notebooks/prob_escape.ipynb

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    "# Compute probabilities of escape\n",
    "In some experiments that involve antibody selections, it is possible to spike in a \"neutralization standard\", which is a set of variants known not to be affected by the antibody.\n",
    "In such cases, it is then possible to compute the probability of escape of each variant, which is just its change in frequency relative to the standard.\n",
    "For instance, if such experiments are done at enough concentrations, it is even possible to reconstruct a conventional neutralization curve.\n",
    "\n",
    "This notebook illustrates how to use `dms_variants` to compute these probabilities of escape:\n",
    "\n",
    "First, import Python modules:"
   ]
  },
  {
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   "source": [
    "import io\n",
    "import textwrap\n",
    "\n",
    "import altair as alt\n",
    "\n",
    "import dms_variants.codonvarianttable\n",
    "import dms_variants.utils\n",
    "\n",
    "import numpy\n",
    "\n",
    "import pandas as pd"
   ]
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  {
   "cell_type": "markdown",
   "id": "594a4091-3768-4a46-bb3d-40a62378b81e",
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   "source": [
    "## Compute escape probabilities\n",
    "Read in the `CodonVariantTable`.\n",
    "These data correspond to snippets of the variant counts from a real experiment on the SARS-CoV-2 spike:"
   ]
  },
  {
   "cell_type": "code",
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   "source": [
    "with open(\"spike.txt\") as f:\n",
    "    spike_seq = f.read().strip()\n",
    "\n",
    "variants = dms_variants.codonvarianttable.CodonVariantTable.from_variant_count_df(\n",
    "    variant_count_df_file=\"prob_escape_codon_variant_table.csv\",\n",
    "    primary_target=\"spike\",\n",
    "    geneseq=spike_seq,\n",
    "    allowgaps=True,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8ef2df0b-e6a1-4946-a8fd-5c0c971ead25",
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   "source": [
    "Set up a data frame giving the antibody / no-antibody sample pairings for each selection:"
   ]
  },
  {
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   "outputs": [],
   "source": [
    "selections_df = pd.read_csv(\n",
    "    io.StringIO(\n",
    "        textwrap.dedent(\n",
    "            \"\"\"\\\n",
    "    library,antibody_sample,no-antibody_sample,antibody_concentration\n",
    "    lib1,thaw-1_REGN10933_0.037_1,thaw-1_no-antibody_control_1,0.037\n",
    "    lib1,thaw-1_REGN10933_0.15_1,thaw-1_no-antibody_control_1,0.15\n",
    "    lib1,thaw-1_REGN10933_0.15_2,thaw-1_no-antibody_control_2,0.15\n",
    "    lib1,thaw-1_REGN10933_0.59_1,thaw-1_no-antibody_control_1,0.59\n",
    "    lib1,thaw-1_REGN10933_0.59_2,thaw-1_no-antibody_control_2,0.59\n",
    "    lib1,thaw-2_279C_0.00088_1,thaw-2_no-antibody_control_1,0.00088\n",
    "    lib1,thaw-2_279C_0.00088_2,thaw-2_no-antibody_control_2,0.00088\n",
    "    lib1,thaw-2_279C_0.0035_1,thaw-2_no-antibody_control_1,0.0035\n",
    "    lib1,thaw-2_279C_0.0035_2,thaw-2_no-antibody_control_2,0.0035\n",
    "    lib1,thaw-2_279C_0.014_1,thaw-2_no-antibody_control_1,0.014\n",
    "    lib1,thaw-2_279C_0.014_2,thaw-2_no-antibody_control_2,0.014\n",
    "    lib2,thaw-1_REGN10933_0.037_1,thaw-1_no-antibody_control_1,0.037\n",
    "    lib2,thaw-1_REGN10933_0.037_2,thaw-1_no-antibody_control_2,0.037\n",
    "    lib2,thaw-1_REGN10933_0.15_1,thaw-1_no-antibody_control_1,0.15\n",
    "    lib2,thaw-1_REGN10933_0.15_2,thaw-1_no-antibody_control_2,0.15\n",
    "    lib2,thaw-1_REGN10933_0.59_1,thaw-1_no-antibody_control_1,0.59\n",
    "    lib2,thaw-1_REGN10933_0.59_2,thaw-1_no-antibody_control_2,0.59\n",
    "    \"\"\"\n",
    "        )\n",
    "    )\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "407e8e6c-b957-4b45-97b0-35f950799c97",
   "metadata": {},
   "source": [
    "Now run `CodonVariantTable.prob_escape` using the above data frame to define which samples to pair in the comparisons:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "b892441c-1171-4cd4-8e81-e57a9248877c",
   "metadata": {
    "execution": {
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    },
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   },
   "outputs": [],
   "source": [
    "prob_escape, neut_standard_fracs, neutralization = variants.prob_escape(\n",
    "    selections_df=selections_df,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b536e296-f40c-4e83-a094-89acdf3aa324",
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    "execution": {
     "iopub.execute_input": "2022-02-03T00:31:21.253145Z",
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    },
    "tags": []
   },
   "source": [
    "## Fraction of reads that are neutralization standard\n",
    "First look at the returned `neut_standard_fracs` data frame, which gives the fraction of all reads corresponding to the neutralization standard for all samples:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "febeca29-7267-4df9-95f1-bb5336116810",
   "metadata": {
    "execution": {
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   "outputs": [
    {
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>library</th>\n",
       "      <th>antibody_sample</th>\n",
       "      <th>no-antibody_sample</th>\n",
       "      <th>antibody_concentration</th>\n",
       "      <th>antibody_count</th>\n",
       "      <th>antibody_frac</th>\n",
       "      <th>no-antibody_count</th>\n",
       "      <th>no-antibody_frac</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.0370</td>\n",
       "      <td>11107</td>\n",
       "      <td>0.0210</td>\n",
       "      <td>16475</td>\n",
       "      <td>0.0098</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.15_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.1500</td>\n",
       "      <td>18045</td>\n",
       "      <td>0.0220</td>\n",
       "      <td>16475</td>\n",
