added parameters for hypergraph function

requirements/requirements.txt

@@ -4,6 +4,5 @@ numpy>=1.19.5
 quantities>=0.14.1
 matplotlib>=3.3.2
 seaborn>=0.9.0
-bokeh>=3.0.0
 holoviews>=1.16.0
 networkx>=3.0.0

viziphant/patterns.py

@@ -399,8 +399,8 @@ def plot_patterns(spiketrains, patterns, circle_sizes=(3, 50, 70),
     axes.yaxis.set_label_coords(-0.01, 0.5)
     return axes
 
-# TODO: add a parameter node_size
-def plot_patterns_hypergraph(patterns, num_neurons=None):
+def plot_patterns_hypergraph(patterns, node_size=3, pattern_size=None, num_neurons=None,\
+                             highlight_patterns=None, mark_neuron=None, node_color='white'):
     """
     Hypergraph visualization of spike patterns.
 
@@ -430,12 +430,19 @@ def plot_patterns_hypergraph(patterns, num_neurons=None):
         :func:`elephant.spade.spade` or
         :func:`elephant.cell_assembly_detection.cell_assembly_detection`
         pattern detectors.
+    node_size (optional): int
+        Change the size of the drawen nodes
+    pattern_size (optional): tuple or int
+        Only draw patterns that are in range of pattern_size
     num_neurons: None or int
         If None, only the neurons that are part of a pattern are shown. If an
         integer is passed, it identifies the total number of recorded neurons
         including non-pattern neurons to be additionally shown in the graph.
         Default: None
-
+    highlight_patterns (optional) : int
+        Highlight pattern which includes neuron x
+    node_color (optional) : String
+        change the color of the nodes
     Returns
     -------
     A handle to a matplotlib figure containing the hypergraph.
@@ -493,11 +500,33 @@ def plot_patterns_hypergraph(patterns, num_neurons=None):
 
     # Create one hypergraph per dataset
     hyperedges = []
+
+    # Create "range" of pattern_size
+    if (isinstance(pattern_size, int)): pattern_size=(pattern_size, pattern_size)
+
     # Create one hyperedge from every pattern
     for pattern in patterns:
         # A hyperedge is the set of neurons of a pattern
-        hyperedges.append(pattern['neurons'])
-
+        if pattern_size is None:
+            hyperedges.append(pattern['neurons'])
+        # check if hyperedge(pattern) is greater or equal to min_pattern_size
+        elif len(pattern['neurons']) >= pattern_size[0] and len(pattern['neurons']) <= pattern_size[1] or highlight_patterns in pattern['neurons']:
+            hyperedges.append(pattern['neurons'])
+
+    # check if neuron to highlight is in hyperedge
+    temp_hyperedges = []
+    if highlight_patterns is not None:
+        if isinstance(highlight_patterns, int):
+            for edge in hyperedges:
+                if highlight_patterns in edge:
+                    temp_hyperedges.append(edge)
+            hyperedges = temp_hyperedges
+
+    # TODO: highlight_patterns as a list 
+
+    if (len(hyperedges) == 0):
+        raise Exception('Could not find any hyperedges that match the given parameters')
+
     # Currently, all hyperedges receive the same weights
     weights = [weight] * len(hyperedges)
 
@@ -507,8 +536,7 @@ def plot_patterns_hypergraph(patterns, num_neurons=None):
                     weights=weights,
                     repulse=repulsive)
     hypergraphs.append(hg)
-
-    view = View(hypergraphs)
+    view = View(hypergraphs, node_size, mark_neuron, node_color)
     fig = view.show(subset_style=VisualizationStyle.COLOR,
                     triangulation_style=VisualizationStyle.INVISIBLE)
 

viziphant/patterns_src/view.py

@@ -35,7 +35,7 @@ class View:
     for the visualization of hypergraphs.
     """
 
-    def __init__(self, hypergraphs, title=None):
+    def __init__(self, hypergraphs, node_size=3, mark_neuron=None, node_color='white', title=None):
         """
         Constructs a View object that handles the visualization
         of the given hypergraphs.
@@ -45,6 +45,15 @@ def __init__(self, hypergraphs, title=None):
         hypergraphs: list of Hypergraph objects
             Hypergraphs to be visualized.
             Each hypergraph should contain data of one data set.
+
+        node_size (optional) : int
+            Size of the nodes in the Hypergraphs
+        
+        mark_neuron (optional) : int
+            Neuron with given number will be highlighted
+        
+        node_color (optional) : String
+            change the color of the nodes
         """
 
         # Hyperedge drawings
@@ -53,12 +62,21 @@ def __init__(self, hypergraphs, title=None):
         # Which color of the color map to use next
         self.current_color = 1
 
-        # Size of the vertices TODO: add as parameter
+        # radius of the hyperedges
         self.node_radius = .2
+
+        # Size of the nodes (vertices of hypergraph)
+        self.node_size = node_size
+
+        # Color of the nodes
+        self.node_color = node_color
 
         # Selected title of the figure
         self.title = title
 
+        # Marked node will be in a different color
+        self.mark_neuron = mark_neuron
+
         # If no data was provided, fill in dummy data
         if hypergraphs:
             self.hypergraphs = hypergraphs
@@ -107,7 +125,7 @@ def _setup_graph_visualization(self):
         # The hv.Graph visualization is used for displaying the data
         # hv.Graph displays the nodes (and optionally binary edges) of a graph
         dynamic_map = hv.DynamicMap(hv.Graph, streams=[pipe])
-
+        
         # Define options for visualization
         dynamic_map.opts(
             # Some space around the Graph in order to avoid nodes being on the
@@ -124,8 +142,7 @@ def _setup_graph_visualization(self):
             # All in black
             cmap=['#ffffff', '#ffffff'] * 50,
             # Size of the nodes
-            node_size=self.node_radius))
-
+            node_size=self.node_size, node_color=self.node_color, show_legend=True))
         return dynamic_map, pipe
 
     def _setup_hyperedge_drawing(self):
@@ -226,10 +243,10 @@ def show(self,
         # Set size of the plot to a square to avoid distortions
         self.plot = plot.redim.range(x=(-1, 11), y=(-1, 11))
         # TODO: how to get axes? currently figure
-        axes = hv.render(plot, backend="matplotlib")
-        return axes
-
-    def draw_hyperedges(self,
+        fig = hv.render(plot, backend="matplotlib")
+        return fig
+        
+    def draw_hyperedges(self, highlight_neuron=None,
                         subset_style=VisualizationStyle.COLOR,
                         triangulation_style=VisualizationStyle.INVISIBLE):
         """
@@ -396,7 +413,7 @@ def _update_nodes(self, data):
         nodes = hv.Nodes((pos_x, pos_y, vertex_ids, vertex_labels),
                          extents=(0.01, 0.01, 0.01, 0.01),
                          vdims='Label')
-
+        
         new_data = ((edge_source, edge_target), nodes)
         self.pipe.send(new_data)