d3graph 2.7.0__tar.gz → 2.8.0__tar.gz

{d3graph-2.7.0/d3graph.egg-info → d3graph-2.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: d3graph
-Version: 2.7.0
+Version: 2.8.0
 Summary: Python package to create interactive network based on d3js.
 Author-email: Erdogan Taskesen <erdogant@gmail.com>
 License-Expression: BSD-3-Clause
@@ -24,7 +24,7 @@ Requires-Dist: networkx>2
 Requires-Dist: ismember
 Requires-Dist: jinja2
 Requires-Dist: packaging
-Requires-Dist: markupsafe==2.0.1
+Requires-Dist: markupsafe
 Requires-Dist: python-louvain
 Requires-Dist: datazets
 Dynamic: license-file

{d3graph-2.7.0 → d3graph-2.8.0}/d3graph/__init__.py

@@ -11,11 +11,13 @@ from d3graph.d3graph import (
     adjmat2dict,
     data_checks,
     check_logger,
+    get_hex_color,
+    import_example,
     )
 
 __author__ = 'Erdogan Tasksen'
 __email__ = 'erdogant@gmail.com'
-__version__ = '2.7.0'
+__version__ = '2.8.0'
 
 # Setup root logger
 _logger = logging.getLogger('d3graph')
@@ -39,13 +41,13 @@ The ouput is a html file that is interactive and stand alone.
 
 Examples
 --------
->>> from d3graph import d3graph, vec2adjmat
+>>> from d3graph import d3graph, vec2adjmat, import_example
 >>>
 >>> # Initialize
 >>> d3 = d3graph()
 >>>
 >>> # Load karate example
->>> df = d3.import_example('energy')
+>>> df = import_example('energy')
 >>> adjmat = vec2adjmat(source=df['source'], target=df['target'], weight=df['weight'])
 >>>
 >>> # Initialize
@@ -58,7 +60,7 @@ Examples
 >>> d3.set_edge_properties(directed=True)
 >>>
 >>> # Plot
->>> d3.show()
+>>> d3.show(node_text_inside=True)
 
 References
 ----------

{d3graph-2.7.0 → d3graph-2.8.0}/d3graph/d3graph.py

@@ -21,6 +21,7 @@ import colourmap as cm
 import networkx as nx
 import numpy as np
 import pandas as pd
+from pandas.arrays import StringArray
 from ismember import ismember
 from jinja2 import Environment, PackageLoader
 from packaging import version
@@ -119,6 +120,7 @@ class d3graph:
              save_button: bool = True,
              link_tension: float = None,
              sticky: bool = None,
+             node_text_inside: bool = False,
              ) -> None:
         """Build and show the graph.
 
@@ -185,6 +187,8 @@ class d3graph:
         self.config['save_button'] = save_button
         self.config['background_color'] = background_color
         self.config['dark_mode'] = dark_mode
+        self.config['node_text_inside'] = node_text_inside
+
         # Allow show() to override the link_tension set at __init__ time
         if link_tension is not None:
             self.config['link_tension'] = link_tension
@@ -192,7 +196,8 @@ class d3graph:
         if sticky is not None:
             self.config['sticky'] = sticky
         # if self.config.get('filepath', None) != 'd3graph.html':
-        self.config['filepath'] = self.set_path(filepath)
+        if filepath is not None or self.config.get('filepath') is None:
+            self.set_path(filepath)
 
         # Create dataframe from co-occurrence matrix
         self.G = make_graph(self.node_properties, self.edge_properties)
@@ -394,7 +399,8 @@ class d3graph:
             * ['label 1','label 2','label 3', ...]
         marker : list of markers (default: 'circle')
             The marker that is used for the Node.
-            * ['circle','rect','rect', ...]
+            * 'circle' or 'hexagon' etc
+            * ['circle', 'star', 'diamond', 'square', 'pentagon', 'hexagon', 'rectangle', 'triangle-down', 'triangle']
         tooltip : list of names (default: None)
             The text that is shown when hovering over the Node.
             If not specified, the text will inherit from the label.
@@ -480,13 +486,13 @@ class d3graph:
         nodecount = self.adjmat.shape[0]
         group = np.zeros_like(node_names).astype(int)
         # Check validity of color.
-        _check_hex_color(color, nodecount)
+        color = _check_hex_color(color, nodecount, cmap=cmap)
         # Store in config
         self.config['cmap'] = 'Paired' if cmap is None else cmap
         self.config['node_scaler'] = scaler
 
         # ############ Set node label #############
-        if isinstance(label, list):
+        if isinstance(label, (list, np.ndarray, pd.Series, pd.Series, StringArray)):
             label = np.array(label).astype(str)
         elif 'numpy' in str(type(label)):
             pass
@@ -499,7 +505,7 @@ class d3graph:
         if len(label) != nodecount: raise ValueError("[label] must be of same length as the number of nodes")
 