       "      <td>0.0098</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.15_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>0.1500</td>\n",
       "      <td>14283</td>\n",
       "      <td>0.0371</td>\n",
       "      <td>11343</td>\n",
       "      <td>0.0103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.59_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.5900</td>\n",
       "      <td>26027</td>\n",
       "      <td>0.0636</td>\n",
       "      <td>16475</td>\n",
       "      <td>0.0098</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.59_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>0.5900</td>\n",
       "      <td>23240</td>\n",
       "      <td>0.0510</td>\n",
       "      <td>11343</td>\n",
       "      <td>0.0103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-2_279C_0.00088_1</td>\n",
       "      <td>thaw-2_no-antibody_control_1</td>\n",
       "      <td>0.0009</td>\n",
       "      <td>8231</td>\n",
       "      <td>0.0157</td>\n",
       "      <td>11134</td>\n",
       "      <td>0.0157</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-2_279C_0.00088_2</td>\n",
       "      <td>thaw-2_no-antibody_control_2</td>\n",
       "      <td>0.0009</td>\n",
       "      <td>8763</td>\n",
       "      <td>0.0177</td>\n",
       "      <td>9002</td>\n",
       "      <td>0.0147</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-2_279C_0.0035_1</td>\n",
       "      <td>thaw-2_no-antibody_control_1</td>\n",
       "      <td>0.0035</td>\n",
       "      <td>9298</td>\n",
       "      <td>0.0200</td>\n",
       "      <td>11134</td>\n",
       "      <td>0.0157</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-2_279C_0.0035_2</td>\n",
       "      <td>thaw-2_no-antibody_control_2</td>\n",
       "      <td>0.0035</td>\n",
       "      <td>9394</td>\n",
       "      <td>0.0231</td>\n",
       "      <td>9002</td>\n",
       "      <td>0.0147</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-2_279C_0.014_1</td>\n",
       "      <td>thaw-2_no-antibody_control_1</td>\n",
       "      <td>0.0140</td>\n",
       "      <td>67940</td>\n",
       "      <td>0.1408</td>\n",
       "      <td>11134</td>\n",
       "      <td>0.0157</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-2_279C_0.014_2</td>\n",
       "      <td>thaw-2_no-antibody_control_2</td>\n",
       "      <td>0.0140</td>\n",
       "      <td>60115</td>\n",
       "      <td>0.1545</td>\n",
       "      <td>9002</td>\n",
       "      <td>0.0147</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.0370</td>\n",
       "      <td>14003</td>\n",
       "      <td>0.0152</td>\n",
       "      <td>11144</td>\n",
       "      <td>0.0103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.037_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>0.0370</td>\n",
       "      <td>12780</td>\n",
       "      <td>0.0233</td>\n",
       "      <td>10877</td>\n",
       "      <td>0.0088</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.15_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.1500</td>\n",
       "      <td>22879</td>\n",
       "      <td>0.0271</td>\n",
       "      <td>11144</td>\n",
       "      <td>0.0103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.15_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>0.1500</td>\n",
       "      <td>20040</td>\n",
       "      <td>0.0263</td>\n",
       "      <td>10877</td>\n",
       "      <td>0.0088</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.59_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.5900</td>\n",
       "      <td>57699</td>\n",
       "      <td>0.0760</td>\n",
       "      <td>11144</td>\n",
       "      <td>0.0103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.59_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>0.5900</td>\n",
       "      <td>52409</td>\n",
       "      <td>0.0671</td>\n",
       "      <td>10877</td>\n",
       "      <td>0.0088</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   library           antibody_sample            no-antibody_sample  \\\n",
       "0     lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "1     lib1   thaw-1_REGN10933_0.15_1  thaw-1_no-antibody_control_1   \n",
       "2     lib1   thaw-1_REGN10933_0.15_2  thaw-1_no-antibody_control_2   \n",
       "3     lib1   thaw-1_REGN10933_0.59_1  thaw-1_no-antibody_control_1   \n",
       "4     lib1   thaw-1_REGN10933_0.59_2  thaw-1_no-antibody_control_2   \n",
       "5     lib1     thaw-2_279C_0.00088_1  thaw-2_no-antibody_control_1   \n",
       "6     lib1     thaw-2_279C_0.00088_2  thaw-2_no-antibody_control_2   \n",
       "7     lib1      thaw-2_279C_0.0035_1  thaw-2_no-antibody_control_1   \n",
       "8     lib1      thaw-2_279C_0.0035_2  thaw-2_no-antibody_control_2   \n",
       "9     lib1       thaw-2_279C_0.014_1  thaw-2_no-antibody_control_1   \n",
       "10    lib1       thaw-2_279C_0.014_2  thaw-2_no-antibody_control_2   \n",
       "11    lib2  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "12    lib2  thaw-1_REGN10933_0.037_2  thaw-1_no-antibody_control_2   \n",
       "13    lib2   thaw-1_REGN10933_0.15_1  thaw-1_no-antibody_control_1   \n",
       "14    lib2   thaw-1_REGN10933_0.15_2  thaw-1_no-antibody_control_2   \n",
       "15    lib2   thaw-1_REGN10933_0.59_1  thaw-1_no-antibody_control_1   \n",
       "16    lib2   thaw-1_REGN10933_0.59_2  thaw-1_no-antibody_control_2   \n",
       "\n",
       "    antibody_concentration  antibody_count  antibody_frac  no-antibody_count  \\\n",
       "0                   0.0370           11107         0.0210              16475   \n",
       "1                   0.1500           18045         0.0220              16475   \n",
       "2                   0.1500           14283         0.0371              11343   \n",
       "3                   0.5900           26027         0.0636              16475   \n",
       "4                   0.5900           23240         0.0510              11343   \n",
       "5                   0.0009            8231         0.0157              11134   \n",
       "6                   0.0009            8763         0.0177               9002   \n",
