Source code for holoviews.plotting.bokeh.graphs

from collections import defaultdict

import numpy as np
import param
from bokeh.models import (

from import Dataset
from ...core.options import Cycle, abbreviated_exception
from ...core.util import dimension_sanitizer, unique_array
from ...util.transform import dim
from ..mixins import ChordMixin, GraphMixin
from ..util import get_directed_graph_paths, process_cmap
from .chart import ColorbarPlot, PointPlot
from .element import CompositeElementPlot, LegendPlot
from .styles import (

[docs]class GraphPlot(GraphMixin, CompositeElementPlot, ColorbarPlot, LegendPlot): arrowhead_length = param.Number(default=0.025, doc=""" If directed option is enabled this determines the length of the arrows as fraction of the overall extent of the graph.""") directed = param.Boolean(default=False, doc=""" Whether to draw arrows on the graph edges to indicate the directionality of each edge.""") selection_policy = param.ObjectSelector(default='nodes', objects=['edges', 'nodes', None], doc=""" Determines policy for inspection of graph components, i.e. whether to highlight nodes or edges when selecting connected edges and nodes respectively.""") inspection_policy = param.ObjectSelector(default='nodes', objects=['edges', 'nodes', None], doc=""" Determines policy for inspection of graph components, i.e. whether to highlight nodes or edges when hovering over connected edges and nodes respectively.""") tools = param.List(default=['hover', 'tap'], doc=""" A list of plugin tools to use on the plot.""") # Deprecated options color_index = param.ClassSelector(default=None, class_=(str, int), allow_None=True, doc=""" Deprecated in favor of color style mapping, e.g. `node_color=dim('color')`""") edge_color_index = param.ClassSelector(default=None, class_=(str, int), allow_None=True, doc=""" Deprecated in favor of color style mapping, e.g. `edge_color=dim('color')`""") # Map each glyph to a style group _style_groups = {'scatter': 'node', 'multi_line': 'edge', 'patches': 'edge', 'bezier': 'edge'} style_opts = (['edge_'+p for p in base_properties+fill_properties+line_properties] + ['node_'+p for p in base_properties+fill_properties+line_properties] + ['node_size', 'cmap', 'edge_cmap', 'node_cmap', 'node_radius', 'node_marker']) _nonvectorized_styles = base_properties + ['cmap', 'edge_cmap', 'node_cmap'] # Filled is only supported for subclasses filled = False # Bezier paths bezier = False # Declares which columns in the data refer to node indices _node_columns = [0, 1] @property def edge_glyph(self): if self.filled: return 'patches_1' elif self.bezier: return 'bezier_1' else: return 'multi_line_1' def _hover_opts(self, element): if self.inspection_policy == 'nodes': dims = element.nodes.dimensions() dims = [(dims[2].pprint_label, '@{index_hover}')]+dims[3:] elif self.inspection_policy == 'edges': kdims = [(kd.pprint_label, '@{%s_values}' % kd) if kd in ('start', 'end') else kd for kd in element.kdims] dims = kdims+element.vdims else: dims = [] return dims, {} def _get_edge_colors(self, element, ranges, edge_data, edge_mapping, style): cdim = element.get_dimension(self.edge_color_index) if not cdim: return elstyle = self.lookup_options(element, 'style') cycle = elstyle.kwargs.get('edge_color') if not isinstance(cycle, Cycle): cycle = None idx = element.get_dimension_index(cdim) field = dimension_sanitizer( cvals = element.dimension_values(cdim) if idx in self._node_columns: factors = element.nodes.dimension_values(2, expanded=False) elif idx == 2 and cvals.dtype.kind in 'uif': factors = None else: factors = unique_array(cvals) default_cmap = 'viridis' if factors is None else 'tab20' cmap = style.get('edge_cmap', style.get('cmap', default_cmap)) nan_colors = {k: rgba_tuple(v) for k, v in self.clipping_colors.items()} if factors is None or (factors.dtype.kind in 'uif' and idx not in self._node_columns): colors, factors = None, None else: if factors.dtype.kind == 'f': cvals = cvals.astype(np.int32) factors = factors.astype(np.int32) if factors.dtype.kind not in 'SU': field += '_str__' cvals = [str(f) for f in cvals] factors = (str(f) for f in factors) factors = list(factors) if isinstance(cmap, dict): colors = [cmap.get(f, nan_colors.get('NaN', self._default_nan)) for f in factors] else: colors = process_cmap(cycle or cmap, len(factors)) if field not in edge_data: edge_data[field] = cvals edge_style = dict(style, cmap=cmap) mapper = self._get_colormapper(cdim, element, ranges, edge_style, factors, colors, 