File size: 2,207 Bytes
9801f83 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | #!/usr/bin/env python3
"""Supplementary Fig. 2a: perfect match rate (left) and motif fragmentation (right)."""
import os
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib.ticker import PercentFormatter
df = pd.read_csv(
"results/summary_by_tokenizer.csv"
).set_index("Tokenizer")
METHODS = ["DNAbert2", "Grover", "cCRE_region_BPE", "motif_region_BPE", "DNAMotifTokenizer"]
LABELS = [
"BPE(orig. DNABERT-2)",
"BPE(orig. Grover)",
"BPE(cCRE-guided)",
"BPE(motif-guided)",
"DNAMotifTokenizer",
]
COLORS = ["#54aa8c", "#ce7f51", "#cca47f", "#c590bd", "#e6bed6"]
mpl.rcParams.update({"font.family": "sans-serif", "font.size": 13})
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(13, 5.2))
def draw(ax, col, title, ylabel, fmt):
vals = df.loc[METHODS, col].values
ax.bar(range(len(vals)), vals, color=COLORS, edgecolor="#555555", linewidth=0.6, width=0.65)
for i, v in enumerate(vals):
ax.text(i, v + max(vals) * 0.015, fmt(v), ha="center", va="bottom", fontsize=13)
ax.set_xticks(range(len(vals)))
ax.set_xticklabels(LABELS, rotation=45, ha="right")
ax.set_title(title, fontsize=14, pad=14)
ax.set_ylabel(ylabel)
ax.set_ylim(0, max(vals) * 1.12)
for s in ["top", "right"]:
ax.spines[s].set_visible(False)
ax.spines["left"].set_color("#bbbbbb")
ax.spines["bottom"].set_color("#bbbbbb")
ax.grid(axis="y", color="#eeeeee", linewidth=0.8)
ax.set_axisbelow(True)
# Perfect match rate is a percentage
draw(ax1, "Perfect_Match_Rate", "Perfect Match Rate", "",
lambda v: f"{v:.2f}" if v >= 1 else f"{v:.4f}")
ax1.yaxis.set_major_formatter(PercentFormatter(decimals=0))
# Fragmentation is a token count, not a percentage
draw(ax2, "Avg_Tokens_Per_Motif", "Motif Fragmentation", "Avg. tokens per motif",
lambda v: f"{v:.2f}")
fig.text(0.01, 0.97, "a", fontsize=15, fontweight="bold", va="top")
fig.tight_layout(rect=(0.02, 0, 1, 0.97), w_pad=4)
out_dir = "figures"
os.makedirs(out_dir, exist_ok=True)
out = os.path.join(out_dir, "supp_fig2a_motif.pdf")
fig.savefig(out, dpi=600)
fig.savefig(out.replace(".pdf", ".png"), dpi=300)
print(f"Saved: {out}")
plt.close(fig)
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