         # ############ tooltip text #############
-        if isinstance(tooltip, list):
+        if isinstance(tooltip, (list, np.ndarray, pd.Series, StringArray)):
             tooltip = np.array(tooltip).astype(str)
         elif 'numpy' in str(type(tooltip)):
             pass
@@ -512,7 +518,7 @@ class d3graph:
         if len(tooltip) != nodecount: raise ValueError("[tooltip text] must be of same length as the number of nodes")
 
         # ############ Set node color #############
-        if isinstance(color, list) and len(color) == nodecount:
+        if isinstance(color, (list, np.ndarray, pd.Series, StringArray)) and len(color) == nodecount:
             color = np.array(color)
         elif 'numpy' in str(type(color)):
             color = _get_hexcolor(color, cmap=self.config['cmap'])
@@ -542,7 +548,7 @@ class d3graph:
         fontsize = _set_node_fontsize(self, fontsize, nodecount)
 
         # ########## Set node color edge #############
-        if isinstance(edge_color, list):
+        if isinstance(edge_color, (list, np.ndarray, pd.Series, StringArray)):
             edge_color = np.array(edge_color)
         elif 'numpy' in str(type(edge_color)):
             pass
@@ -574,7 +580,7 @@ class d3graph:
         marker = _set_marker(self, marker, nodecount)
 
         # ############ Set node edge size #############
-        if isinstance(edge_size, list):
+        if isinstance(edge_size, (list, np.ndarray, pd.Series, StringArray)):
             edge_size = np.array(edge_size)
         elif 'numpy' in str(type(edge_size)):
             pass
@@ -597,16 +603,16 @@ class d3graph:
                                           'marker': marker[i],
                                           'label': label[i],
                                           'tooltip': tooltip[i],
-                                          'color': color[i].astype(str),
-                                          'opacity': opacity[i].astype(str),
-                                          'fontcolor': fontcolor[i].astype(str),
-                                          'fontsize': fontsize[i].astype(int),
+                                          'color': str(color[i]),
+                                          'opacity': str(opacity[i]),
+                                          'fontcolor': str(fontcolor[i]),
+                                          'fontsize': str(fontsize[i]),
                                           'size': size[i],
                                           'edge_size': edge_size[i],
                                           'edge_color': edge_color[i],
                                           'group': group[i]}
 
-        logger.info('Number of unique nodes: %.0d', len(self.node_properties.keys()))
+        logger.info(f'Number of unique nodes: {len(self.node_properties.keys())}')
 
     # compute clusters
     def get_cluster_color(self, node_names: list = None, color: str = '#000080') -> tuple:
@@ -713,13 +719,13 @@ class d3graph:
 
         Examples
         --------
-        >>> from d3graph import d3graph
+        >>> from d3graph import d3graph, import_example
         >>>
         >>> # Initialize
         >>> d3 = d3graph()
         >>>
         >>> # Load karate example
-        >>> adjmat, df = d3.import_example('karate')
+        >>> adjmat, df = import_example('karate')
         >>>
         >>> # Initialize
         >>> d3.graph(adjmat)
@@ -793,6 +799,7 @@ class d3graph:
                    'collision': self.config['collision'],
                    'link_tension': self.config.get('link_tension', 1.0),
                    'sticky': self.config.get('sticky', False),
+                   'node_text_inside': self.config.get('node_text_inside', False),
                    'CLICK_COMMENT': CLICK_COMMENT,
                    'CLICK_FILL': click_properties['fill'],
                    'CLICK_STROKE': click_properties['stroke'],
@@ -863,7 +870,8 @@ class d3graph:
         os.makedirs(dirname, exist_ok=True)
         filepath = os.path.abspath(os.path.join(dirname, filename))
         logger.debug(f'filepath is set to [{filepath}]')
-        return Path(filepath)
+        # Set to config
+        self.config['filepath'] = Path(filepath)
 
     def import_example(self, data='energy', url=None, sep=','):
         """Import example dataset from github source.
@@ -887,38 +895,7 @@ class d3graph:
             * https://github.com/erdogant/datazets
 