'edge', 'edge_colormapper') transform = {'field': field, 'transform': mapper} color_type = 'fill_color' if self.filled else 'line_color' edge_mapping['edge_'+color_type] = transform edge_mapping['edge_nonselection_'+color_type] = transform edge_mapping['edge_selection_'+color_type] = transform def _get_edge_paths(self, element, ranges): path_data, mapping = {}, {} xidx, yidx = (1, 0) if self.invert_axes else (0, 1) if element._edgepaths is not None: edges = element._split_edgepaths.split(datatype='array', dimensions=element.edgepaths.kdims) if len(edges) == len(element): path_data['xs'] = [path[:, xidx] for path in edges] path_data['ys'] = [path[:, yidx] for path in edges] mapping = {'xs': 'xs', 'ys': 'ys'} else: raise ValueError("Edge paths do not match the number of supplied edges." "Expected %d, found %d paths." % (len(element), len(edges))) elif self.directed: xdim, ydim = element.nodes.kdims[:2] x_range = ranges[]['combined'] y_range = ranges[]['combined'] arrow_len = np.hypot(y_range[1]-y_range[0], x_range[1]-x_range[0])*self.arrowhead_length arrows = get_directed_graph_paths(element, arrow_len) path_data['xs'] = [arr[:, 0] for arr in arrows] path_data['ys'] = [arr[:, 1] for arr in arrows] return path_data, mapping
[docs] def get_data(self, element, ranges, style): # Force static source to False static = self.static_source self.handles['static_source'] = static self.static_source = False # Get node data nodes = element.nodes.dimension_values(2) node_positions = element.nodes.array([0, 1]) # Map node indices to integers if nodes.dtype.kind not in 'uif': node_indices = {v: i for i, v in enumerate(nodes)} index = np.array([node_indices[n] for n in nodes], dtype=np.int32) layout = {node_indices[k]: (y, x) if self.invert_axes else (x, y) for k, (x, y) in zip(nodes, node_positions)} else: index = nodes.astype(np.int32) layout = {k: (y, x) if self.invert_axes else (x, y) for k, (x, y) in zip(index, node_positions)} point_data = {'index': index} # Handle node colors fixed_color = style.pop('node_color', None) cycle = self.lookup_options(element, 'style').kwargs.get('node_color') if isinstance(cycle, Cycle) and 'cmap' not in style: colors = cycle else: colors = None cdata, cmapping = self._get_color_data( element.nodes, ranges, style, name='node_fill_color', colors=colors, int_categories=True ) if fixed_color is not None and not cdata: style['node_color'] = fixed_color point_data.update(cdata) point_mapping = cmapping if 'node_fill_color' in point_mapping: style = {k: v for k, v in style.items() if k not in ['node_fill_color', 'node_nonselection_fill_color']} point_mapping['node_nonselection_fill_color'] = point_mapping['node_fill_color'] # Handle edge colors edge_mapping = {} nan_node = index.max()+1 if len(index) else 0 start, end = (element.dimension_values(i) for i in range(2)) if nodes.dtype.kind == 'f': start, end = start.astype(np.int32), end.astype(np.int32) elif nodes.dtype.kind not in 'ui': start = np.array([node_indices.get(x, nan_node) for x in start], dtype=np.int32) end = np.array([node_indices.get(y, nan_node) for y in end], dtype=np.int32) path_data = dict(start=start, end=end) self._get_edge_colors(element, ranges, path_data, edge_mapping, style) if not static: pdata, pmapping = self._get_edge_paths(element, ranges) path_data.update(pdata) edge_mapping.update(pmapping) # Get hover data if 'hover' in self.handles: if self.inspection_policy == 'nodes': index_dim = element.nodes.get_dimension(2) point_data['index_hover'] = [index_dim.pprint_value(v) for v in element.nodes.dimension_values(2)] for d in element.nodes.dimensions()[3:]: point_data[dimension_sanitizer(] = element.nodes.dimension_values(d) elif self.inspection_policy == 'edges': for d in element.dimensions(): dim_name = dimension_sanitizer( if dim_name in ('start', 'end'): dim_name += '_values' path_data[dim_name] = element.dimension_values(d) data = {'scatter_1': point_data, self.edge_glyph: path_data, 'layout': layout} mapping = {'scatter_1': point_mapping, self.edge_glyph: edge_mapping} return data, mapping, style
