wepy.analysis.network_layouts.tree module

Class for generating layouts for resampling trees.

Routines

ResamplingTreeLayout.layout

class wepy.analysis.network_layouts.tree.ResamplingTreeLayout(node_radius=1.0, row_spacing=5.0, step_spacing=20.0, central_axis=0.0)[source]

Bases: object

Class that wraps the parameters for generating resampling tree layouts.

Use the ‘layout’ method to generate inputs to a LayoutGraph for rendering.

node_radius

Default node radius to use.

Type

float

row_spacing

Spacing between nodes in a single row in layout.

Type

float

step_spacing

Spacing between the rows of nodes in each step of the layout.

Type

float

central_axis

X coordinate value to center each row around in the tree layout.

Type

float

Constructing the object is just a setting of the parameters and collection of methods for generating layout positions.

Parameters

  • node_radius (float, optional) –

    Default node radius to use.

    (Default value = 1.0)

  • row_spacing (float) –

    Spacing between nodes in a single row in layout.

    (Default value = 5.0)

  • step_spacing (float) –

    Spacing between the rows of nodes in each step of the layout.

    (Default value = 20.0)

  • central_axis (float) –

    X coordinate value to center each row around in the tree layout.

    (Default value = 0.0)

_overlaps(positions, node_radii, node_idx)[source]
Parameters

  • positions –

  • node_radii –

  • node_idx –

_node_row_length(node_positions, node_radii)[source]

Get the edge to edge length of a row of nodes.

Parameters

  • node_positions –

  • node_radii –

Returns

row_length

Return type

float

_simple_gen_distribution(nodes_x, node_radii)[source]
Parameters

  • nodes_x –

  • node_radii –

Returns

Return type

new_nodes_positions

_simple_next_gen(parents_x, children_parent_idxs, node_radii)[source]
Parameters

  • parents_x –

  • children_parent_idxs –

  • node_radii –

Returns

Return type

children_x

_initial_parent_distribution(node_radii)[source]
Parameters

node_radii –

Returns

Return type

positions

_center_row(positions, radii, center)[source]

Centers the midpoint of a row of nodes around a number.

Parameters

  • positions –

  • radii –

  • center (float) –

Returns

Return type

centered_positions

_layout_array(parent_table, radii_array)[source]

Generates the structured array of positions for nodes in the parent forest tree layout given the corresponding radii.

Parameters

  • parent_table –

  • radii_array –

Returns

Return type

node_positions

layout(parent_forest, node_radii=None)[source]

Given a parent forest object, returns a dictionary mapping nodes to their xyz layout coordinates.

If the node radii are given (as a dictionary mapping node ID to the desired radius) these are used as the the node radii and the default node radius parameter of the layout object is ignored.

Radii are needed to calculate the proper positions so there is no overlaps between nodes.

Parameters

  • parent_forest (ParentForest object) –

  • node_radii (dict of node_id: float) –

    A dictionary mapping the nodes to node radii.

    (Default value = None)

Returns

node_coords – x, y, z coordinates for all nodes. Z will be 0 for all.

Return type

dict of node_id: array_like of float of dim (3,)

Raises

ValueError – If an invalid node_id is given.

Warns

  • If some but not all nodes were given assigned radii. Uses

  • default value for unspecified nodes.