def _render_parasite_branches(fig: plot_tools.FigureWrapper, node: tree.Node,
recon_obj: recon.Reconciliation,
host_lookup: dict, parasite_lookup: dict):
"""
Very basic branch drawing
:param fig: Figure object that visualizes trees using MatplotLib
:param node: Node object representing the parasite event being rendered
:param recon_obj: Reconciliation object that represents an edge-to-edge mapping from a parasite tree to a host tree
:param host_lookup: Dictionary with host node names as the key and host node objects as the values
:param parasite_lookup: Dictionary with parasite node names as the key and parasite node objects as the values
"""
node_pos = plot_tools.Position(node.layout.x, node.layout.y)
left_node, right_node = _get_children(node, recon_obj, parasite_lookup)
right_pos = plot_tools.Position(right_node.layout.x, right_node.layout.y)
mapping_node = recon_obj.mapping_of(node.name)
event = recon_obj.event_of(mapping_node)
if event.event_type is recon.EventType.COSPECIATION:
_render_cospeciation_branch(node, host_lookup, parasite_lookup,
recon_obj, fig)
elif event.event_type is recon.EventType.DUPLICATION:
_connect_children(node, host_lookup, parasite_lookup, recon_obj, fig)
elif event.event_type is recon.EventType.TRANSFER:
_render_transfer_branch(node_pos, right_pos, fig, node, host_lookup,
recon_obj, right_node)
_connect_child_to_parent(node, left_node, host_lookup, recon_obj, fig)
else:
raise ValueError('%s is not an known event type' % event.event_type)
def _is_sharing_track(node: tree.Node, host_name: str,
recon_obj: recon.Reconciliation):
"""
Determines if a node is sharing it's horizontal track with its children
:param node: Node object representing a parasite event
:param host_name: Name of host node
:param recon_obj: Reconciliation Object
"""
left_host_name = recon_obj.mapping_of(node.left_node.name).host
right_host_name = recon_obj.mapping_of(node.right_node.name).host
return host_name == left_host_name or host_name == right_host_name
def dict_to_reconciliation(old_recon: Dict[Tuple, List],
event_scores: Dict[tuple, float] = None):
"""
Convert the old reconciliation graph format to Reconciliation.
Example of old format:
old_recon = {
('n0', 'm2'): [('S', ('n2', 'm3'), ('n1', 'm4'))],
('n1', 'm4'): [('C', (None, None), (None, None))],
('n2', 'm3'): [('T', ('n3', 'm3'), ('n4', 'm1'))],
('n3', 'm3'): [('C', (None, None), (None, None))],
('n4', 'm1'): [('C', (None, None), (None, None))],
}
"""
roots = _find_roots(old_recon)
if len(roots) > 1:
raise ValueError("old_recon has many roots")
root = roots[0]
recon = Reconciliation(root)
event = None
for mapping in old_recon:
host, parasite = mapping
if len(old_recon[mapping]) != 1:
raise ValueError(
'old_recon mapping node has no or multiple events')
event_tuple = old_recon[mapping][0]
etype, left, right = event_tuple
mapping_node = MappingNode(host, parasite)
if etype in 'SDT':
left_parasite, left_host = left
right_parasite, right_host = right
left_mapping = MappingNode(left_parasite, left_host)
right_mapping = MappingNode(right_parasite, right_host)
if etype == 'S':
event = Cospeciation(left_mapping, right_mapping)
if etype == 'D':
event = Duplication(left_mapping, right_mapping)
if etype == 'T':
event = Transfer(left_mapping, right_mapping)
elif etype == 'L':
child_parasite, child_host = left
child_mapping = MappingNode(child_parasite, child_host)
event = Loss(child_mapping)
elif etype == 'C':
event = TipTip()
else:
raise ValueError('%s not in "SDTLC"' % etype)
if event_scores is not None:
event._freq = event_scores[event_tuple]
recon.set_event(mapping_node, event)
return recon
def _get_children(node: tree.Node, recon_obj: recon.Reconciliation,
parasite_lookup: dict):
"""
Gets the children of a node in the order they appear in the mapping node.
