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

Return type:

new_nodes_positions

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

  • parents_x

  • children_parent_idxs

  • node_radii

Return type:

children_x

_initial_parent_distribution(node_radii)[source]
Parameters:

node_radii

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)

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

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.