def _update_datasource(self, source, data): """ Update datasource with data for a new frame. """ if isinstance(source, ColumnDataSource): if self.handles['static_source']: source.trigger('data',, data) else: else: source.graph_layout = data def _init_filled_edges(self, renderer, properties, edge_mapping): "Replace edge renderer with filled renderer" glyph_model = Patches if self.filled else Bezier allowed_properties = for glyph_type in ('', 'selection_', 'nonselection_', 'hover_', 'muted_'): glyph = getattr(renderer.edge_renderer, glyph_type+'glyph', None) if glyph is None: continue group_properties = dict(properties) props = self._process_properties(self.edge_glyph, group_properties, {}) filtered = self._filter_properties(props, glyph_type, allowed_properties) new_glyph = glyph_model(**dict(filtered, **edge_mapping)) setattr(renderer.edge_renderer, glyph_type+'glyph', new_glyph) def _get_graph_properties(self, plot, element, data, mapping, ranges, style): "Computes the args and kwargs for the GraphRenderer" sources = [] properties, mappings = {}, {} for key in ('scatter_1', self.edge_glyph): gdata = data.pop(key, {}) group_style = dict(style) style_group = self._style_groups.get('_'.join(key.split('_')[:-1])) with abbreviated_exception(): group_style = self._apply_transforms(element, gdata, ranges, group_style, style_group) # Get source source = self._init_datasource(gdata) self.handles[key+'_source'] = source sources.append(source) # Get style others = [sg for sg in self._style_groups.values() if sg != style_group] glyph_props = self._glyph_properties( plot, element, source, ranges, group_style, style_group) for k, p in glyph_props.items(): if any(k.startswith(o) for o in others): continue properties[k] = p mappings.update(mapping.pop(key, {})) properties = {p: v for p, v in properties.items() if p != 'source' and 'legend' not in p} properties.update(mappings) # Initialize graph layout layout = data.pop('layout', {}) layout = StaticLayoutProvider(graph_layout=layout) self.handles['layout_source'] = layout return tuple(sources+[layout]), properties def _reorder_renderers(self, plot, renderer, mapping): "Reorders renderers based on the defined draw order" renderers = dict({r: self.handles[r+'_glyph_renderer'] for r in mapping}, graph=renderer) other = [r for r in plot.renderers if r not in renderers.values()] graph_renderers = [renderers[k] for k in self._draw_order if k in renderers] plot.renderers = other + graph_renderers def _set_interaction_policies(self, renderer): if self.selection_policy == 'nodes': renderer.selection_policy = NodesAndLinkedEdges() elif self.selection_policy == 'edges': renderer.selection_policy = EdgesAndLinkedNodes() else: renderer.selection_policy = NodesOnly() if self.inspection_policy == 'nodes': renderer.inspection_policy = NodesAndLinkedEdges() elif self.inspection_policy == 'edges': renderer.inspection_policy = EdgesAndLinkedNodes() else: renderer.inspection_policy = NodesOnly() def _init_glyphs(self, plot, element, ranges, source): # Get data and initialize data source style =[self.cyclic_index] data, mapping, style = self.get_data(element, ranges, style) self.handles['previous_id'] = element._plot_id # Initialize GraphRenderer edge_mapping = {k: v for k, v in mapping[self.edge_glyph].items() if 'color' not in k} graph_args, properties = self._get_graph_properties( plot, element, data, mapping, ranges, style) renderer = plot.graph(*graph_args, **properties) if self.filled or self.bezier: self._init_filled_edges(renderer, properties, edge_mapping) self._set_interaction_policies(renderer) # Initialize other renderers if data and mapping: CompositeElementPlot._init_glyphs( self, plot, element, ranges, source, data, mapping, style) # Reorder renderers if self._draw_order: self._reorder_renderers(plot, renderer, mapping) self.handles['glyph_renderer'] = renderer self.handles['scatter_1_glyph_renderer'] = renderer.node_renderer self.handles[self.edge_glyph+'_glyph_renderer'] = renderer.edge_renderer self.handles['scatter_1_glyph'] = renderer.node_renderer.glyph self.handles[self.edge_glyph+'_glyph'] = renderer.edge_renderer.glyph if 'hover' in self.handles: if self.handles['hover'].renderers == 'auto': self.handles['hover'].renderers = [] self.handles['hover'].renderers.append(renderer) if self.colorbar: for k, v in list(self.handles.items()): if not k.endswith('color_mapper'): continue self._draw_colorbar(plot, v, k.replace('color_mapper', ''))