       "7                   0.0035            9298         0.0200              11134   \n",
       "8                   0.0035            9394         0.0231               9002   \n",
       "9                   0.0140           67940         0.1408              11134   \n",
       "10                  0.0140           60115         0.1545               9002   \n",
       "11                  0.0370           14003         0.0152              11144   \n",
       "12                  0.0370           12780         0.0233              10877   \n",
       "13                  0.1500           22879         0.0271              11144   \n",
       "14                  0.1500           20040         0.0263              10877   \n",
       "15                  0.5900           57699         0.0760              11144   \n",
       "16                  0.5900           52409         0.0671              10877   \n",
       "\n",
       "    no-antibody_frac  \n",
       "0             0.0098  \n",
       "1             0.0098  \n",
       "2             0.0103  \n",
       "3             0.0098  \n",
       "4             0.0103  \n",
       "5             0.0157  \n",
       "6             0.0147  \n",
       "7             0.0157  \n",
       "8             0.0147  \n",
       "9             0.0157  \n",
       "10            0.0147  \n",
       "11            0.0103  \n",
       "12            0.0088  \n",
       "13            0.0103  \n",
       "14            0.0088  \n",
       "15            0.0103  \n",
       "16            0.0088  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "neut_standard_fracs.round(4)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "86712764-798c-47e0-89f3-bb2ae00f517b",
   "metadata": {},
   "source": [
    "Now plot the fraction of all reads corresponding to the neutralization standard for all samples, making an interactive `altair` plot where you can mouse over points for details and select which libraries to show with the drop down at the bottom.\n",
    "Note the plot uses a symlog scale:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "af439f45-3285-4a1c-8d1f-c404a3fbd33a",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:26.660090Z",
     "iopub.status.busy": "2023-03-19T13:39:26.659915Z",
     "iopub.status.idle": "2023-03-19T13:39:26.669258Z",
     "shell.execute_reply": "2023-03-19T13:39:26.668644Z",
     "shell.execute_reply.started": "2023-03-19T13:39:26.660070Z"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "# make tidy version of neut_standard_fracs\n",
    "melt_cols = [\"antibody_frac\", \"no-antibody_frac\"]\n",
    "neut_standard_fracs_tidy = neut_standard_fracs.melt(\n",
    "    id_vars=[c for c in neut_standard_fracs.columns if c not in melt_cols],\n",
    "    value_vars=melt_cols,\n",
    "    value_name=\"neut_standard_frac\",\n",
    "    var_name=\"sample_type\",\n",
    ").assign(\n",
    "    sample_type=lambda x: x[\"sample_type\"].str.replace(\"_frac\", \"\"),\n",
    "    library_sample=lambda x: x[\"library\"] + \" \" + x[\"antibody_sample\"],\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "62958bdf-0a4e-4f69-a950-0ad32bd2f06d",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:26.672247Z",
     "iopub.status.busy": "2023-03-19T13:39:26.672066Z",
     "iopub.status.idle": "2023-03-19T13:39:26.759771Z",
     "shell.execute_reply": "2023-03-19T13:39:26.759102Z",
     "shell.execute_reply.started": "2023-03-19T13:39:26.672227Z"
    },
    "tags": []
   },
   "outputs": [
    {
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      ],
      "text/plain": [
       "alt.Chart(...)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# NBVAL_IGNORE_OUTPUT\n",
    "\n",
    "# set up selections over other columns of interest, in this case just library:\n",
    "selections = [\n",
    "    alt.selection_point(\n",
    "        fields=[col],\n",
    "        bind=alt.binding_select(\n",
    "            options=[None] + neut_standard_fracs_tidy[col].unique().tolist(),\n",
    "            labels=[\"all\"] + [str(x) for x in neut_standard_fracs_tidy[col].unique()],\n",
    "            name=col,\n",
    "        ),\n",
    "    )\n",
    "    for col in [\"library\"]\n",
    "]\n",
    "\n",
    "neut_standard_fracs_chart = (\n",
    "    alt.Chart(neut_standard_fracs_tidy)\n",
    "    .encode(\n",
    "        x=alt.X(\n",
    "            \"neut_standard_frac\",\n",
    "            title=\"neutralization standard fraction\",\n",
    "            scale=alt.Scale(type=\"symlog\", constant=0.02, domainMax=1),\n",
    "        ),\n",
    "        y=alt.Y(\"library_sample\", title=None),\n",
    "        color=\"sample_type\",\n",
    "        shape=\"sample_type\",\n",
    "        tooltip=[\n",
    "            alt.Tooltip(c, format=\".2g\") if c == \"neut_standard_frac\" else c\n",
    "            for c in neut_standard_fracs_tidy.columns\n",
    "        ],\n",
    "    )\n",
    "    .mark_point()\n",
    "    .properties(width=275, height=alt.Step(14))\n",
    "    .add_params(*selections)\n",
    "    .configure_axis(labelLimit=500)\n",
    ")\n",
    "for selection in selections:\n",
    "    neut_standard_fracs_chart = neut_standard_fracs_chart.transform_filter(selection)\n",
    "\n",
    "neut_standard_fracs_chart"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2f3f5bc2-4eed-4c44-a272-5550c959da38",
   "metadata": {},
   "source": [
    "## Neutralization averaged over all variants with given number of mutations\n",
    "Now look at `neutralization`, which gives the extent of neutralization averages over all variants with each number of amino-acid mutations:"
   ]
  },
  {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>library</th>\n",
       "      <th>antibody_sample</th>\n",
       "      <th>no-antibody_sample</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "      <th>antibody_neut_standard_count</th>\n",
       "      <th>no-antibody_neut_standard_count</th>\n",
       "      <th>antibody_count</th>\n",
       "      <th>no-antibody_count</th>\n",
       "      <th>prob_escape_uncensored</th>\n",