:param node: Node object representing a parasite event
:param recon_obj: Reconciliation Object
:param parasite_lookup: Dictionary with parasite node names as the key and parasite node objects as the values
:return A tuple consisting of the left node and right node
"""
mapping_node = recon_obj.mapping_of(node.name)
event = recon_obj.event_of(mapping_node)
left_mapping_node = event.left
right_mapping_node = event.right
left_node_name = left_mapping_node.parasite
right_node_name = right_mapping_node.parasite
left_node = parasite_lookup[left_node_name]
right_node = parasite_lookup[right_node_name]
return left_node, right_node
def _populate_host_tracks(node: tree.Node, recon_obj: recon.Reconciliation,
host_lookup: dict):
"""
:param node: Node object
:param recon_obj: Reconciliation object that represents an edge-to-edge mapping from a parasite tree to a host tree
:param host_lookup: Dictionary with host node names as the key and host node objects as the values
"""
mapping_node = recon_obj.mapping_of(node.name)
event = recon_obj.event_of(mapping_node)
host_name = mapping_node.host
host_node = host_lookup[host_name]
if not (event.event_type is recon.EventType.DUPLICATION
or event.event_type is recon.EventType.TRANSFER):
host_node.update_count()
else:
if not (_is_sharing_track(node, host_name, recon_obj)):
host_node.update_count()
if not (node.is_leaf()):
_populate_host_tracks(node.left_node, recon_obj, host_lookup)
_populate_host_tracks(node.right_node, recon_obj, host_lookup)
def _connect_child_to_parent(node: tree.Node,
child_node: tree.Node,
host_lookup: dict,
recon_obj: recon.Reconciliation,
fig: plot_tools.FigureWrapper,
stop_row: float = None):
"""
Connects a child node to its parent node
:param node: Node object representing a parasite event
:param child_node: The child node object of a given node
:param host_lookup: Dictionary with host node names as the key and host node objects as the values
:param recon_obj: Reconciliation object that represents an edge-to-edge mapping from a parasite tree to a host tree
:param fig: Figure object that visualizes trees using MatplotLib
:param stop_row: row number to stop line drawing on
"""
mapping_node = recon_obj.mapping_of(child_node.name)
host_node = host_lookup[mapping_node.host]
if stop_row == None:
stop_row = node.layout.row
current_pos = plot_tools.Position(child_node.layout.x, child_node.layout.y)
while host_node.layout.row != stop_row and host_node.parent_node:
parent_node = host_node.parent_node
if parent_node.layout.row < host_node.layout.row:
v_track = parent_node.get_and_update_track(
tree.Track.UPPER_VERTICAL)
else:
v_track = parent_node.get_and_update_track(
tree.Track.LOWER_VERTICAL)
while v_track < parent_node.layout.upper_v_track:
v_track = parent_node.get_and_update_track(
tree.Track.LOWER_VERTICAL)
h_track = parent_node.get_and_update_track(tree.Track.HORIZONTAL)
offset = parent_node.layout.offset
sub_parent_pos = plot_tools.Position(parent_node.layout.x - (offset * v_track), \
parent_node.layout.y + (offset * h_track))
_render_loss_branch(sub_parent_pos, current_pos, fig)
host_node = parent_node
current_pos = sub_parent_pos
node_pos = plot_tools.Position(node.layout.x, node.layout.y)
mid_pos = plot_tools.Position(node_pos.x, current_pos.y)
fig.line(node_pos, mid_pos, render_settings.PARASITE_EDGE_COLOR)
fig.line(mid_pos, current_pos, render_settings.PARASITE_EDGE_COLOR)
def _fix_transfer(node: tree.Node,
left_node,
right_node: tree.Node,
host_node: tree.Node,
host_lookup: dict,
parasite_lookup: dict,
recon_obj: recon.Reconciliation,
node_col: float = None,
offset_number: int = 1):
"""
Checks to see in tranfer node is inconsistent and the tries to fix node if it can be slid down the host edge
The tries to push a given node forward if possible to correct the assumed inconsistency
:param node: Node object representing the parasite event being rendered
