added new

Author: Sayitobar

examples/another_usage.py

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+import pandas as pd
+import matplotlib.pyplot as plt
+from fishplotpy import FishPlotData, fishplot, draw_legend
+
+timepoints = [0.0, 2.0, 3.0, 4.0]
+frac_table = pd.DataFrame([
+    [15,  40,  50, 100],
+    [1, 15,  20,  60],
+    [  1,  5,  20, 20],
+    [  0,  0,  3, 20]
+], columns=timepoints)
+parents = [0, 1, 1, 3]  # first root (0), second and third inside the first one, fourth is inside the third one.
+
+custom_labels = ["Founder (WT)", "Gain(Chr3)", "Mut(GeneA)", "DoubleHit+Resist"]
+custom_colors = ['#FFFFFF', '#4682B4', '#FF4500', '#2E8B57']
+
+custom_annots_base = ["First", "Second", "Third", "Fourth"]
+
+fish_data = FishPlotData(
+    frac_table=frac_table,
+    parents=parents,
+    timepoints=timepoints,
+    clone_labels=custom_labels,
+    colors=custom_colors,
+    clone_annots=custom_annots_base,
+    clone_annots_angle=45,
+    clone_annots_pos=5,
+    clone_annots_offset=0.6,
+    clone_annots_col='#111111',
+    clone_annots_cex=0.9
+)
+
+fish_data.layout_clones()
+
+fig, ax = plt.subplots(figsize=(9, 6.5))
+fig.subplots_adjust(left=0.05, right=0.95, bottom=0.22, top=0.88)
+
+fishplot(
+    fish_data,
+    ax=ax,
+    shape="spline",
+    pad_left_frac=0.1,
+    vlines=timepoints,
+    vlab=[f"T={int(t)}" for t in timepoints],
+    cex_vlab=0.75,
+    col_vline="#cccccc",
+    border=0.6,
+    col_border="#666666",
+    bg_type='solid',
+    bg_col='#f0f0f0',
+    use_annot_outline=True
+)
+
+ax.set_title("Muller Graphs Testing", fontsize=14, weight='bold', pad=25)
+
+ax.text(ax.get_xlim()[0] - fish_data.timepoints[-1]*0.02, 50, 'Clonal Fraction (%)',
+        ha='right', va='center', fontsize=9, rotation=90, color='#444444')
+
+draw_legend(
+    fish_data,
+    fig=fig,
+    ncol=4,
+    frameon=True,
+    title="Clone Identity",
+    loc='upper center',
+    bbox_to_anchor=(0.5, 0.15),
+    cex=0.9
+)
+
+plt.show()

requirements.txt

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+contourpy==1.3.1
+cycler==0.12.1
+fonttools==4.57.0
+iniconfig==2.1.0
+Jinja2==3.1.6
+kiwisolver==1.4.8
+MarkupSafe==3.0.2
+matplotlib==3.10.1
+numpy==2.2.4
+packaging==24.2
+pandas==2.2.3
+pillow==11.1.0
+pluggy==1.5.0
+pyparsing==3.2.3
+python-dateutil==2.9.0.post0
+pytz==2025.2
+scipy==1.15.2
+six==1.17.0
+tzdata==2025.2