       "      <th>prob_escape</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0</td>\n",
       "      <td>11107</td>\n",
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       "      <td>140698</td>\n",
       "      <td>0.446</td>\n",
       "      <td>0.446</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>1</td>\n",
       "      <td>11107</td>\n",
       "      <td>16475</td>\n",
       "      <td>102466</td>\n",
       "      <td>340357</td>\n",
       "      <td>0.447</td>\n",
       "      <td>0.447</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>2</td>\n",
       "      <td>11107</td>\n",
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       "      <td>124509</td>\n",
       "      <td>404439</td>\n",
       "      <td>0.457</td>\n",
       "      <td>0.457</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>3</td>\n",
       "      <td>11107</td>\n",
       "      <td>16475</td>\n",
       "      <td>106742</td>\n",
       "      <td>342394</td>\n",
       "      <td>0.462</td>\n",
       "      <td>0.462</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>4</td>\n",
       "      <td>11107</td>\n",
       "      <td>16475</td>\n",
       "      <td>141667</td>\n",
       "      <td>442459</td>\n",
       "      <td>0.475</td>\n",
       "      <td>0.475</td>\n",
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       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>80</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.59_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>0</td>\n",
       "      <td>52409</td>\n",
       "      <td>10877</td>\n",
       "      <td>70691</td>\n",
       "      <td>174569</td>\n",
       "      <td>0.084</td>\n",
       "      <td>0.084</td>\n",
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       "    <tr>\n",
       "      <th>81</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.59_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>1</td>\n",
       "      <td>52409</td>\n",
       "      <td>10877</td>\n",
       "      <td>179056</td>\n",
       "      <td>361718</td>\n",
       "      <td>0.103</td>\n",
       "      <td>0.103</td>\n",
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       "    <tr>\n",
       "      <th>82</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.59_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>2</td>\n",
       "      <td>52409</td>\n",
       "      <td>10877</td>\n",
       "      <td>201992</td>\n",
       "      <td>331201</td>\n",
       "      <td>0.127</td>\n",
       "      <td>0.127</td>\n",
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       "    <tr>\n",
       "      <th>83</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.59_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>3</td>\n",
       "      <td>52409</td>\n",
       "      <td>10877</td>\n",
       "      <td>141530</td>\n",
       "      <td>219133</td>\n",
       "      <td>0.134</td>\n",
       "      <td>0.134</td>\n",
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       "    <tr>\n",
       "      <th>84</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_REGN10933_0.59_2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>4</td>\n",
       "      <td>52409</td>\n",
       "      <td>10877</td>\n",
       "      <td>135208</td>\n",
       "      <td>136249</td>\n",
       "      <td>0.206</td>\n",
       "      <td>0.206</td>\n",
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       "   library           antibody_sample            no-antibody_sample  \\\n",
       "0     lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "1     lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "2     lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "3     lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "4     lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "..     ...                       ...                           ...   \n",
       "80    lib2   thaw-1_REGN10933_0.59_2  thaw-1_no-antibody_control_2   \n",
       "81    lib2   thaw-1_REGN10933_0.59_2  thaw-1_no-antibody_control_2   \n",
       "82    lib2   thaw-1_REGN10933_0.59_2  thaw-1_no-antibody_control_2   \n",
       "83    lib2   thaw-1_REGN10933_0.59_2  thaw-1_no-antibody_control_2   \n",
       "84    lib2   thaw-1_REGN10933_0.59_2  thaw-1_no-antibody_control_2   \n",
       "\n",
       "    n_aa_substitutions  antibody_neut_standard_count  \\\n",
       "0                    0                         11107   \n",
       "1                    1                         11107   \n",
       "2                    2                         11107   \n",
       "3                    3                         11107   \n",
       "4                    4                         11107   \n",
       "..                 ...                           ...   \n",
       "80                   0                         52409   \n",
       "81                   1                         52409   \n",
       "82                   2                         52409   \n",
       "83                   3                         52409   \n",
       "84                   4                         52409   \n",
       "\n",
       "    no-antibody_neut_standard_count  antibody_count  no-antibody_count  \\\n",
       "0                             16475           42343             140698   \n",
       "1                             16475          102466             340357   \n",
       "2                             16475          124509             404439   \n",
       "3                             16475          106742             342394   \n",
       "4                             16475          141667             442459   \n",
       "..                              ...             ...                ...   \n",
       "80                            10877           70691             174569   \n",
       "81                            10877          179056             361718   \n",
       "82                            10877          201992             331201   \n",
       "83                            10877          141530             219133   \n",