:param node: Right node of the node object
:param left_node: Left node of the node object
:param right_node: Right node of the node object
:param host_node: Node object represeting a host that the parasite node is mapped to
:param host_lookup: Dictionary with host node names as the key and host node objects as the values
:param parasite_lookup: Dictionary with parasite node names as the key and parasite node objects as the values
:param recon_obj: Reconciliation object that represents an edge-to-edge mapping from a parasite tree to a host tree
:param node_col: Column of the node, used when function is called recursively to check the next available transfer spot
:param offset_number: Used to push node to an available transfer spot
"""
min_col = host_lookup[recon_obj.mapping_of(
right_node.name).host].parent_node.layout.col
max_col = host_node.layout.col
node_col = node.layout.col
max_col = min(host_node.layout.col, left_node.layout.col)
if not (node_col):
node_col = node.layout.col
# Checks to see if transfer is inconsistent and if the inconsistency can be fixed by sliding the transfer node down the host edge
if min_col >= node_col and min_col < max_col and not (_is_sharing_track(
node, host_node.name, recon_obj)):
node.set_layout(col=min_col + 0.5, x=min_col + 0.5)
if min_col < max_col:
new_value = min_col + render_settings.PUSHED_NODE_OFFSET * offset_number
if _is_col_taken(new_value, host_lookup, parasite_lookup):
_fix_transfer(node,
left_node,
right_node,
host_node,
host_lookup,
parasite_lookup,
recon_obj,
node_col=new_value,
offset_number=offset_number + 1)
else:
node.set_layout(col=new_value, x=new_value)
def _render_transfer_branch(node_pos: plot_tools.Position,
right_pos: plot_tools.Position,
fig: plot_tools.FigureWrapper, node: tree.Node,
host_lookup: dict, recon_obj: recon.Reconciliation,
right_node: tree.Node):
"""
Renders a transfer branch
:param node_xy: x and y position of a node
:param right_pos: x and y position of the right child of a node
:param fig: Figure object that visualizes trees using MatplotLib
:param node: Node object representing the parasite event being rendered
:param host_lookup: Dictionary with host node names as the key and host node objects as the values
:param recon_obj: Reconciliation object that represents an edge-to-edge mapping from a parasite tree to a host tree
:param right_node: The right node object of node
"""
child_mapping_node = recon_obj.mapping_of(right_node.name)
child_host_node = host_lookup[child_mapping_node.host]
# Check temporal consistency of transfer event
if child_host_node.parent_node.layout.col < node.layout.col:
# Draw right node, which is transfered
mid_pos = plot_tools.Position(node_pos.x,
right_pos.y) # xy coords of midpoint
y_midpoint = abs(
mid_pos.y +
node_pos.y) / 2 # value of midpoint between mid_xy and parent node
# Determine if transfer is upwards or downwards, and draw triangle accordingly
is_upwards = True if y_midpoint < mid_pos.y else False
arrow_pos = plot_tools.Position(node_pos.x, y_midpoint)
if is_upwards:
fig.triangle(arrow_pos, render_settings.PARASITE_EDGE_COLOR)
else:
fig.triangle(arrow_pos,
render_settings.PARASITE_EDGE_COLOR,
rotation=render_settings.DOWN_ARROW_ROTATION)
# Draw branch to midpoint, then draw branch to child
fig.line(node_pos, mid_pos, render_settings.PARASITE_EDGE_COLOR)
fig.line(mid_pos, right_pos, render_settings.PARASITE_EDGE_COLOR)
else:
transfer_edge_color = plot_tools.transparent_color(
render_settings.PARASITE_EDGE_COLOR,
render_settings.TRANSFER_TRANSPARENCY)
fig.arrow_segment(node_pos, right_pos, transfer_edge_color)
fig.line(node_pos, right_pos, transfer_edge_color)
def _render_cospeciation_branch(node: tree.Node, host_lookup: dict,
parasite_lookup: dict,
recon_obj: recon.Reconciliation,
fig: plot_tools.FigureWrapper):
"""
Renders the cospeciation branch.
