spike-diffs.ipynb

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    "# Plot spike amino-acid differences between SARS-CoV-2 clades\n",
    "\n",
    "This is a Jupyter notebook written by Jesse Bloom that plots spike amino-acid differences among SARS-CoV-2 Pango clades.\n",
    "This notebook is found in the GitHub repo at [https://github.com/jbloom/SARS2-clade-spike-diffs](https://github.com/jbloom/SARS2-clade-spike-diffs), and can be run interactively using `mybinder` by going to [https://mybinder.org/v2/gh/jbloom/SARS2-clade-spike-diffs/main?labpath=spike-diffs.ipynb](https://mybinder.org/v2/gh/jbloom/SARS2-clade-spike-diffs/main?labpath=spike-diffs.ipynb).\n",
    "\n",
    "It reads Pango clade definitions from the [clade definition JSON file](https://raw.githubusercontent.com/corneliusroemer/pango-sequences/main/data/pango-consensus-sequences_summary.json) maintained [by Cornelius Roemer](https://github.com/corneliusroemer/pango-sequences).\n",
    "\n",
    "To use, specify the Pango clades you want to plot in the list below.\n",
    "Then run the rest of the notebook, and it will create an interactive [altair](https://altair-viz.github.io/) plot of the differences.\n",
    "There is an option at the bottom of this plot to show all sites that differ in any of the clades from the Wuhan-Hu-1 reference, or just sites that differ among the clades of interest.\n",
    "You can download a SVG of the plot by clicking the circle with the three small dots in the upper right of the plot.\n",
    "Note that a limitation of these plots is that they show substitutions and deletions, but **not** insertions."
   ]
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    "# Specify the clades to plot. These must either be standard Pango names listed\n",
    "# in Cornelius Roemer's JSON defintions OR specified in `custom_clades` below\n",
    "clades = [\"BA.2\", \"XBB.1.5\", \"HK.3.1\", \"JN.1\", \"BA.2.87.1\"]\n",
    "\n",
    "# Specify any clades not in the Pango site, as a dict giving the clade names followed\n",
    "# by the space de-limited mutations in the form E484A. Below is an example.\n",
    "# Note the clade is not plotted as it is not listed in `my_clades` above\n",
    "custom_clades = {\n",
    "    \"my_clade\": \"Y453F E484A\",\n",
    "}"
   ]
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  {
   "cell_type": "markdown",
   "id": "98a6b7ed-b6d5-4d7c-b5d2-e22e973046d4",
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   "source": [
    "Read the Pango clade information:"
   ]
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   "source": [
    "import json\n",
    "import urllib.request\n",
    "\n",
    "import altair as alt\n",
    "\n",
    "import pandas as pd\n",
    "\n",
    "pango_json = \"https://raw.githubusercontent.com/corneliusroemer/pango-sequences/main/data/pango-consensus-sequences_summary.json\"\n",
    "with urllib.request.urlopen(pango_json) as url:\n",
    "    pango_clades = json.load(url)\n",
    "    \n",
    "if len(clades) != len(set(clades)):\n",
    "    raise ValueError(f\"duplicate clades in {clades}\")\n",
    "\n",
    "clade_spike_muts = {}\n",
    "for clade in clades:\n",
    "    if clade in pango_clades:\n",
    "        clade_spike_muts[clade] = [\n",
    "            m.split(\":\")[1]\n",
    "            for m in pango_clades[clade][\"aaSubstitutions\"] + pango_clades[clade][\"aaDeletions\"]\n",
    "            if m.startswith(\"S:\")\n",
    "        ]\n",
    "        if clade in custom_clades:\n",
    "            raise ValueError(f\"{clade} is in {pango_json} and {my_clades}\")\n",
    "    elif clade in custom_clades:\n",
    "        clade_spike_muts[clade] = custom_clades[clade].split()\n",
    "    else:\n",
    "        raise ValueError(f\"Cannot find {clade=} in {pango_json=}\")"
   ]
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   "cell_type": "markdown",
   "id": "c158b3a4-b677-4650-8c79-d16485cc2e65",
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   "source": [
    "Make a data frame of the mutations to plot:"
   ]
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   "execution_count": 3,
   "id": "ef612434-5bec-4f95-93b7-433a8e9aae20",
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    "def domain(r):\n",
    "    if 13 <= r <= 305:\n",
    "        return \"NTD\"\n",
    "    elif 331 <= r <= 528:\n",
    "        return \"RBD\"\n",
