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Fix tree distance graphs #97

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Fix tree distance graphs #97

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fa1f027
fix_tree_distance_graphs
BadPrograms Dec 10, 2025
2b9831e
do not add pos if none specified for add_root
BadPrograms Dec 10, 2025
b392320
Merge branch 'fix_the_add_root' into fix_tree_distance_graphs
BadPrograms Dec 10, 2025
739cdc1
reorder sibliings for minimal time cost, for one dataset
BadPrograms Dec 10, 2025
0a0cc9d
reorder branches end
BadPrograms Dec 10, 2025
f1b58c1
no_leaves
BadPrograms Dec 10, 2025
77941dd
slightly faster
BadPrograms Dec 11, 2025
d579744
fix
BadPrograms Dec 11, 2025
dc320bb
Merge branch 'no_more_leaves' into fix_tree_distance_graphs
BadPrograms Dec 11, 2025
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3 changes: 2 additions & 1 deletion src/lineagetree/_core/_modifier.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,8 @@ def add_root(lT: LineageTree, t: int, pos: list | None = None) -> int:
lT._successor[C_next] = ()
lT._predecessor[C_next] = ()
lT._time[C_next] = t
lT.pos[C_next] = pos if isinstance(pos, list) else []
if isinstance(pos, (list, tuple)):
lT.pos[C_next] = list(pos)
lT._changed_roots = True
return C_next

Expand Down
59 changes: 57 additions & 2 deletions src/lineagetree/lineage_tree_manager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -617,10 +617,37 @@ def plot_tree_distance_graphs(
matched_left = []
colors1 = {}
colors2 = {}
to_reverse_back = []

if style not in ("full", "downsampled"):
for m in btrc:
if m._left != -1 and m._right != -1:
cyc1 = tree1.lT.get_chain_of_node(corres1[m._left])
node_1 = corres1[m._left]
node_2 = corres2[m._right]
if (
node_1 not in tree1.lT.roots
and node_2 not in tree2.lT.roots
):
if tree1.lT.successor[
tree1.lT.predecessor[node_1][0]
].index(node_1) != tree2.lT.successor[
tree2.lT.predecessor[node_2][0]
].index(
node_2
):
tree2.lT._successor[
tree2.lT.predecessor[node_2][0]
] = list(
reversed(
tree2.lT.successor[
tree2.lT.predecessor[node_2][0]
]
)
)
to_reverse_back.append(
tree2.lT.predecessor[node_2][0]
)
cyc1 = tree1.lT.get_chain_of_node(node_1)
if len(cyc1) > 1:
node_1, *_, l_node_1 = cyc1
matched_left.append(node_1)
Expand All @@ -629,7 +656,7 @@ def plot_tree_distance_graphs(
node_1 = l_node_1 = cyc1.pop()
matched_left.append(node_1)

cyc2 = tree2.lT.get_chain_of_node(corres2[m._right])
cyc2 = tree2.lT.get_chain_of_node(node_2)
if len(cyc2) > 1:
node_2, *_, l_node_2 = cyc2
matched_right.append(node_2)
Expand Down Expand Up @@ -659,8 +686,32 @@ def plot_tree_distance_graphs(
else:
for m in btrc:
if m._left != -1 and m._right != -1:

node_1 = tree1.lT.get_chain_of_node(corres1[m._left])[0]
node_2 = tree2.lT.get_chain_of_node(corres2[m._right])[0]
if (
node_1 not in tree1.lT.roots
and node_2 not in tree2.lT.roots
):
if tree1.lT.successor[
tree1.lT.predecessor[node_1][0]
].index(node_1) != tree2.lT.successor[
tree2.lT.predecessor[node_2][0]
].index(
node_2
):
tree2.lT._successor[
tree2.lT.predecessor[node_2][0]
] = list(
reversed(
tree2.lT.successor[
tree2.lT.predecessor[node_2][0]
]
)
)
to_reverse_back.append(
tree2.lT.predecessor[node_2][0]
)
if (
tree1.lT.get_chain_of_node(node_1)[0] == node_1
or tree2.lT.get_chain_of_node(node_2)[0] == node_2
Expand Down Expand Up @@ -733,6 +784,10 @@ def plot_tree_distance_graphs(
lw=lw,
ax=ax[1],
)
for node in to_reverse_back:
tree2.lT._successor[node] = list(
reversed(tree2.lT._successor[node])
)
return ax[0].get_figure(), ax