:param node: Node object representing the parasite event being rendered
:param host_lookup: Dictionary with host node names as the key and host node objects as the values
:param parasite_lookup: Dictionary with parasite node names as the key and parasite node objects as the values
:param recon_obj: Reconciliation object that represents an edge-to-edge mapping from a parasite tree to a host tree
:param fig: Figure object that visualizes trees using MatplotLib
"""
left_node, right_node = _get_children(node, recon_obj, parasite_lookup)
node_pos = plot_tools.Position(node.layout.x, node.layout.y)
left_pos = plot_tools.Position(left_node.layout.x, left_node.layout.y)
right_pos = plot_tools.Position(right_node.layout.x, right_node.layout.y)
mapping_node = recon_obj.mapping_of(node.name)
host_node = host_lookup[mapping_node.host]
# Update h_track
host_node.get_and_update_track(tree.Track.HORIZONTAL)
left_mapping_node = recon_obj.mapping_of(left_node.name)
left_host_node = host_lookup[left_mapping_node.host]
right_mapping_node = recon_obj.mapping_of(right_node.name)
right_host_node = host_lookup[right_mapping_node.host]
# Draw left node
offset = host_node.layout.offset
if host_node.left_node.name == left_host_node.name:
_render_curved_line_to(node_pos, left_pos, fig)
if host_node.layout.lower_v_track < (host_node.layout.x -
node_pos.x) / offset:
host_node.layout.lower_v_track += (host_node.layout.x -
node_pos.x) / offset + offset
else:
stop_row = host_node.left_node.layout.row
_connect_child_to_parent(node,
left_node,
host_lookup,
recon_obj,
fig,
stop_row=stop_row)
# Draw Right node
if host_node.right_node.name == right_host_node.name:
_render_curved_line_to(node_pos, right_pos, fig)
if host_node.layout.upper_v_track < (host_node.layout.x -
node_pos.x) / offset:
host_node.layout.upper_v_track += (host_node.layout.x -
node_pos.x) / offset + offset
else:
stop_row = host_node.right_node.layout.row
_connect_child_to_parent(node,
right_node,
host_lookup,
recon_obj,
fig,
stop_row=stop_row)
def _render_parasite_helper(fig: plot_tools.FigureWrapper, node: tree.Node,
recon_obj: recon.Reconciliation, host_lookup: dict,
parasite_lookup: dict, show_internal_labels: bool,
show_freq: bool, font_size: float,
longest_host_name: int):
"""
Helper function for rendering the parasite tree.
:param fig: Figure object that visualizes trees using MatplotLib
:param node: Node object representing the parasite event being rendered
:param recon_obj: Reconciliation object that represents an edge-to-edge mapping from a parasite tree to a host tree
:param host_lookup: Dictionary with host node names as the key and host node objects as the values
:param parasite_lookup: Dictionary with parasite node names as the key and parasite node objects as the values
:param show_internal_labels: Boolean that determines whether or not the internal labels are shown
:param show_freq: Boolean that determines wheter or not the frequencies are shown
:param font_size: Font size for the text of the tips and internal nodes of the tree
:param longest_host_name: The number of symbols in the longest host tree tip name
"""
# mapping_node is of type MappingNode which associates
# a parasite to a host in a reconciliation
mapping_node = recon_obj.mapping_of(node.name)
# A reconciliation has an event_of method which is an object of
# type Event.
event = recon_obj.event_of(mapping_node)
host_name = mapping_node.host
# host_lookup is a dictionary computed in the Tree class
# that associates a host name (a string) with the correspond node
# object for that host. The node object contains layout information
# which we need here.
host_node = host_lookup[host_name]
# Set parasite node layout
host_row = host_node.layout.row
# host_col = host_node.layout.col
# host_x = host_node.layout.x
host_y = host_node.layout.y
node.set_layout(row=host_row, x=node.layout.col, y=host_y)
# Render parasite node and recurse if not a leaf
if node.is_leaf():
node.layout.y += host_node.get_and_update_track(
tree.Track.HORIZONTAL) * host_node.layout.offset
_render_parasite_node(fig, node, event, font_size, longest_host_name)
return
# If the Node is in their own track, change their position
if not (_is_sharing_track(node, host_name, recon_obj)):
node.layout.y += host_node.layout.h_track * host_node.layout.offset
left_node, right_node = _get_children(node, recon_obj, parasite_lookup)
_render_parasite_helper(fig, left_node, recon_obj, host_lookup,
parasite_lookup, show_internal_labels, show_freq,
font_size, longest_host_name)
_render_parasite_helper(fig, right_node, recon_obj, host_lookup,
parasite_lookup, show_internal_labels, show_freq,
font_size, longest_host_name)
# Checking to see if left node is mapped to the same host node as parent
if node.layout.row == left_node.layout.row:
node.set_layout(y=left_node.layout.y)
elif node.layout.row == right_node.layout.row:
node.set_layout(y=right_node.layout.y)
elif event.event_type is recon.EventType.TRANSFER:
node.layout.y = host_node.layout.y + host_node.layout.h_track * host_node.layout.offset
#Checks to see if transfer node is inconsistent and if it can be fixed
if event.event_type is recon.EventType.TRANSFER:
min_col = host_lookup[recon_obj.mapping_of(
right_node.name).host].parent_node.layout.col
if min_col >= node.layout.col:
_fix_transfer(node, left_node, right_node, host_node, host_lookup,
parasite_lookup, recon_obj)
_render_parasite_branches(fig, node, recon_obj, host_lookup,
parasite_lookup)
_render_parasite_node(fig, node, event, font_size, longest_host_name,
show_internal_labels, show_freq)
