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Use same root branch for ts #581

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Use same root branch for ts #581

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b88da05
Properly use node labels
hyanwong May 5, 2020
d135e06
Only add root branch to trees with mutations over root
hyanwong May 5, 2020
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24 changes: 16 additions & 8 deletions python/tskit/drawing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -194,8 +194,8 @@ def __init__(
mutation_label_attrs=None,
root_svg_attributes=None,
style=None,
root_branch=None,
):
self.ts = ts
if size is None:
size = (200 * ts.num_trees, 200)
if root_svg_attributes is None:
Expand All @@ -206,9 +206,15 @@ def __init__(
self.drawing = svgwrite.Drawing(
size=self.image_size, debug=True, **root_svg_attributes
)
if node_labels is None:
node_labels = {u: str(u) for u in range(ts.num_nodes)}
if style is not None:
self.drawing.defs.add(self.drawing.style(style))
self.node_labels = {u: str(u) for u in range(ts.num_nodes)}
if root_branch is None:
root_branch = any(
any(tree.parent(mut.node) == NULL for mut in tree.mutations())
for tree in ts.trees()
)
# TODO add general padding arguments following matplotlib's terminology.
self.axes_x_offset = 15
self.axes_y_offset = 10
Expand All @@ -231,6 +237,7 @@ def __init__(
node_label_attrs=node_label_attrs,
mutation_attrs=mutation_attrs,
mutation_label_attrs=mutation_label_attrs,
root_branch=root_branch,
)
for tree in ts.trees()
]
Expand Down Expand Up @@ -285,7 +292,7 @@ class SvgTree:
"""
A class to draw a tree in SVG format.

See :meth:`Tree.draw_svg` for a description of usage and parameters.
See :meth:`Tree.draw_svg` for a description of usage and frequently used parameters.
"""

def __init__(
Expand All @@ -303,6 +310,7 @@ def __init__(
mutation_label_attrs=None,
root_svg_attributes=None,
style=None,
root_branch=None,
):
self.tree = tree
if size is None:
Expand All @@ -314,6 +322,10 @@ def __init__(
self.drawing = self.setup_drawing()
if style is not None:
self.drawing.defs.add(self.drawing.style(style))
if root_branch is None:
# put a root branch in if we have mutations over the root
root_branch = any(tree.parent(mut.node) == NULL for mut in tree.mutations())
self.root_branch = root_branch
self.treebox_x_offset = 10
self.treebox_y_offset = 10
self.treebox_width = size[0] - 2 * self.treebox_x_offset
Expand Down Expand Up @@ -434,13 +446,9 @@ def assign_y_coordinates(self, tree_height_scale, max_tree_height):
# node labels within the treebox
label_padding = 10
y_padding = self.treebox_y_offset + 2 * label_padding
mutations_over_root = any(
any(tree.parent(mut.node) == NULL for mut in tree.mutations())
for tree in ts.trees()
)
root_branch_length = 0
height = self.image_size[1]
if mutations_over_root:
if self.root_branch:
# Allocate a fixed about of space to show the mutations on the
# 'root branch'
root_branch_length = height / 10 # FIXME just draw branch??
Expand Down