def labelled_mappings(
Expand Down
26 changes: 24 additions & 2 deletions src/lineagetree/measure/uted.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from __future__ import annotations

import copy
import warnings
from collections.abc import Callable
from functools import partial
Expand Down Expand Up @@ -445,10 +446,21 @@ def plot_tree_distance_graphs(
matched_right = []
matched_left = []
colors = {}
to_reverse_back = []
if style not in ("full", "downsampled"):
for m in btrc:
if m._left != -1 and m._right != -1:
cyc1 = lT.get_chain_of_node(corres1[m._left])
node_1 = corres1[m._left]
node_2 = corres2[m._right]
if node_1 not in lT.roots and node_2 not in lT.roots:
if lT.successor[lT.predecessor[node_1][0]].index(
node_1
) != lT.successor[lT.predecessor[node_2][0]].index(node_2):
lT._successor[lT.predecessor[node_2][0]] = list(
reversed(lT.successor[lT.predecessor[node_2][0]])
)
to_reverse_back.append(lT.predecessor[node_2][0])
cyc1 = lT.get_chain_of_node(node_1)
if len(cyc1) > 1:
node_1, *_, l_node_1 = cyc1
matched_left.append(node_1)
Expand All @@ -457,7 +469,7 @@ def plot_tree_distance_graphs(
node_1 = l_node_1 = cyc1.pop()
matched_left.append(node_1)

cyc2 = lT.get_chain_of_node(corres2[m._right])
cyc2 = lT.get_chain_of_node(node_2)
if len(cyc2) > 1:
node_2, *_, l_node_2 = cyc2
matched_right.append(node_2)
Expand Down Expand Up @@ -487,6 +499,14 @@ def plot_tree_distance_graphs(
if m._left != -1 and m._right != -1:
node_1 = corres1[m._left]
node_2 = corres2[m._right]
if node_1 not in lT.roots and node_2 not in lT.roots:
if lT.successor[lT.predecessor[node_1][0]].index(
node_1
) != lT.successor[lT.predecessor[node_2][0]].index(node_2):
lT._successor[lT.predecessor[node_2][0]] = list(
reversed(lT.successor[lT.predecessor[node_2][0]])
)
to_reverse_back.append(lT.predecessor[node_2][0])

if (
lT.get_chain_of_node(node_1)[0] == node_1
Expand Down Expand Up @@ -547,6 +567,8 @@ def plot_tree_distance_graphs(
lw=lw,
ax=ax[1],
)
for node in to_reverse_back:
lT._successor[node] = list(reversed(lT._successor[node]))
return ax[0].get_figure(), ax


Expand Down
14 changes: 10 additions & 4 deletions src/lineagetree/plot.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from __future__ import annotations

import copy
import warnings
from collections.abc import Iterable
from typing import Literal, TYPE_CHECKING
Expand All @@ -20,20 +21,24 @@ def __plot_nodes(
color: str | dict | list,
size: int | float,
ax: plt.Axes,
leaves: set,
default_color: str = "black",
**kwargs,
) -> None:
"""
Private method that plots the nodes of the tree.
"""

hier_no_leaves = copy.copy(hier)
for leaf in leaves:
hier_no_leaves.pop(leaf, None)
if isinstance(color, dict):
color = [color.get(k, default_color) for k in hier]
color = [color.get(k, default_color) for k in hier_no_leaves]
elif isinstance(color, str | list):
color = [
color if node in selected_nodes else default_color for node in hier
color if node in selected_nodes else default_color
for node in hier_no_leaves
]
hier_pos = np.array(list(hier.values()))
hier_pos = np.array(list(hier_no_leaves.values()))
ax.scatter(*hier_pos.T, s=size, zorder=10, color=color, **kwargs)


Expand Down Expand Up @@ -142,6 +147,7 @@ def draw_tree_graph(
size=size,
ax=ax,
default_color=default_color,
leaves={k for k, v in lnks_tms["links"].items() if not v},
**kwargs,
)
if not color_of_edges:
Expand Down
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