       "84                            10877          135208             136249   \n",
       "\n",
       "    prob_escape_uncensored  prob_escape  \n",
       "0                    0.446        0.446  \n",
       "1                    0.447        0.447  \n",
       "2                    0.457        0.457  \n",
       "3                    0.462        0.462  \n",
       "4                    0.475        0.475  \n",
       "..                     ...          ...  \n",
       "80                   0.084        0.084  \n",
       "81                   0.103        0.103  \n",
       "82                   0.127        0.127  \n",
       "83                   0.134        0.134  \n",
       "84                   0.206        0.206  \n",
       "\n",
       "[85 rows x 10 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "neutralization.round(3)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f42d253c-a8f1-4f58-88da-5ddf0c0f241b",
   "metadata": {},
   "source": [
    "Now plot neutralization.\n",
    "First, get the neutralization data ready to plot by melting, and doing a few other transformations:"
   ]
  },
  {
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   "source": [
    "cols_to_melt = [\"prob_escape\", \"prob_escape_uncensored\"]\n",
    "neutralization_to_plot = (\n",
    "    neutralization.melt(\n",
    "        id_vars=[c for c in neutralization.columns if c not in cols_to_melt],\n",
    "        var_name=\"censored\",\n",
    "        value_name=\"fraction not neutralized\",\n",
    "    )\n",
    "    .assign(\n",
    "        library_sample=lambda x: x[\"library\"] + \" \" + x[\"antibody_sample\"],\n",
    "        censored=lambda x: x[\"censored\"] == \"prob_escape\",\n",
    "        n_aa_substitutions=lambda x: (\n",
    "            x[\"n_aa_substitutions\"].map(\n",
    "                lambda n: f\">{n - 1}\" if n == x[\"n_aa_substitutions\"].max() else str(n)\n",
    "            )\n",
    "        ),\n",
    "    )\n",
    "    .rename(\n",
    "        columns={\n",
    "            c: c.replace(\"_\", \" \")\n",
    "            for c in neutralization.columns\n",
    "            if c.endswith(\"count\")\n",
    "        }\n",
    "    )\n",
    "    .merge(selections_df, validate=\"many_to_one\")\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e49d2c40-609b-4c4c-89c5-a8e0ae03e423",
   "metadata": {},
   "source": [
    "Now make the plot.\n",
    "You can mouseover points for details, click on the legend to get values for a specific number of amino-acid substitutions, and use the drop-down to show censored (to [0, 1]) values or raw values, and subset which data to show:"
   ]
  },
  {
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   "id": "36d3edd6-7a60-47eb-94ef-06a4159905f3",
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     "shell.execute_reply": "2023-03-19T13:39:26.970706Z",
     "shell.execute_reply.started": "2023-03-19T13:39:26.802953Z"
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22879, \"no-antibody neut standard count\": 11144, \"antibody count\": 156451, \"no-antibody count\": 189903, \"censored\": true, \"fraction not neutralized\": 0.4012828349021588, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_1\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \">3\", \"antibody neut standard count\": 22879, \"no-antibody neut standard count\": 11144, \"antibody count\": 108684, \"no-antibody count\": 122988, \"censored\": true, \"fraction not neutralized\": 0.4304343674746719, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_1\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"0\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 101205, \"no-antibody count\": 174569, \"censored\": false, \"fraction not neutralized\": 0.3146634184386299, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"1\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 205185, \"no-antibody count\": 361718, \"censored\": false, \"fraction not neutralized\": 0.30788384319832574, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"2\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 202587, \"no-antibody count\": 331201, \"censored\": false, \"fraction not neutralized\": 0.3319948487420134, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"3\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 134660, \"no-antibody count\": 219133, \"censored\": false, \"fraction not neutralized\": 0.3335356321168181, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \">3\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 98279, \"no-antibody count\": 136249, \"censored\": false, \"fraction not neutralized\": 0.3915063556510346, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"0\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 101205, \"no-antibody count\": 174569, \"censored\": true, \"fraction not neutralized\": 0.3146634184386299, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"1\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 205185, \"no-antibody count\": 361718, \"censored\": true, \"fraction not neutralized\": 0.30788384319832574, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"2\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 202587, \"no-antibody count\": 331201, \"censored\": true, \"fraction not neutralized\": 0.3319948487420134, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"3\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 134660, \"no-antibody count\": 219133, \"censored\": true, \"fraction not neutralized\": 0.3335356321168181, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \">3\", \"antibody neut standard count\": 20040, \"no-antibody neut standard count\": 10877, \"antibody count\": 98279, \"no-antibody count\": 136249, \"censored\": true, \"fraction not neutralized\": 0.3915063556510346, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\", \"antibody_concentration\": 0.15}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \"0\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 74318, \"no-antibody count\": 150802, \"censored\": false, \"fraction not