Plotting Merger Trees

Some relatively simple visualizations of merger trees can be made with the TreePlot command.

Additional Dependencies

Making merger tree plots with ytree requires the pydot and graphviz packages. pydot can be installed with pip and the graphviz website provides a number of installation options.

Making Tree Plots

The TreePlot command can be used to create a digraph depicting halos as filled circles with sizes proportional to their mass. The main progenitor line will be colored red.

>>> import ytree
>>> a = ytree.load("ahf_halos/snap_N64L16_000.parameter",
...                hubble_constant=0.7)
>>> p = ytree.TreePlot(a[0], dot_kwargs={'rankdir': 'LR', 'size': '"12,4"'})
>>> p.save('tree.png')
_images/tree.png

Plot Modifications

Four TreePlot attributes can be set to modify the default plotting behavior. These are:

  • size_field: The field to determine the size of each circle. Default: ‘mass’.

  • size_log: Whether to scale circle sizes based on log of size field. Default: True.

  • min_mass: The minimum halo mass to be included in the plot. If given as a float, units are assumed to be Msun. Default: None.

  • min_mass_ratio: The minimum ratio between a halo’s mass and the mass of the main halo to be included in the plot. Default: None.

>>> import ytree
>>> a = ytree.load("ahf_halos/snap_N64L16_000.parameter",
...                hubble_constant=0.7)
>>> p = ytree.TreePlot(a[0], dot_kwargs={'rankdir': 'LR', 'size': '"12,4"'})
>>> p.min_mass_ratio = 0.01
>>> p.save('tree_small.png')
_images/tree_small.png

Customizing Node Appearance

The appearance of the nodes can be customized by providing a function that returns a dictionary of keywords that will be used to create the pydot node. This should accept a single argument that is a TreeNode object representing the halo to be plotted. For example, the following function will add labels of the halo id and mass and make the node shape square. It will also color the most massive progenitor red.

def my_node(halo):
    prog = list(halo.find_root()['prog', 'uid'])
    if halo['uid'] in prog:
        color = 'red'
    else:
        color = 'black'

    label = \
    """
    id: %d
    mass: %.2e Msun
    """ % (halo['uid'], halo['mass'].to('Msun'))

    my_kwargs = {"label": label, "fontsize": 8,
                 "shape": "square", "color": color}
    return my_kwargs

This function is then provided with the node_function keyword.

>>> p = ytree.TreePlot(tree, dot_kwargs={'rankdir': "BT"},
...                    node_function=my_node)
>>> p.save('tree_custom_node.png')
_images/tree_custom_node.png

Customizing Edge Appearance

The edges of the plot are the lines connecting each of the nodes. Similar to the nodes, their appearance can be customized by providing a function that returns a dictionary of keywords that will be used to create the pydot edge. This should accept two TreeNode arguments representing the ancestor and descendent halos being connected by the edge. The example below colors the edges blue when the descendent is less massive than its ancestor and green when the descendent is more than 10 times more massive than its ancestor.

def my_edge(ancestor, descendent):
    if descendent['mass'] < ancestor['mass']:
        color = 'blue'
    elif descendent['mass'] / ancestor['mass'] > 10:
        color = 'green'
    else:
        color = 'black'

    my_kwargs = {"color": color, "penwidth": 5}
    return my_kwargs

This function is then provided with the edge_function keyword.

>>> p = ytree.TreePlot(tree, dot_kwargs={'rankdir': "BT"},
...                    node_function=my_node,
...                    edge_function=my_edge)
>>> p.save('tree_custom_edge.png')
_images/tree_custom_edge.png

Supported Output Formats

Plots can be saved to any format supported by graphviz by giving a filename with the appropriate extension. See here for a list of currently supported formats.