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Proposal for Beeswarm to overlap points when out of space #3744

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Proposal for Beeswarm to overlap points when out of space #3744

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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -14,3 +14,5 @@ htmlcov/
.DS_Store
notes/
notebooks/
mytest.py
*.png
111 changes: 80 additions & 31 deletions seaborn/categorical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -535,6 +535,11 @@ def plot_swarms(

if "marker" in plot_kws and not MarkerStyle(plot_kws["marker"]).is_filled():
plot_kws.pop("edgecolor", None)

keep_gutters = True
if "keep_gutters" in plot_kws:
keep_gutters = plot_kws.pop("keep_gutters")
plot_kws.pop("keep_gutters", None)

for sub_vars, sub_data in self.iter_data(iter_vars,
from_comp_data=True,
Expand All @@ -557,7 +562,7 @@ def plot_swarms(
if not sub_data.empty:
point_collections[(ax, sub_data[self.orient].iloc[0])] = points

beeswarm = Beeswarm(width=width, orient=self.orient, warn_thresh=warn_thresh)
beeswarm = Beeswarm(width=width, orient=self.orient, warn_thresh=warn_thresh, keep_gutters=keep_gutters)
for (ax, center), points in point_collections.items():
if points.get_offsets().shape[0] > 1:

Expand Down Expand Up @@ -3223,11 +3228,14 @@ def catplot(

class Beeswarm:
"""Modifies a scatterplot artist to show a beeswarm plot."""
def __init__(self, orient="x", width=0.8, warn_thresh=.05):
def __init__(self, orient="x", width=0.8, warn_thresh=.05, keep_gutters=True):

self.orient = orient
self.width = width
self.warn_thresh = warn_thresh
self.gutters = False #BetterBeeswarm modification
self.shrink_factor = 0.9 #BetterBeeswarm modification
self.keep_gutters = keep_gutters #BetterBeeswarm modification

def __call__(self, points, center):
"""Swarm `points`, a PathCollection, around the `center` position."""
Expand Down Expand Up @@ -3259,35 +3267,58 @@ def __call__(self, points, center):
sizes = np.repeat(sizes, orig_xy.shape[0])
edge = points.get_linewidth().item()
radii = (np.sqrt(sizes) + edge) / 2 * (dpi / 72)
orig_xy = np.c_[orig_xy, radii]

# Sort along the value axis to facilitate the beeswarm
sorter = np.argsort(orig_xy[:, 1])
orig_xyr = orig_xy[sorter]
#BetterBeeswarm modified added while loop to check for gutters
checking_gutters = True
radius_shrink_factor = self.shrink_factor
original_radius_fraction = 1.0
orig_xy_copy = orig_xy.copy()

# Adjust points along the categorical axis to prevent overlaps
new_xyr = np.empty_like(orig_xyr)
new_xyr[sorter] = self.beeswarm(orig_xyr)
while checking_gutters:

# Transform the point coordinates back to data coordinates
if self.orient == "y":
new_xy = new_xyr[:, [1, 0]]
else:
new_xy = new_xyr[:, :2]
new_x_data, new_y_data = ax.transData.inverted().transform(new_xy).T
orig_xy = np.c_[orig_xy_copy, radii] #BetterBeeswarm modified by changing orig_xy to orig_xy_copy

# Add gutters
t_fwd, t_inv = _get_transform_functions(ax, self.orient)
if self.orient == "y":
self.add_gutters(new_y_data, center, t_fwd, t_inv)
else:
self.add_gutters(new_x_data, center, t_fwd, t_inv)
# Sort along the value axis to facilitate the beeswarm
sorter = np.argsort(orig_xy[:, 1])
orig_xyr = orig_xy[sorter]

# Reposition the points so they do not overlap
if self.orient == "y":
points.set_offsets(np.c_[orig_x_data, new_y_data])
else:
points.set_offsets(np.c_[new_x_data, orig_y_data])
# Adjust points along the categorical axis to prevent overlaps
new_xyr = np.empty_like(orig_xyr)
new_xyr[sorter] = self.beeswarm(orig_xyr)

# Transform the point coordinates back to data coordinates
if self.orient == "y":
new_xy = new_xyr[:, [1, 0]]
else:
new_xy = new_xyr[:, :2]
new_x_data, new_y_data = ax.transData.inverted().transform(new_xy).T

# Add gutters
t_fwd, t_inv = _get_transform_functions(ax, self.orient)
if self.orient == "y":
self.add_gutters(new_y_data, center, t_fwd, t_inv)
else:
self.add_gutters(new_x_data, center, t_fwd, t_inv)

# Reposition the points so they do not overlap
if self.orient == "y":
points.set_offsets(np.c_[orig_x_data, new_y_data])
else:
points.set_offsets(np.c_[new_x_data, orig_y_data])

# if keep_gutters is True then we will keep the gutters and stop the while loop
if self.keep_gutters:
break

else:
# Check if gutters were added
if self.gutters:
# Shrink the radii and try again
radii = radii * radius_shrink_factor
original_radius_fraction = original_radius_fraction * radius_shrink_factor
print(f"Shrinking radii to the {original_radius_fraction:.1%} of the original point size.")
else:
checking_gutters = False

def beeswarm(self, orig_xyr):
"""Adjust x position of points to avoid overlaps."""
Expand Down Expand Up @@ -3398,12 +3429,30 @@ def add_gutters(self, points, center, trans_fwd, trans_inv):
points[off_high] = high_gutter

gutter_prop = (off_high + off_low).sum() / len(points)


if gutter_prop > self.warn_thresh:
msg = (
"{:.1%} of the points cannot be placed; you may want "
"to decrease the size of the markers or use stripplot."
).format(gutter_prop)
warnings.warn(msg, UserWarning)

self.gutters = True

if self.keep_gutters:
msg = (
"{:.1%} of the points cannot be placed; you may want "
"to decrease the size of the markers, use stripplot, or "
"set 'keep_gutters=False' to increase point density."
).format(gutter_prop)
warnings.warn(msg, UserWarning)

else:
print(f"{gutter_prop:.1%} of the points cannot be placed. Iteratively shrinking radii distance by {(1 - self.shrink_factor):.1%}")
# msg = (
# "{:.1%} of the points cannot be placed. "
# f"Iteratively shrinking radii distance by {(1 - self.shrink_factor) * 100:.1f}%"
# ).format(gutter_prop)
# warnings.warn(msg, UserWarning)

else:
self.gutters = False

return points

Expand Down