neutralized\": 0.09518307463271658, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \"1\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 173340, \"no-antibody count\": 319332, \"censored\": false, \"fraction not neutralized\": 0.10484052047324502, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \"2\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 183505, \"no-antibody count\": 283629, \"censored\": false, \"fraction not neutralized\": 0.12495973208317888, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \"3\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 144675, \"no-antibody count\": 189903, \"censored\": false, \"fraction not neutralized\": 0.1471412640251833, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \">3\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 125906, \"no-antibody count\": 122988, \"censored\": false, \"fraction not neutralized\": 0.19772268739437646, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \"0\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 74318, \"no-antibody count\": 150802, \"censored\": true, \"fraction not neutralized\": 0.09518307463271658, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \"1\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 173340, \"no-antibody count\": 319332, \"censored\": true, \"fraction not neutralized\": 0.10484052047324502, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \"2\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 183505, \"no-antibody count\": 283629, \"censored\": true, \"fraction not neutralized\": 0.12495973208317888, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \"3\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 144675, \"no-antibody count\": 189903, \"censored\": true, \"fraction not neutralized\": 0.1471412640251833, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"n_aa_substitutions\": \">3\", \"antibody neut standard count\": 57699, \"no-antibody neut standard count\": 11144, \"antibody count\": 125906, \"no-antibody count\": 122988, \"censored\": true, \"fraction not neutralized\": 0.19772268739437646, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"0\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 70691, \"no-antibody count\": 174569, \"censored\": false, \"fraction not neutralized\": 0.08404275035563254, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"1\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 179056, \"no-antibody count\": 361718, \"censored\": false, \"fraction not neutralized\": 0.10273584867979824, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"2\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 201992, \"no-antibody count\": 331201, \"censored\": false, \"fraction not neutralized\": 0.1265743731718183, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"3\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 141530, \"no-antibody count\": 219133, \"censored\": false, \"fraction not neutralized\": 0.1340429501522916, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \">3\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 135208, \"no-antibody count\": 136249, \"censored\": false, \"fraction not neutralized\": 0.20595499090797922, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"0\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 70691, \"no-antibody count\": 174569, \"censored\": true, \"fraction not neutralized\": 0.08404275035563254, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"1\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 179056, \"no-antibody count\": 361718, \"censored\": true, \"fraction not neutralized\": 0.10273584867979824, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"2\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 201992, \"no-antibody count\": 331201, \"censored\": true, \"fraction not neutralized\": 0.1265743731718183, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \"3\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 141530, \"no-antibody count\": 219133, \"censored\": true, \"fraction not neutralized\": 0.1340429501522916, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"n_aa_substitutions\": \">3\", \"antibody neut standard count\": 52409, \"no-antibody neut standard count\": 10877, \"antibody count\": 135208, \"no-antibody count\": 136249, \"censored\": true, \"fraction not neutralized\": 0.20595499090797922, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\", \"antibody_concentration\": 0.59}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.Chart(...)"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# NBVAL_SKIP\n",
    "\n",
    "censored_selection = alt.selection_point(\n",
    "    fields=[\"censored\"],\n",
    "    value=[{\"censored\": True}],\n",
    "    bind=alt.binding_select(\n",
    "        options=[True, False],\n",
    "        name=\"censored to be between 0 and 1\",\n",
    "    ),\n",
    ")\n",
    "\n",
    "n_aa_substitutions_selection = alt.selection_point(\n",
    "    fields=[\"n_aa_substitutions\"],\n",
    "    bind=\"legend\",\n",
    ")\n",
    "\n",
    "neutralization_chart = (\n",
    "    alt.Chart(neutralization_to_plot)\n",
    "    .encode(\n",
    "        x=alt.X(\"fraction not neutralized\"),\n",
    "        y=alt.Y(\"library_sample\", title=None),\n",
    "        color=\"n_aa_substitutions:N\",\n",
    "        opacity=alt.condition(\n",
    "            n_aa_substitutions_selection, alt.value(0.7), alt.value(0)\n",
    "        ),\n",
    "        tooltip=[\n",
    "            (\n",
    "                alt.Tooltip(c, format=\".3g\")\n",
    "                if c.endswith(\"_count\")\n",
    "                or c.startswith(\"fraction\")\n",
    "                or c == \"antibody_concentration\"\n",
    "                else c\n",
    "            )\n",
    "            for c in neutralization_to_plot.columns\n",
    "            if c not in [\"library_sample\"]\n",
    "        ],\n",
    "    )\n",
    "    .mark_point(filled=True, size=50)\n",
    "    .properties(width=275, height=alt.Step(14))\n",
    "    .add_params(censored_selection, n_aa_substitutions_selection, *selections)\n",