    "    elif 682 <= r <= 1211:\n",
    "        return \"S2\"\n",
    "    else:\n",
    "        return \"other\"\n",
    "\n",
    "mutations = (\n",
    "    pd.Series(clade_spike_muts, name=\"mutation\")\n",
    "    .rename_axis(\"clade\")\n",
    "    .reset_index()\n",
    "    .explode(\"mutation\")\n",
    "    .assign(\n",
    "        reference_aa=lambda x: x[\"mutation\"].str[0],\n",
    "        site=lambda x: x[\"mutation\"].str[1: -1].astype(int),\n",
    "        mutant_aa=lambda x: x[\"mutation\"].str[-1],\n",
    "        is_deletion=lambda x: x[\"mutant_aa\"] == \"-\",\n",
    "        reference_site=lambda x: x[\"reference_aa\"] + x[\"site\"].astype(str),\n",
    "        domain=lambda x: x[\"site\"].map(domain),\n",
    "        differ_among_clades=lambda x: (\n",
    "            x.groupby(\"site\")[\"mutant_aa\"].transform(lambda s: (len(s) != len(clades)) or (s.nunique() > 1))\n",
    "        )\n",
    "    )\n",
    ")\n",
    "\n",
    "assert len(mutations.groupby([\"site\", \"reference_aa\"])) == mutations[\"site\"].nunique()"
   ]
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    "Draw the plot using `altair`.\n",
    "Save a SVG by clicking on the three dots in the upper right of the plot below:"
   ]
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\"is_deletion\": true, \"reference_site\": \"V16\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"N17-\", \"reference_aa\": \"N\", \"site\": 17, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"N17\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"L18-\", \"reference_aa\": \"L\", \"site\": 18, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"L18\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"T19-\", \"reference_aa\": \"T\", \"site\": 19, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"T19\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"T20-\", \"reference_aa\": \"T\", \"site\": 20, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"T20\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"R21-\", \"reference_aa\": \"R\", \"site\": 21, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"R21\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"T22-\", \"reference_aa\": \"T\", \"site\": 22, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"T22\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"Q23-\", \"reference_aa\": \"Q\", \"site\": 23, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"Q23\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"L24-\", \"reference_aa\": \"L\", \"site\": 24, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"L24\", \"domain\": \"NTD\", \"differ_among_clades\": false}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"P25-\", \"reference_aa\": \"P\", \"site\": 25, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"P25\", \"domain\": \"NTD\", \"differ_among_clades\": false}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"P26-\", \"reference_aa\": \"P\", \"site\": 26, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"P26\", \"domain\": \"NTD\", \"differ_among_clades\": false}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"H69-\", \"reference_aa\": \"H\", \"site\": 69, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"H69\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"V70-\", \"reference_aa\": \"V\", \"site\": 70, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"V70\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"C136-\", \"reference_aa\": \"C\", \"site\": 136, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"C136\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"N137-\", \"reference_aa\": \"N\", \"site\": 137, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"N137\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"D138-\", \"reference_aa\": \"D\", \"site\": 138, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"D138\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"P139-\", \"reference_aa\": \"P\", \"site\": 139, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"P139\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"F140-\", \"reference_aa\": \"F\", \"site\": 140, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"F140\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"L141-\", \"reference_aa\": \"L\", \"site\": 141, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"L141\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"G142-\", \"reference_aa\": \"G\", \"site\": 142, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"G142\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"V143-\", \"reference_aa\": \"V\", \"site\": 143, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"V143\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"Y144-\", \"reference_aa\": \"Y\", \"site\": 144, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"Y144\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"Y145-\", \"reference_aa\": \"Y\", \"site\": 145, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"Y145\", \"domain\": \"NTD\", \"differ_among_clades\": true}, {\"clade\": \"BA.2.87.1\", \"mutation\": \"H146-\", \"reference_aa\": \"H\", \"site\": 146, \"mutant_aa\": \"-\", \"is_deletion\": true, \"reference_site\": \"H146\", \"domain\": \"NTD\", \"differ_among_clades\": true}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.VConcatChart(...)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cell_width = 11\n",
    "\n",
    "differ_among_clades = alt.selection_point(\n",
    "    fields=[\"differ_among_clades\"],\n",
    "    bind=alt.binding_radio(\n",
    "        options=[None, True],\n",
    "        labels=[\"differ from Wuhan-Hu-1 reference in any of the clades\", \"differ among the clades\"],\n",
    "        name=\"show sites that:\",\n",
    "    ),\n",
    "    value=None,\n",
    ")\n",
    "\n",
    "chart_base = alt.Chart(mutations).add_params(differ_among_clades).transform_filter(differ_among_clades)\n",
    "\n",
    "heatmap_base = (\n",
    "    chart_base\n",
    "    .encode(\n",
    "        alt.X(\"reference_site\", sort=alt.SortField(\"site\"), title=\"site (indicating amino-acid in Wuhan-Hu-1)\"),\n",
    "        alt.Y(\"clade\", sort=list(clades)),\n",
    "        alt.Fill(\"is_deletion\", legend=None, scale=alt.Scale(scheme=\"set1\")),\n",
    "        alt.Text(\"mutant_aa\"),\n",
    "        tooltip=[\"site\", \"mutation\", \"clade\"],\n",
    "    )\n",
    "    .properties(\n",
    "        width=alt.Step(cell_width),\n",
    "        height=alt.Step(15),\n",
    "    )\n",
    ")\n",
    "\n",
    "domain_overlay = (\n",
    "    chart_base\n",
    "    .transform_calculate(y=\"'domain'\")\n",
    "    .encode(\n",
    "        alt.X(\"reference_site\", sort=alt.SortField(\"site\"), title=None, axis=None),\n",
    "        alt.Y(\"y:N\", title=None),\n",
    "        alt.Color(\n",
    "            \"domain\",\n",
    "            legend=alt.Legend(orient=\"top\", titleOrient=\"left\", offset=10),\n",
    "            scale=alt.Scale(scheme=\"accent\"),\n",
    "        ),\n",
    "        tooltip=[\"site\", \"reference_aa\", \"domain\"],\n",
    "    )\n",
    "    .properties(\n",
    "        width=alt.Step(cell_width),\n",
    "        height=10,\n",
    "    )\n",
    "    .mark_rect(stroke=\"gray\")\n",
    ")\n",
    "\n",
    "heatmap = heatmap_base.mark_rect(stroke=\"gray\", fillOpacity=0.4)\n",
    "\n",
    "aas = heatmap_base.mark_text(stroke=\"black\", size=10)\n",
    "\n",
    "chart = alt.vconcat(domain_overlay, (heatmap + aas), spacing=3).properties(\n",
    "    title=alt.TitleParams(\n",
    "        \"Spike amino-acid differences among clades.\",\n",
    "        subtitle=[\n",
    "            \"Use option at bottom to show all sites that differ from the Wuhan-Hu-1 reference, or just sites that differ among plotted clades.\",\n",
    "            \"For Jesse Bloom's code to make these plots, see https://github.com/jbloom/SARS2-clade-spike-diffs\",\n",
    "            \"Clade sequences taken from Cornelius Roemer's definitions at https://github.com/corneliusroemer/pango-sequences\",\n",
    "            \"Note that only substitutions and deletions but NOT insertions are are shown.\",\n",
    "            \"Sites are numbered using Wuhan-Hu-1 reference numbering.\",\n",
    "        ],\n",
    "        dy=-15,\n",
    "    ),\n",
    ")\n",
    "\n",
    "chart"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a611bac6-dc2f-414d-b7e9-dfff4b0b3d15",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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    "name": "ipython",
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   "file_extension": ".py",
   "mimetype": "text/x-python",
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   "nbconvert_exporter": "python",
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