TreeLayout

class visualife.diagrams.TreeLayout(id, viewport, max_screen_x, max_screen_y, **kwargs)

Bases: object

Base class for drawing a tree

Parameters:id – (string) a string that is used to identify graphical elements of this tree.

ID of a node will be created as ID-idx where ID is the ID of this layout object and idx is the index of a node :param viewport: (SvgViewport) or its derivative :param max_screen_x: (int) - right screen coordinate :param max_screen_y: (int) - bottom screen coordinate :param kwargs: - see below

Keyword Arguments (**kwargs)(**kwargs):  

• width (number) – width of each node in pixels
• height (number) – height of each node in pixels
• separation (number) – minimum separation between nodes in pixels
• x_margin (number) – white space margin for the diagram on both sides along X axis (in viewport units, e.g. pixels)
• y_margin (number) – white space margin for the diagram on both sides along Y axis

Attributes Summary

id	Returns ID string that identifies this drawing

Methods Summary

draw(root_node)	Draws a binary tree given by its root node :param root_node: (BTreeNode) - root of the tree
get_edge_color(node)	Returns the color of a line that connects a given node The color is defined by self.edge_color property of this class as follows: - self.edge_color is callable : self.edge_color(node.id) will be returned - self.edge_color is a list : self.edge_color[node.id] will be returned - self.edge_color is a string : self.edge_color will be returned :param node: (TreeNode) - a node that defines the line color :return: color (str)
set_style(**kwargs)	parses parameters to style this tree :param kwargs: see below

Attributes Documentation

id

Returns ID string that identifies this drawing

Methods Documentation

draw(root_node: visualife.diagrams.TreeNode.TreeNode)

Draws a binary tree given by its root node :param root_node: (BTreeNode) - root of the tree

get_edge_color(node)

Returns the color of a line that connects a given node The color is defined by self.edge_color property of this class as follows:

• self.edge_color is callable : self.edge_color(node.id) will be returned
• self.edge_color is a list : self.edge_color[node.id] will be returned
• self.edge_color is a string : self.edge_color will be returned

Parameters:node – (TreeNode) - a node that defines the line color Returns:color (str)

set_style(**kwargs)

parses parameters to style this tree :param kwargs: see below

Keyword Arguments:  

• leaves_on_axis (boolean) –

  if True, all leaves (singletons) will be placed on X axis; otherwise they will be plotted on the Y coordinate accordingly to the clustering hierarchy

• scale_edges (boolean) –

  if True, the length of radial edges will be determined proportionally to the distances stored in a given phylogenetic trees

• node_shape (char) –

  a single character defining the shape of each mid-node: t and s draw triangles and squares respectively; both o and c draw circles

• node_color (string, list[string] or callable) –

  color of a mid-tree node

• node_size (float) –

  size of a mid-tree node, e.g. circle radius

• node_stroke (string) –

  color of a mid-tree node outline

• node_stroke_width (float) –

  width of a mid-tree node outline

• leaf_shape (char) –

  a single character defining the shape of each leaf node: t and s draw triangles and squares respectively; both o and c draw circles

• leaf_color (string, list[string] or callable) –

  color of a leaf node (i.e. representing a specie or a sequence)

• leaf_size (float) –

  size of a leaf node, e.g. circle radius

• leaf_stroke (string) –

  color of leaf node outline

• leaf_stroke_width (float) –

  width of leaf node outline

• label_color (string, list[string] or callable) –

  color of a label string, if drawn