    "    .transform_filter(censored_selection)\n",
    "    .configure_axis(labelLimit=500)\n",
    ")\n",
    "for selection in selections:\n",
    "    neutralization_chart = neutralization_chart.transform_filter(selection)\n",
    "\n",
    "neutralization_chart"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "aade6882-4d01-4cbd-9838-90a3fbee3327",
   "metadata": {},
   "source": [
    "## Variant-level probabilities of escape\n",
    "Now we examine the variant-level probabilities of escape."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "aa460d67-9d0c-472c-b94e-c205ec587458",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:26.974658Z",
     "iopub.status.busy": "2023-03-19T13:39:26.974515Z",
     "iopub.status.idle": "2023-03-19T13:39:26.998696Z",
     "shell.execute_reply": "2023-03-19T13:39:26.997988Z",
     "shell.execute_reply.started": "2023-03-19T13:39:26.974643Z"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>library</th>\n",
       "      <th>antibody_sample</th>\n",
       "      <th>no-antibody_sample</th>\n",
       "      <th>codon_substitutions</th>\n",
       "      <th>n_codon_substitutions</th>\n",
       "      <th>aa_substitutions</th>\n",
       "      <th>n_aa_substitutions</th>\n",
       "      <th>barcode</th>\n",
       "      <th>prob_escape</th>\n",
       "      <th>prob_escape_uncensored</th>\n",
       "      <th>antibody_count</th>\n",
       "      <th>no-antibody_count</th>\n",
       "      <th>antibody_neut_standard_count</th>\n",
       "      <th>no-antibody_neut_standard_count</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>AAG180AGG CAT653CAG</td>\n",
       "      <td>2</td>\n",
       "      <td>K180R H653Q</td>\n",
       "      <td>2</td>\n",
       "      <td>AACTCAAAATCCTTAG</td>\n",
       "      <td>0.510</td>\n",
       "      <td>0.510</td>\n",
       "      <td>1794</td>\n",
       "      <td>5218</td>\n",
       "      <td>11107</td>\n",
       "      <td>16475</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>CAC146CAG TCC151--- GCT417GCA AGC475ATC ACC111...</td>\n",
       "      <td>6</td>\n",
       "      <td>H146Q S151- S475I I1208T</td>\n",
       "      <td>4</td>\n",
       "      <td>AAGGTCCCGGAGTAAC</td>\n",
       "      <td>0.628</td>\n",
       "      <td>0.628</td>\n",
       "      <td>1733</td>\n",
       "      <td>4094</td>\n",
       "      <td>11107</td>\n",
       "      <td>16475</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>AGA450AAG TTG580AAC AGC744AGT CAG955AAG</td>\n",
       "      <td>4</td>\n",
       "      <td>R450K L580N Q955K</td>\n",
       "      <td>3</td>\n",
       "      <td>AAAGCTGGAGTACGTA</td>\n",
       "      <td>0.593</td>\n",
       "      <td>0.593</td>\n",
       "      <td>1428</td>\n",
       "      <td>3574</td>\n",
       "      <td>11107</td>\n",
       "      <td>16475</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>AGC98CAC GTG306ATC AGC475ATC GAT1082AAT CTG119...</td>\n",
       "      <td>5</td>\n",
       "      <td>S98H V306I S475I D1082N L1191M</td>\n",
       "      <td>5</td>\n",
       "      <td>AACCCAGCACCGTTGA</td>\n",
       "      <td>0.669</td>\n",
       "      <td>0.669</td>\n",
       "      <td>1350</td>\n",
       "      <td>2994</td>\n",
       "      <td>11107</td>\n",
       "      <td>16475</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td></td>\n",
       "      <td>0</td>\n",
       "      <td>AATCACAACCTTTACC</td>\n",
       "      <td>0.478</td>\n",
       "      <td>0.478</td>\n",
       "      <td>1318</td>\n",
       "      <td>4087</td>\n",
       "      <td>11107</td>\n",
       "      <td>16475</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  library           antibody_sample            no-antibody_sample  \\\n",
       "0    lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "1    lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "2    lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "3    lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "4    lib1  thaw-1_REGN10933_0.037_1  thaw-1_no-antibody_control_1   \n",
       "\n",
       "                                 codon_substitutions  n_codon_substitutions  \\\n",
       "0                                AAG180AGG CAT653CAG                      2   \n",
       "1  CAC146CAG TCC151--- GCT417GCA AGC475ATC ACC111...                      6   \n",
       "2            AGA450AAG TTG580AAC AGC744AGT CAG955AAG                      4   \n",
       "3  AGC98CAC GTG306ATC AGC475ATC GAT1082AAT CTG119...                      5   \n",
       "4                                                                         0   \n",
       "\n",
       "                 aa_substitutions  n_aa_substitutions           barcode  \\\n",
       "0                     K180R H653Q                   2  AACTCAAAATCCTTAG   \n",
       "1        H146Q S151- S475I I1208T                   4  AAGGTCCCGGAGTAAC   \n",
       "2               R450K L580N Q955K                   3  AAAGCTGGAGTACGTA   \n",
       "3  S98H V306I S475I D1082N L1191M                   5  AACCCAGCACCGTTGA   \n",
       "4                                                   0  AATCACAACCTTTACC   \n",
       "\n",
       "   prob_escape  prob_escape_uncensored  antibody_count  no-antibody_count  \\\n",
       "0        0.510                   0.510            1794               5218   \n",
       "1        0.628                   0.628            1733               4094   \n",
       "2        0.593                   0.593            1428               3574   \n",
       "3        0.669                   0.669            1350               2994   \n",
       "4        0.478                   0.478            1318               4087   \n",
       "\n",
       "   antibody_neut_standard_count  no-antibody_neut_standard_count  \n",
       "0                         11107                            16475  \n",
       "1                         11107                            16475  \n",
       "2                         11107                            16475  \n",
       "3                         11107                            16475  \n",