         """
-        if data == 'small':
-            source = ['node A', 'node F', 'node B', 'node B', 'node B', 'node A', 'node C', 'node Z']
-            target = ['node F', 'node B', 'node J', 'node F', 'node F', 'node M', 'node M', 'node A']
-            weight = [5.56, 0.5, 0.64, 0.23, 0.9, 3.28, 0.5, 0.45]
-            adjmat = vec2adjmat(source, target, weight=weight)
-            return adjmat, None
-        elif data == 'bigbang':
-            df = dz.get(data=data)
-            adjmat = vec2adjmat(df['source'], df['target'], weight=df['weight'])
-            return adjmat
-        elif data == 'karate':
-            import scipy
-            if version.parse(scipy.__version__) < version.parse('1.8.0'):
-                raise ImportError(
-                    '[d3graph] >Error: This release requires scipy version >= 1.8.0. Try: pip install -U scipy>=1.8.0')
-
-            G = nx.karate_club_graph()
-            adjmat = nx.adjacency_matrix(G).todense()
-            adjmat = pd.DataFrame(index=range(adjmat.shape[0]), data=adjmat, columns=range(adjmat.shape[0]))
-            adjmat.columns = adjmat.columns.astype(str)
-            adjmat.index = adjmat.index.astype(str)
-            adjmat.iloc[3, 4] = 5
-            adjmat.iloc[4, 5] = 6
-            adjmat.iloc[5, 6] = 7
-
-            df = pd.DataFrame(index=adjmat.index)
-            df['degree'] = np.array([*G.degree()])[:, 1]
-            df['label'] = [G.nodes[i]['club'] for i in range(len(G.nodes))]
-
-            return adjmat, df
-        else:
-            return dz.get(data=data, url=url, sep=sep)
+        return import_example(data=data, url=url, sep=sep)
 
 
 # %%
@@ -1427,6 +1404,8 @@ def _get_hexcolor(label, cmap: str = 'Paired'):
 
     return label
 
+def get_hex_color(labels, cmap='Set1', opaque_type='per_class', gradient=None):
+    return cm.fromlist(labels, scheme='hex', opaque_type=opaque_type, gradient=gradient)
 
 # %% Do checks
 def library_compatibility_checks() -> None:
@@ -1437,7 +1416,7 @@ def library_compatibility_checks() -> None:
     None.
 
     """
-    if not version.parse(nx.__version__) >= version.parse('2.5'):
+    if not version.parse(nx.__version__) >= version.parse('2.5.0'):
         logger.error('Networkx version should be >= 2.5')
         logger.info('Hint: pip install -U networkx')
 
@@ -1623,15 +1602,21 @@ def adjmat2vec(adjmat, min_weight: float = 1.0) -> pd.DataFrame:
     return adjmat
 
 
-def _check_hex_color(color, n=None):
-    if isinstance(color, str) and len(color) != 7: raise ValueError(
-        'Input parameter [color] has wrong format. Must be like color="#000000"')
-    if isinstance(color, list) and len(color) == 0: raise ValueError(
-        'Input parameter [color] has wrong format and length. Must be like: color=["#000000", "...", "#000000"]')
-    if isinstance(color, list) and (not np.all(list(map(lambda x: len(x) == 7, color)))): raise ValueError(
-        '[color] contains incorrect length of hex-color! Hex must be of length 7: ["#000000", "#000000", etc]')
-    if (n is not None) and isinstance(color, list) and len(color) != n:
-        raise ValueError(f'Input parameter [color] has wrong length. Must be of length: {str(n)}')
+def _check_hex_color(color, n=None, cmap='Set1'):
+    if isinstance(color, str) and len(color) != 7:
+        logger.warning('Input parameter [color] has wrong format. Must be like color="#000000" <auto-fixing>')
+        return get_hex_color(color, cmap=cmap)[0]
+    if isinstance(color, (list, np.ndarray, pd.Series, pd.Series, StringArray)) and len(color) == 0:
+        logger.warning('Input parameter [color] has wrong format and length. Must be like: color=["#000000", "...", "#000000"] <auto-fixing>')
+        return get_hex_color(color, cmap=cmap)[0]
+    if isinstance(color, (list, np.ndarray, pd.Series, pd.Series, StringArray)) and (not np.all(list(map(lambda x: len(x) == 7, color)))):
+        logger.warning('[color] contains incorrect hex-colors. Hex must be of length 7: ["#000000", "#000000", etc] <auto-fixing>')
+        return get_hex_color(color, cmap=cmap)[0]
+    if (n is not None) and isinstance(color, (list, np.ndarray, pd.Series, pd.Series, StringArray)) and len(color) != n:
+        logger.warning(f'Input parameter [color] has wrong length. Must be of length: {str(n)} <auto-fixing>')
+        return get_hex_color(color, cmap=cmap)[0]
+    # Return original input
+    return color
 
 
 def _set_opacity(self, opacity, nodecount, node_names):
@@ -1673,20 +1658,63 @@ def _compute_centrality(adjmat):
     # opacity = opacity[:-2]
     return opacity
 
