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‎MANIFEST.in‎

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include LICENSE
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include README.md

‎docs/README.md‎

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‎docs/index.md‎

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‎docs/tutorials/case_studies/cdr_plots.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "41895583",
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"metadata": {},
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"outputs": [],
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"source": [
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"# import libraries\n",
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"\n",
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"import numpy as np\n",
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"import matplotlib.pyplot as plt\n",
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"import plotly.graph_objects as go\n",
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"from matplotlib.patches import Rectangle"
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]
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},
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{
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"cell_type": "raw",
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"id": "00339492",
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"metadata": {
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"vscode": {
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"languageId": "raw"
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}
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},
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"source": [
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"seq = \"QVQLQESGGGLVQPGGSLRLSCAASGSASSMYTLAWYRQAPGKQRELVALITSGHMTHYEDSVKGRFTISRDNAKEVLYLQMNSLKPEDTAVYFCNLHRLTSSDDDGRTWGQGTQVTVSSAAADYKDHDGDYKDHDIDYKDDDDKGAAHHHHHH\"\n",
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"\n",
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"cdrs = {\n",
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" \"CDR1\": seq[30:35],\n",
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" \"CDR2\": seq[49:66], \n",
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" \"CDR3\": seq[98:115], \n",
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"}\n",
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"\n",
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"for cdr, seq_part in cdrs.items():\n",
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" print(f\"{cdr}: {seq_part}\")\n",
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"\n",
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"# Styling\n",
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"font_family = \"Courier New\"\n",
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"highlight_colors = {\n",
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" \"CDR1\": \"#f4a261\",\n",
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" \"CDR2\": \"#2a9d8f\",\n",
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" \"CDR3\": \"#457b9d\"\n",
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"}"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "1785f8e1",
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"metadata": {},
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"outputs": [],
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"source": [
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"def plot_psm_depth_with_cdrs(\n",
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" protein_sequence,\n",
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" mapped_psms,\n",
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" cdrs,\n",
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" highlight_colors,\n",
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" output_file=\"fig_depth_psms_cdrs.svg\",\n",
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" title=\"PSM depth across the protein sequence with CDR regions\",\n",
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"):\n",
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" \"\"\"\n",
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" Plot PSM depth along a protein sequence with CDR regions highlighted.\n",
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"\n",
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" Args:\n",
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" protein_sequence (str): Normalized protein sequence.\n",
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" mapped_psms (list of tuples): Each tuple should contain (start, end, ..., ...).\n",
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" cdrs (dict): Dictionary of CDR labels and their (start, end) positions.\n",
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" highlight_colors (dict): CDR labels mapped to their highlight colors.\n",
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" output_file (str): Path to save the SVG file.\n",
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" title (str): Plot title.\n",
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" \"\"\"\n",
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" depth = np.zeros(len(protein_sequence), dtype=int)\n",
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" for _, (start, end, _, _) in mapped_psms:\n",
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" depth[start:end] += 1\n",
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"\n",
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" fig = go.Figure()\n",
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" fig.add_trace(\n",
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" go.Scatter(\n",
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" x=list(range(len(protein_sequence))),\n",
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" y=depth,\n",
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" mode=\"lines\",\n",
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" line=dict(color=\"steelblue\", width=2),\n",
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" fill=\"tozeroy\",\n",
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" fillcolor=\"rgba(70, 130, 180, 0.2)\",\n",
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" name=\"PSM Depth\",\n",
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" )\n",
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" )\n",
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"\n",
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" for label, (start, end) in cdrs.items():\n",
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" fig.add_shape(\n",
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" type=\"rect\",\n",
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" x0=start,\n",
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" x1=end,\n",
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" y0=0,\n",
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" y1=max(depth),\n",
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" fillcolor=highlight_colors.get(label, \"gray\"),\n",
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" opacity=0.3,\n",
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" line=dict(width=0),\n",
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" layer=\"below\",\n",