[docs]class ChordPlot(ChordMixin, GraphPlot): labels = param.ClassSelector(class_=(str, dim), doc=""" The dimension or dimension value transform used to draw labels from.""") show_frame = param.Boolean(default=False, doc=""" Whether or not to show a complete frame around the plot.""") # Deprecated options label_index = param.ClassSelector(default=None, class_=(str, int), allow_None=True, doc=""" Index of the dimension from which the node labels will be drawn""") # Map each glyph to a style group _style_groups = {'scatter': 'node', 'multi_line': 'edge', 'text': 'label'} style_opts = (GraphPlot.style_opts + ['label_'+p for p in base_properties+text_properties]) _draw_order = ['multi_line_2', 'graph', 'text_1'] def _sync_arcs(self): arc_renderer = self.handles['multi_line_2_glyph_renderer'] scatter_renderer = self.handles['scatter_1_glyph_renderer'] for gtype in ('selection_', 'nonselection_', 'muted_', 'hover_', ''): glyph = getattr(scatter_renderer, gtype+'glyph') arc_glyph = getattr(arc_renderer, gtype+'glyph') if not glyph or not arc_glyph: continue scatter_props = glyph.properties_with_values(include_defaults=False) styles = {k.replace('fill', 'line'): v for k, v in scatter_props.items() if 'fill' in k} arc_glyph.update(**styles) def _init_glyphs(self, plot, element, ranges, source): super()._init_glyphs(plot, element, ranges, source) # Ensure that arc glyph matches node style if 'multi_line_2_glyph' in self.handles: arc_renderer = self.handles['multi_line_2_glyph_renderer'] scatter_renderer = self.handles['scatter_1_glyph_renderer'] arc_renderer.view = scatter_renderer.view arc_renderer.data_source = scatter_renderer.data_source self.handles['multi_line_2_source'] = scatter_renderer.data_source self._sync_arcs() def _update_glyphs(self, element, ranges, style): if 'multi_line_2_glyph' in self.handles: self._sync_arcs() super()._update_glyphs(element, ranges, style)
[docs] def get_data(self, element, ranges, style): offset = style.pop('label_offset', 1.05) data, mapping, style = super().get_data(element, ranges, style) angles = element._angles arcs = defaultdict(list) for i in range(len(element.nodes)): start, end = angles[i:i+2] vals = np.linspace(start, end, 20) xs, ys = np.cos(vals), np.sin(vals) arcs['arc_xs'].append(xs) arcs['arc_ys'].append(ys) data['scatter_1'].update(arcs) data['multi_line_2'] = data['scatter_1'] mapping['multi_line_2'] = {'xs': 'arc_xs', 'ys': 'arc_ys', 'line_width': 10} label_dim = element.nodes.get_dimension(self.label_index) labels = self.labels if label_dim and labels: self.param.warning( "Cannot declare style mapping for 'labels' option " "and declare a label_index; ignoring the label_index.") elif label_dim: labels = label_dim elif isinstance(labels, str): labels = element.nodes.get_dimension(labels) if labels is None: return data, mapping, style nodes = element.nodes if element.vdims: values = element.dimension_values(element.vdims[0]) if values.dtype.kind in 'uif': edges = Dataset(element)[values>0] nodes = list(np.unique([edges.dimension_values(i) for i in range(2)])) nodes =**{element.nodes.kdims[2].name: nodes}) xs, ys = (nodes.dimension_values(i)*offset for i in range(2)) if isinstance(labels, dim): text = labels.apply(element, flat=True) else: text = element.nodes.dimension_values(labels) text = [labels.pprint_value(v) for v in text] angles = np.arctan2(ys, xs) data['text_1'] = dict(x=xs, y=ys, text=[str(l) for l in text], angle=angles) mapping['text_1'] = dict(text='text', x='x', y='y', angle='angle', text_baseline='middle') return data, mapping, style
[docs]class NodePlot(PointPlot): """ Simple subclass of PointPlot which hides x, y position on hover. """ def _hover_opts(self, element): return element.dimensions()[2:], {}
[docs]class TriMeshPlot(GraphPlot): filled = param.Boolean(default=False, doc=""" Whether the triangles should be drawn as filled.""") style_opts = (['edge_'+p for p in base_properties+line_properties+fill_properties] + ['node_'+p for p in base_properties+fill_properties+line_properties] + ['node_size', 'cmap', 'edge_cmap', 'node_cmap']) # Declares that three columns in TriMesh refer to edges _node_columns = [0, 1, 2] def _process_vertices(self, element): style =[self.cyclic_index] edge_color = style.get('edge_color') if edge_color not in element.nodes: edge_color = self.edge_color_index simplex_dim = element.get_dimension(edge_color) vertex_dim = element.nodes.get_dimension(edge_color) if vertex_dim and not simplex_dim: simplices = element.array([0, 1, 2]) z = element.nodes.dimension_values(vertex_dim) z = z[simplices].mean(axis=1) element = element.add_dimension(vertex_dim, len(element.vdims), z, vdim=True) element._initialize_edgepaths() return element def _init_glyphs(self, plot, element, ranges, source): element = self._process_vertices(element) super()._init_glyphs(plot, element, ranges, source) def _update_glyphs(self, element, ranges, style): element = self._process_vertices(element) super()._update_glyphs(element, ranges, style)