+MARKERS_SUPPORTED = {
+    'circle',
+    'ellipse',
+    'rect', 'rectangle', 'square',
+    'rect-wide', 'rectangle-wide',
+    'triangle', 'triangle-up', 'triangle-down',
+    'diamond',
+    'star',
+    'hexagon',
+    'pentagon',
+}
+
+
 def _set_marker(self, marker, nodecount):
-    if isinstance(marker, type(None)):
+    """Validate and broadcast the node marker/shape.
+
+    Supported shapes
+    ----------------
+    'circle'                         : Circle (default)
+    'ellipse'                        : Ellipse (wider than tall)
+    'rect' / 'rectangle' / 'square' : Square
+    'rect-wide' / 'rectangle-wide'  : Wide rectangle
+    'triangle' / 'triangle-up'      : Triangle pointing up
+    'triangle-down'                  : Triangle pointing down
+    'diamond'                        : Diamond (rotated square)
+    'star'                           : 5-pointed star
+    'hexagon'                        : Regular hexagon
+    'pentagon'                       : Regular pentagon
+    """
+    if marker is None:
         marker = 'circle'
 
-    if isinstance(marker, list) and len(marker)==nodecount:
-        marker = np.array(marker)
-    elif 'numpy' in str(type(marker)) and len(marker)==nodecount:
+    if isinstance(marker, (list, np.ndarray, pd.Series)) and len(marker) == nodecount:
+        marker = np.array([str(m).lower() for m in marker])
+        invalid = set(marker) - MARKERS_SUPPORTED
+        if invalid:
+            logger.warning(
+                'Unknown marker(s) %s. Supported: %s. Falling back to "circle" for those.',
+                sorted(invalid), sorted(MARKERS_SUPPORTED)
+            )
+            marker = np.where(np.isin(marker, list(MARKERS_SUPPORTED)), marker, 'circle')
+    elif 'numpy' in str(type(marker)) and len(marker) == nodecount:
         pass
     elif isinstance(marker, str):
+        marker = marker.lower()
+        if marker not in MARKERS_SUPPORTED:
+            logger.warning(
+                'Unknown marker "%s". Supported: %s. Falling back to "circle".',
+                marker, sorted(MARKERS_SUPPORTED)
+            )
+            marker = 'circle'
         marker = np.repeat(marker, nodecount)
+    else:
+        marker = np.repeat('circle', nodecount)
 
-    # Make check
-    if len(marker) != nodecount: raise ValueError("Node size must be of same length as the number of nodes")
-    # Return
+    if len(marker) != nodecount:
+        raise ValueError("Node marker must be of same length as the number of nodes")
     return marker
 
 def _set_node_size(self, size, minmax, nodecount):
@@ -1755,6 +1783,61 @@ def _set_node_fontcolor(self, fontcolor, color, node_names, nodecount):
     # return
     return fontcolor
 
+def import_example(data='energy', url=None, sep=','):
+    """Import example dataset from github source.
+
+    Import one of the few datasets from github source or specify your own download url link.
+
+    Parameters
+    ----------
+    data : str
+        Name of datasets: 'sprinkler', 'titanic', 'student', 'fifa', 'cancer', 'waterpump', 'retail'
+    url : str
+        url link to to dataset.
+
+    Returns
+    -------
+    pd.DataFrame()
+        Dataset containing mixed features.
+
+    References
+    ----------
+        * https://github.com/erdogant/datazets
+
+    """
+    if data == 'small':
+        source = ['node A', 'node F', 'node B', 'node B', 'node B', 'node A', 'node C', 'node Z']
+        target = ['node F', 'node B', 'node J', 'node F', 'node F', 'node M', 'node M', 'node A']
+        weight = [5.56, 0.5, 0.64, 0.23, 0.9, 3.28, 0.5, 0.45]
+        adjmat = vec2adjmat(source, target, weight=weight)
+        return adjmat, None
+    elif data == 'bigbang':
+        df = dz.get(data=data)
+        adjmat = vec2adjmat(df['source'], df['target'], weight=df['weight'])
+        return adjmat
+    elif data == 'karate':
+        import scipy
+        if version.parse(scipy.__version__) < version.parse('1.8.0'):
+            raise ImportError(
+                '[d3graph] >Error: This release requires scipy version >= 1.8.0. Try: pip install -U scipy>=1.8.0')
+
+        G = nx.karate_club_graph()
+        adjmat = nx.adjacency_matrix(G).todense()
+        adjmat = pd.DataFrame(index=range(adjmat.shape[0]), data=adjmat, columns=range(adjmat.shape[0]))
+        adjmat.columns = adjmat.columns.astype(str)
+        adjmat.index = adjmat.index.astype(str)
+        adjmat.iloc[3, 4] = 5
+        adjmat.iloc[4, 5] = 6
+        adjmat.iloc[5, 6] = 7
+
+        df = pd.DataFrame(index=adjmat.index)
+        df['degree'] = np.array([*G.degree()])[:, 1]
+        df['label'] = [G.nodes[i]['club'] for i in range(len(G.nodes))]
+
+        return adjmat, df
+    else:
+        return dz.get(data=data, url=url, sep=sep)
+
 
 def get_support(support):
     """Support."""