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" )\n",
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" fig.add_annotation(\n",
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" x=(start + end) / 2,\n",
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" y=max(depth) + 8,\n",
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" text=label,\n",
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" showarrow=False,\n",
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" font=dict(size=14, color=\"black\"),\n",
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" xanchor=\"center\",\n",
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" )\n",
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"\n",
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" fig.update_layout(\n",
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" title=title,\n",
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" xaxis=dict(\n",
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" title=\"Amino acid position\",\n",
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" tickmode=\"linear\",\n",
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" dtick=10,\n",
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" showline=True,\n",
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" linecolor=\"black\",\n",
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" linewidth=2,\n",
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" showgrid=False,\n",
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" ),\n",
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" yaxis=dict(\n",
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" title=\"Depth (Number of matching PSMs per position)\",\n",
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" showline=True,\n",
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" linecolor=\"black\",\n",
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" linewidth=2,\n",
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" showgrid=False,\n",
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" ),\n",
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" template=\"plotly_white\",\n",
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" height=450,\n",
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" width=1000,\n",
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" margin=dict(t=60),\n",
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" showlegend=False,\n",
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" )\n",
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"\n",
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" fig.show()\n",
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" fig.write_image(output_file, format=\"svg\", scale=2)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "3347a030",
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"metadata": {},
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"source": [
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"To run the previous function you need to create mapped_psms and protein_norm first you can find in the main pipeline."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "857db62a",
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"metadata": {},
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"outputs": [],
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"source": [
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"cdrs = {\"CDR1\": (31, 35), \"CDR2\": (50, 66), \"CDR3\": (99, 115)}\n",
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"highlight_colors = {\"CDR1\": \"orange\", \"CDR2\": \"lightgreen\", \"CDR3\": \"deepskyblue\"}\n",
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"\n",
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"plot_psm_depth_with_cdrs(\n",
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" protein_sequence=protein_norm,\n",
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" mapped_psms=mapped_psms,\n",
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" cdrs=cdrs,\n",
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" highlight_colors=highlight_colors,\n",
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" output_file=\"fig_4C_depth_psms_cdrs.svg\",\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "43d014e1",
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"metadata": {},
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"outputs": [],
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"source": [
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"def plot_cdr_scaffolds(\n",
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" reference_seq,\n",
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" scaffold_info,\n",
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" cdrs,\n",
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" highlight_colors,\n",
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" font_family=\"monospace\",\n",
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" font_size=25,\n",
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" letter_spacing=1.5,\n",
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" save_path=None,\n",
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"):\n",
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" \"\"\"\n",
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" Plot reference sequence and full scaffold sequences aligned, highlighting CDR regions,\n",
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" with adjustable letter spacing for sequence letters.\n",
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"\n",
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" \"\"\"\n",
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"\n",
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" def chars_equal(a, b):\n",
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" return (a in [\"L\", \"I\"] and b in [\"L\", \"I\"]) or a == b\n",
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"\n",
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" def find_alignment_offset(ref, seq):\n",
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" for pos in range(len(ref) - len(seq) + 1):\n",
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" if all(chars_equal(ref[pos + i], seq[i]) for i in range(len(seq))):\n",
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" return pos\n",
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" return 0\n",
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"\n",
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" fig_width = max(10, len(reference_seq) * letter_spacing / 8)\n",
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" fig, ax = plt.subplots(figsize=(fig_width, 6))\n",
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" ax.axis(\"off\")\n",
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"\n",
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" for name, (start, end) in cdrs.items():\n",
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" x0 = (start - 1) * letter_spacing + 1\n",
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" width = (end - start + 1) * letter_spacing\n",
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" ax.add_patch(\n",
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" Rectangle((x0, 4.5), width, 0.8, color=highlight_colors[name], alpha=0.3)\n",
