta symmetrization (theta = {}).".format(self.theta))
+            K = self.theta * elementwise_minimum(K, K.T) + \
+                (1 - self.theta) * elementwise_maximum(K, K.T)
         elif self.kernel_symm is None:
             tasklogger.log_debug("Using no symmetrization.")
             pass
         else:
             # this should never happen
             raise ValueError(
-                "Expected kernel_symm in ['+', '*', 'gamma' or None]. "
-                "Got {}".format(self.gamma))
+                "Expected kernel_symm in ['+', '*', 'theta' or None]. "
+                "Got {}".format(self.theta))
         return K
 
     def get_params(self):
         """Get parameters from this object
         """
         return {'kernel_symm': self.kernel_symm,
-                'gamma': self.gamma}
+                'theta': self.theta}
 
     def set_params(self, **params):
         """Set parameters on this object
@@ -429,7 +438,7 @@ def set_params(self, **params):
         Valid parameters:
         Invalid parameters: (these would require modifying the kernel matrix)
         - kernel_symm
-        - gamma
+        - theta
 
         Parameters
         ----------
@@ -439,8 +448,8 @@ def set_params(self, **params):
         -------
         self
         """
-        if 'gamma' in params and params['gamma'] != self.gamma:
-            raise ValueError("Cannot update gamma. Please create a new graph")
+        if 'theta' in params and params['theta'] != self.theta:
+            raise ValueError("Cannot update theta. Please create a new graph")
         if 'kernel_symm' in params and \
                 params['kernel_symm'] != self.kernel_symm:
             raise ValueError(
@@ -535,6 +544,42 @@ def build_kernel(self):
         """
         raise NotImplementedError
 
+    def to_pygsp(self, **kwargs):
+        """Convert to a PyGSP graph
+
+        For use only when the user means to create the graph using
+        the flag `use_pygsp=True`, and doesn't wish to recompute the kernel.
+        Creates a graphtools.graphs.TraditionalGraph with a precomputed
+        affinity matrix which also inherits from pygsp.graphs.Graph.
+
+        Parameters
+        ----------
+        kwargs
+            keyword arguments for graphtools.Graph
+
+        Returns
+        -------
+        G : graphtools.base.PyGSPGraph, graphtools.graphs.TraditionalGraph
+        """
+        from . import api
+        if 'precomputed' in kwargs:
+            if kwargs['precomputed'] != 'affinity':
+                warnings.warn(
+                    "Cannot build PyGSPGraph with precomputed={}. "
+                    "Using 'affinity' instead.".format(kwargs['precomputed']),
+                    UserWarning)
+            del kwargs['precomputed']
+        if 'use_pygsp' in kwargs:
+            if kwargs['use_pygsp'] is not True:
+                warnings.warn(
+                    "Cannot build PyGSPGraph with use_pygsp={}. "
+                    "Use True instead.".format(kwargs['use_pygsp']),
+                    UserWarning)
+            del kwargs['use_pygsp']
+        return api.Graph(self.K,
+                         precomputed="affinity", use_pygsp=True,
+                         **kwargs)
+
 
 class PyGSPGraph(with_metaclass(abc.ABCMeta, pygsp.graphs.Graph, Base)):
     """Interface between BaseGraph and PyGSP.