Example #1
0
def equal_arc_layout(T, B):
    """
    @param T: tree topology
    @param B: branch lengths
    @return: a map from vertex to location
    """
    # arbitrarily root the tree
    R = Ftree.T_to_R_canonical(T)
    r = Ftree.R_to_root(R)
    # map vertices to subtree tip count
    v_to_sinks = Ftree.R_to_v_to_sinks(R)
    v_to_count = {}
    for v in Ftree.R_to_postorder(R):
        sinks = v_to_sinks.get(v, [])
        if sinks:
            v_to_count[v] = sum(v_to_count[sink] for sink in sinks)
        else:
            v_to_count[v] = 1
    # create the equal arc angles
    v_to_theta = {}
    _force_equal_arcs(
            v_to_sinks, v_to_count, v_to_theta,
            r, -math.pi, math.pi)
    # convert angles to coordinates
    v_to_source = Ftree.R_to_v_to_source(R)
    v_to_location = {}
    _update_locations(
            R, B,
            v_to_source, v_to_sinks, v_to_theta, v_to_location,
            r, (0, 0), 0)
    return v_to_location
Example #2
0
def RB_to_v_to_age(R, B):
    """
    @param R: directed topology
    @param B: branch lengths in time units
    @return: map from vertex to age
    """
    sources, sinks = zip(*R)
    leaves = set(sinks) - set(sources)
    v_to_age = dict((v, 0) for v in leaves)
    v_to_source = Ftree.R_to_v_to_source(R)
    for v in Ftree.R_to_postorder(R):
        p = v_to_source.get(v, None)
        if p is not None:
            v_to_age[p] = v_to_age[v] + B[frozenset([v, p])]
    return v_to_age