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" )\n",
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" ax.text(\n",
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" x0 + width / 2,\n",
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" 5.5,\n",
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" name,\n",
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" ha=\"center\",\n",
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" va=\"bottom\",\n",
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" fontsize=font_size,\n",
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" fontweight=\"bold\",\n",
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" color=highlight_colors[name],\n",
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" )\n",
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"\n",
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" ax.text(-5, 5, \"Reference\", fontfamily=font_family, fontsize=font_size, ha=\"right\")\n",
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" for i, aa in enumerate(reference_seq):\n",
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" x = i * letter_spacing + 1\n",
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" ax.text(x, 5, aa, fontfamily=font_family, fontsize=font_size, color=\"black\")\n",
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"\n",
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" y_positions = [4, 3, 2]\n",
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" for idx, (scaf_name, seq) in enumerate(scaffold_info):\n",
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" cdr_name = f\"CDR{idx+1}\"\n",
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" color = highlight_colors[cdr_name]\n",
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" offset = find_alignment_offset(reference_seq, seq)\n",
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"\n",
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" start, end = cdrs[cdr_name]\n",
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" rel_start = max(start - 1 - offset, 0)\n",
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" rel_end = min(end - 1 - offset, len(seq) - 1)\n",
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"\n",
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" ax.text(\n",
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" -5,\n",
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" y_positions[idx],\n",
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" f\"{cdr_name} ({scaf_name})\",\n",
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" fontfamily=font_family,\n",
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" fontsize=font_size,\n",
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" ha=\"right\",\n",
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" )\n",
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"\n",
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" for i, aa in enumerate(seq):\n",
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" x = (offset + i) * letter_spacing + 1\n",
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" ax.text(\n",
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" x,\n",
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" y_positions[idx],\n",
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" aa,\n",
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" fontfamily=font_family,\n",
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" fontsize=font_size,\n",
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" color=\"black\",\n",
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" )\n",
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"\n",
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" if rel_end >= rel_start:\n",
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" x0 = (offset + rel_start) * letter_spacing + 1\n",
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" width = (rel_end - rel_start + 1) * letter_spacing\n",
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" ax.add_patch(\n",
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" Rectangle(\n",
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" (x0, y_positions[idx] - 0.2), width, 0.8, color=color, alpha=0.3\n",
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" )\n",
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" )\n",
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"\n",
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" ax.set_xlim(0, len(reference_seq) * letter_spacing + 5)\n",
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" ax.set_ylim(1.5, 6)\n",
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"\n",
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" plt.tight_layout()\n",
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" if save_path:\n",
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" plt.savefig(save_path, format=\"svg\", dpi=600, bbox_inches=\"tight\")\n",
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" plt.show()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "849fc33e",
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"metadata": {},
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"outputs": [],
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"source": [
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"reference_seq = \"QVQLQESGGGLVQPGGSLRLSCAASGSASSMYTLAWYRQAPGKQRELVALITSGHMTHYEDSVKGRFTISRDNAKEVLYLQMNSLKPEDTAVYFCNLHRLTSSDDDGRTWGQGTQVTVSSAAADYKDHDGDYKDHDIDYKDDDDKGAAHHHHHH\"\n",
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"\n",
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"cdrs = {\"CDR1\": (31, 35), \"CDR2\": (50, 66), \"CDR3\": (99, 115)}\n",
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"highlight_colors = {\"CDR1\": \"orange\", \"CDR2\": \"lightgreen\", \"CDR3\": \"deepskyblue\"}\n",
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"scaffold_info = [\n",
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" (\n",
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" \"scaffold_5\",\n",
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" \"QVQLQESGGGLVQPGGSLRLSCAASGSASSMYTLAWYRQAPGKQRELVALLTSGHMTHYEDSVKGRFY\",\n",
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" ),\n",
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" (\"scaffold_10\", \"SYFCNLHRLTSSDDDGRTWGQGTQVTVSSAAADYKDHDGDYKDHDLDYKDDDDKGAAH\"),\n",
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"]\n",
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"\n",
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"plot_cdr_scaffolds(\n",
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" reference_seq,\n",
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" scaffold_info,\n",
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" cdrs,\n",
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" highlight_colors,\n",
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" font_size=20,\n",
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" letter_spacing=3, # increased spacing\n",
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" save_path=\"cdrs_scaffolds.svg\",\n",
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")"
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]
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}
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],
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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