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Merged
ammarcsj merged 2 commits into from
May 25, 2026
Merged

Add graphviz pure-Python fallback layout for treeviz #128

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f868690
Add graphviz pure-Python fallback layout for treeviz
ammarcsj May 25, 2026
6b6172d
Minor fcviz cleanup
ammarcsj May 25, 2026
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15 changes: 14 additions & 1 deletion alphaquant/plotting/fcviz.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,10 @@ def __init__(self, label_rotation = 90, add_stripplot = False, narrowing_factor_
shortened_xticklabels = False,
remove_leaf_labels_in_tree = False,
hide_root_in_tree = False,
exclude_outlier_fragments = True):
exclude_outlier_fragments = True,
highlight_excluded_nodes = True,
show_excluded_node_counts = True,
show_exclusion_legend = True):
"""
Configuration class for plotting.

Expand All @@ -139,6 +142,10 @@ def __init__(self, label_rotation = 90, add_stripplot = False, narrowing_factor_
exclude_outlier_fragments (bool): Whether to exclude fragment ions marked as outliers from plots.
When True (default), only fragments used in statistical aggregation are displayed.
Mirrors the fragment_outlier_filtering behavior from the analysis pipeline.
highlight_excluded_nodes (bool): Whether tree plots should highlight nodes excluded from aggregation.
show_excluded_node_counts (bool): Whether visible parents should annotate how many hidden descendants
were excluded from aggregation.
show_exclusion_legend (bool): Whether tree plots should include a legend for exclusion highlighting.
"""
self.label_rotation = label_rotation
self.add_stripplot = add_stripplot
Expand All @@ -158,6 +165,9 @@ def __init__(self, label_rotation = 90, add_stripplot = False, narrowing_factor_
self.remove_leaf_labels_in_tree = remove_leaf_labels_in_tree
self.hide_root_in_tree = hide_root_in_tree
self.exclude_outlier_fragments = exclude_outlier_fragments
self.highlight_excluded_nodes = highlight_excluded_nodes
self.show_excluded_node_counts = show_excluded_node_counts
self.show_exclusion_legend = show_exclusion_legend

# Node annotation configuration
self.show_node_annotations = show_node_annotations
Expand All @@ -180,6 +190,9 @@ def __init__(self, label_rotation = 90, add_stripplot = False, narrowing_factor_
'min_reps': 'reps={}',
'fraction_consistent': 'cons={:.2f}',
'is_included': 'incl={}',
'exclude_residual_decorrelation': 'decorr excl={}',
'is_outlier_fragment': 'frag excl={}',
'is_outlier_peptide': 'pep excl={}',
'missingval': 'miss={}'
}
else:
Expand Down
165 changes: 132 additions & 33 deletions alphaquant/plotting/treeviz.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
import networkx as nx
import anytree
import re
import shlex
from matplotlib import gridspec
from matplotlib.lines import Line2D
import matplotlib.pyplot as plt
import alphaquant.cluster.cluster_utils as aqcluster_utils
import alphaquant.plotting.base_functions as aqviz
Expand Down Expand Up @@ -77,7 +79,7 @@ def _define_colorlist(self):
self._colorlist_hex = [aqviz.rgb_to_hex(x) for x in self._plotconfig.colorlist]

def _format_graph(self):
pos = nx.drawing.nx_agraph.graphviz_layout(self.graph, **self._graph_parameters.layout_params)
pos = _graphviz_layout(self.graph, self._graph_parameters.layout_params)

root_id = id(self._protein)
hide_root = getattr(self._plotconfig, 'hide_root_in_tree', False)
Expand All @@ -87,14 +89,8 @@ def _format_graph(self):

for node in nodes_to_draw:
matching_anynode = self._id2anytree_node[node]
is_included = matching_anynode.is_included
if not is_included:
self._graph_parameters.node_options["alpha"] = self._graph_parameters.alpha_excluded
self._graph_parameters.node_options["node_color"] = self._determine_cluster_color(matching_anynode)
# Allow overriding node size from plotconfig
if hasattr(self._plotconfig, 'node_size') and self._plotconfig.node_size is not None:
self._graph_parameters.node_options["node_size"] = self._plotconfig.node_size
nx.draw_networkx_nodes(self.graph, pos, nodelist=[node], ax=self._ax, **self._graph_parameters.node_options)
node_options = self._get_node_options(matching_anynode)
nx.draw_networkx_nodes(self.graph, pos, nodelist=[node], ax=self._ax, **node_options)

label_dict = nx.get_node_attributes(self.graph, 'label')

