Beeswarm Plot

Patient Recovery Time by Treatment Protocol

Clinical trial recovery days across treatment groups

Output
Patient Recovery Time by Treatment Protocol
Python
import numpy as np
import matplotlib.pyplot as plt

np.random.seed(302)
BG_COLOR = '#0a0a0f'
TEXT_COLOR = 'white'
COLORS = ['#4927F5', '#F5276C', '#27F5B0']

def simple_beeswarm(y, nbins=None, width=1.):
    y = np.asarray(y)
    if nbins is None:
        nbins = np.ceil(len(y) / 6).astype(int)
    nn, ybins = np.histogram(y, bins=nbins)
    nmax = nn.max()
    x = np.zeros(len(y))
    ibs = []
    for ymin, ymax in zip(ybins[:-1], ybins[1:]):
        i = np.nonzero((y > ymin) * (y <= ymax))[0]
        ibs.append(i)
    dx = width / (nmax // 2) if nmax > 1 else width
    for i in ibs:
        yy = y[i]
        if len(i) > 1:
            j = len(i) % 2
            i = i[np.argsort(yy)]
            a = i[j::2]
            b = i[j+1::2]
            x[a] = (0.5 + j / 3 + np.arange(len(b))) * dx
            x[b] = (0.5 + j / 3 + np.arange(len(b))) * -dx
    return x

treatments = ['Placebo', 'Drug A', 'Drug B']
data = {
    'Placebo': np.random.gamma(5, 4, 50),
    'Drug A': np.random.gamma(3, 3, 55),
    'Drug B': np.random.gamma(2.5, 2.5, 52)
}

fig, ax = plt.subplots(figsize=(10, 6), facecolor=BG_COLOR)
ax.set_facecolor(BG_COLOR)

boxplot_data = []
for i, (treat, values) in enumerate(data.items()):
    x = simple_beeswarm(values, width=0.35)
    ax.scatter(x + i + 1, values, c=COLORS[i], alpha=0.7, s=50, edgecolors='white', linewidth=0.5)
    boxplot_data.append(values)

bp = ax.boxplot(boxplot_data, positions=range(1, len(treatments)+1), widths=0.5, patch_artist=True)
for patch in bp['boxes']:
    patch.set_facecolor('none')
    patch.set_edgecolor('#666')
for element in ['whiskers', 'caps', 'medians']:
    for item in bp[element]:
        item.set_color('#666')

ax.set_xticks(range(1, len(treatments)+1))
ax.set_xticklabels(treatments, color=TEXT_COLOR)
ax.set_xlabel('Treatment Group', fontsize=12, color=TEXT_COLOR, fontweight='500')
ax.set_ylabel('Recovery Time (days)', fontsize=12, color=TEXT_COLOR, fontweight='500')
ax.set_title('Patient Recovery by Treatment', fontsize=14, color=TEXT_COLOR, fontweight='bold', pad=15)

ax.tick_params(colors='#888', labelsize=10)
for spine in ax.spines.values():
    spine.set_color('#333')

plt.tight_layout()
plt.show()
Library

Matplotlib

Category

Statistical

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