Expand All @@ -112,9 +108,10 @@ def _format_graph(self):
rotation = self._plotconfig.label_rotation if len(matching_anynode.children) == 0 else 0

self._ax.text(x, y, labelstring, verticalalignment='center', horizontalalignment='center', fontsize=self._plotconfig.node_fontsize, family='monospace',
weight = "bold", rotation = rotation)
weight = "bold", rotation = rotation, color=self._get_label_color(matching_anynode))

nx.draw_networkx_edges(self.graph, pos, edgelist=edges_to_draw, ax=self._ax, **self._graph_parameters.edge_options)
self._add_exclusion_legend(nodes_to_draw)

# Add vertical padding to avoid cutting labels at top/bottom and hide axis frame
try:
Expand All @@ -133,25 +130,97 @@ def _format_graph(self):
def _determine_cluster_color(self, anynode):
return self._colorlist_hex[anynode.cluster]

def _get_node_options(self, anynode):
node_options = dict(self._graph_parameters.node_options)

if hasattr(self._plotconfig, 'node_size') and self._plotconfig.node_size is not None:
node_options["node_size"] = self._plotconfig.node_size

node_options["node_color"] = self._determine_cluster_color(anynode)
node_options["alpha"] = self._graph_parameters.alpha_included
node_options["edgecolors"] = self._graph_parameters.included_edge_color
node_options["linewidths"] = self._graph_parameters.included_linewidth

if self._should_highlight_exclusions() and self._is_directly_excluded(anynode):
node_options["node_color"] = self._graph_parameters.excluded_color
node_options["alpha"] = self._graph_parameters.alpha_excluded
node_options["edgecolors"] = self._graph_parameters.excluded_edge_color
node_options["linewidths"] = self._graph_parameters.excluded_linewidth

return node_options

def _get_label_color(self, anynode):
if self._should_highlight_exclusions() and self._is_directly_excluded(anynode):
return self._graph_parameters.excluded_label_color
return self._graph_parameters.included_label_color

def _should_highlight_exclusions(self):
return getattr(self._plotconfig, "highlight_excluded_nodes", True)

@classmethod
def _is_directly_excluded(cls, anynode):
return (
not getattr(anynode, "is_included", True)
or getattr(anynode, "exclude_residual_decorrelation", False)
or getattr(anynode, "is_outlier_fragment", False)
or getattr(anynode, "is_outlier_peptide", False)
)

def _add_exclusion_legend(self, nodes_to_draw):
if not (
self._should_highlight_exclusions()
and getattr(self._plotconfig, "show_exclusion_legend", True)
):
return

drawn_anynodes = [self._id2anytree_node[node] for node in nodes_to_draw]
has_direct = any(self._is_directly_excluded(node) for node in drawn_anynodes)
if not has_direct:
return

legend_handles = []
if has_direct:
legend_handles.append(
Line2D(
[0],
[0],
marker="o",
linestyle="",
markerfacecolor=self._graph_parameters.excluded_color,
markeredgecolor=self._graph_parameters.excluded_edge_color,
markeredgewidth=self._graph_parameters.excluded_linewidth,
markersize=8,
label="excluded from aggregation",
)
)

self._ax.legend(
handles=legend_handles,
loc="upper right",
frameon=False,
fontsize=max(7, self._plotconfig.node_fontsize - 3),
)

@staticmethod
def render_tree(root):
for pre, _, node in anytree.RenderTree(root):
print("%s%s" % (pre, node.name))


class GraphParameters():
def __init__(self):
self.included_color = "skyblue"
self.excluded_color = "lightgrey"
self.excluded_color = "#D9D9D9"
self.included_edge_color = "#404040"
self.excluded_edge_color = "#808080"
self.included_label_color = "#202020"
self.excluded_label_color = "#333333"
self.alpha_included = 0.6 # More transparent nodes
self.alpha_excluded = 0.3 # More transparent excluded nodes
self.alpha_excluded = 0.8
self.included_linewidth = 1
self.excluded_linewidth = 2.0

self.node_options = {
"node_color": self.included_color,
"node_size": 1500,
"linewidths": 1,
"linewidths": self.included_linewidth,
"edgecolors": self.included_edge_color,
"alpha": self.alpha_included, # default alpha
}

Expand All @@ -171,6 +240,38 @@ def __init__(self):
}


def _graphviz_layout(graph, layout_params):
try:
return nx.drawing.nx_agraph.graphviz_layout(graph, **layout_params)
except ImportError:
return _graphviz_plain_layout(graph, layout_params)


def _graphviz_plain_layout(graph, layout_params):
import graphviz

prog = layout_params.get("prog", "dot")
graph_attr = {}
for token in shlex.split(layout_params.get("args", "")):
if token.startswith("-G") and "=" in token:
key, value = token[2:].split("=", 1)
graph_attr[key] = value

dot = graphviz.Digraph(engine=prog, graph_attr=graph_attr)
for node in graph.nodes:
dot.node(str(node))
for parent, child in graph.edges:
dot.edge(str(parent), str(child))

plain = dot.pipe(format="plain").decode("utf-8")
pos = {}
for line in plain.splitlines():
parts = line.split()
if len(parts) >= 4 and parts[0] == "node":
pos[int(parts[1])] = (float(parts[2]) * 72.0, float(parts[3]) * 72.0)
return pos



class TreeLabelFormatter:
@classmethod
Expand Down Expand Up @@ -252,8 +353,17 @@ def get_annotation_lines(cls, node, plotconfig):
formatted = f"{attr}={value}"

annotations.append(formatted)

return annotations

@classmethod
def get_exclusion_annotation_lines(cls, node):
"""Return compact annotations for aggregation-excluded nodes."""
if GraphCreator._is_directly_excluded(node):
return ["excluded"]

return []


class AnnotatedGraphCreator(GraphCreator):
"""Enhanced GraphCreator that supports configurable node annotations."""
Expand All @@ -264,7 +374,7 @@ def __init__(self, protein, ax, plotconfig):

def _format_graph(self):
"""Override _format_graph to use the enhanced label formatter."""
pos = nx.drawing.nx_agraph.graphviz_layout(self.graph, **self._graph_parameters.layout_params)
pos = _graphviz_layout(self.graph, self._graph_parameters.layout_params)

root_id = id(self._protein)
hide_root = getattr(self._plotconfig, 'hide_root_in_tree', False)
Expand All @@ -274,17 +384,8 @@ def _format_graph(self):

for node in nodes_to_draw:
matching_anynode = self._id2anytree_node[node]
is_included = matching_anynode.is_included
if not is_included:
self._graph_parameters.node_options["alpha"] = self._graph_parameters.alpha_excluded
else:
self._graph_parameters.node_options["alpha"] = self._graph_parameters.alpha_included

self._graph_parameters.node_options["node_color"] = self._determine_cluster_color(matching_anynode)
# Allow overriding node size from plotconfig
if hasattr(self._plotconfig, 'node_size') and self._plotconfig.node_size is not None:
self._graph_parameters.node_options["node_size"] = self._plotconfig.node_size
nx.draw_networkx_nodes(self.graph, pos, nodelist=[node], ax=self._ax, **self._graph_parameters.node_options)
node_options = self._get_node_options(matching_anynode)
nx.draw_networkx_nodes(self.graph, pos, nodelist=[node], ax=self._ax, **node_options)

label_dict = nx.get_node_attributes(self.graph, 'label')

Expand Down Expand Up @@ -316,9 +417,10 @@ def _format_graph(self):

self._ax.text(x, y, labelstring, verticalalignment='center', horizontalalignment='center',
fontsize=fontsize, family='monospace', weight="bold",
rotation=rotation)
rotation=rotation, color=self._get_label_color(matching_anynode))

nx.draw_networkx_edges(self.graph, pos, edgelist=edges_to_draw, ax=self._ax, **self._graph_parameters.edge_options)
self._add_exclusion_legend(nodes_to_draw)

# Add vertical padding to avoid cutting labels at top/bottom and hide axis frame
try:
Expand Down Expand Up @@ -389,6 +491,3 @@ def define_tree_fig_and_ax(self):
fig_width = min(max(8, num_leaves * 1.3),100)
fig_height = max(8, max_depth * 2)
self.fig, self.ax_tree = plt.subplots(figsize=(fig_width, fig_height))



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