       "4                         11107                            16475  "
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "prob_escape.round(3).head()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bd076943-14c7-4021-ae18-b02d8e41f77c",
   "metadata": {},
   "source": [
    "First, we filter on pre-selection counts (counts in the no-antibody condition) and pre-selection fraction (fraction in no-antibody condition among all variants).\n",
    "This enables us to calculate a minimum threshold for each sample, which is the larger of this counts or fraction threshold for that sample:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "cf6d993c-6db8-4bf4-a1cd-faeb7f970b9f",
   "metadata": {
    "execution": {
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     "shell.execute_reply": "2023-03-19T13:39:27.027343Z",
     "shell.execute_reply.started": "2023-03-19T13:39:27.001794Z"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "\n",
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>library</th>\n",
       "      <th>no-antibody_sample</th>\n",
       "      <th>total_no_antibody_count</th>\n",
       "      <th>threshold</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>5011041</td>\n",
       "      <td>50</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>2186016</td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-2_no-antibody_control_1</td>\n",
       "      <td>2096481</td>\n",
       "      <td>21</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-2_no-antibody_control_2</td>\n",
       "      <td>1812264</td>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>3199962</td>\n",
       "      <td>32</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>lib2</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>3668610</td>\n",
       "      <td>37</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "  library            no-antibody_sample  total_no_antibody_count  threshold\n",
       "0    lib1  thaw-1_no-antibody_control_1                  5011041         50\n",
       "1    lib1  thaw-1_no-antibody_control_2                  2186016         22\n",
       "2    lib1  thaw-2_no-antibody_control_1                  2096481         21\n",
       "3    lib1  thaw-2_no-antibody_control_2                  1812264         20\n",
       "4    lib2  thaw-1_no-antibody_control_1                  3199962         32\n",
       "5    lib2  thaw-1_no-antibody_control_2                  3668610         37"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "min_no_antibody_counts = 20  # pre-selection counts must be >= this\n",
    "min_no_antibody_frac = 0.00001  # pre-selection counts must >= this fraction of total\n",
    "\n",
    "min_no_antibody_count_threshold_df = (\n",
    "    prob_escape.groupby([\"library\", \"no-antibody_sample\"], as_index=False)\n",
    "    .aggregate(total_no_antibody_count=pd.NamedAgg(\"no-antibody_count\", \"sum\"))\n",
    "    .assign(\n",
    "        threshold=lambda x: (x[\"total_no_antibody_count\"] * min_no_antibody_frac)\n",
    "        .clip(lower=min_no_antibody_counts)\n",
    "        .round()\n",
    "        .astype(int),\n",
    "    )\n",
    ")\n",
    "\n",
    "min_no_antibody_count_threshold_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "772e3df3-c72d-4db5-acb0-6fbfebaae279",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2022-03-01T00:08:03.949907Z",
     "iopub.status.busy": "2022-03-01T00:08:03.949278Z",
     "iopub.status.idle": "2022-03-01T00:08:03.957073Z",
     "shell.execute_reply": "2022-03-01T00:08:03.956257Z",
     "shell.execute_reply.started": "2022-03-01T00:08:03.949856Z"
    }
   },
   "source": [
    "Now draw a box plot on the pre-selection (no-antibody) counts with black line at median, boxes spanning 25th to 75th percentile, whiskers spanning minimum to maximum, and a red line indicating the threshold.\n",
    "You can mouseover bars for details:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "6178e1c6-36f6-4260-a7d6-f9cd891ca6ac",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:27.029135Z",
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     "shell.execute_reply": "2023-03-19T13:39:27.085451Z",
     "shell.execute_reply.started": "2023-03-19T13:39:27.029115Z"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "no_antibody_count_boxplot_df = (\n",
    "    prob_escape.groupby(\n",
    "        [\"library\", \"antibody_sample\", \"no-antibody_sample\"], as_index=False\n",
    "    )\n",
    "    .aggregate(\n",
    "        median=pd.NamedAgg(\"no-antibody_count\", \"median\"),\n",
    "        percentile_25=pd.NamedAgg(\"no-antibody_count\", lambda s: s.quantile(0.25)),\n",
    "        percentile_75=pd.NamedAgg(\"no-antibody_count\", lambda s: s.quantile(0.75)),\n",
    "        min=pd.NamedAgg(\"no-antibody_count\", \"min\"),\n",
    "        max=pd.NamedAgg(\"no-antibody_count\", \"max\"),\n",
    "    )\n",
    "    .merge(\n",
    "        min_no_antibody_count_threshold_df.drop(columns=\"total_no_antibody_count\"),\n",
    "        validate=\"many_to_one\",\n",
    "    )\n",
    "    .assign(library_sample=lambda x: x[\"library\"] + \" \" + x[\"antibody_sample\"])\n",
    ")\n",
    "assert (\n",
    "    len(no_antibody_count_boxplot_df)\n",
    "    == no_antibody_count_boxplot_df[\"library_sample\"].nunique()\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "02e9ad78-59d3-4f07-88e9-5feb16e3c6eb",
   "metadata": {
    "execution": {
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     "iopub.status.idle": "2023-03-19T13:39:27.176117Z",
     "shell.execute_reply": "2023-03-19T13:39:27.175442Z",
     "shell.execute_reply.started": "2023-03-19T13:39:27.087261Z"
    },
    "tags": []
   },
   "outputs": [
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       "</script>"
      ],
      "text/plain": [
       "alt.LayerChart(...)"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# NBVAL_SKIP\n",
    "\n",
    "no_antibody_count_base = alt.Chart(no_antibody_count_boxplot_df).encode(\n",
    "    y=alt.Y(\"library_sample\", title=None),\n",
    "    tooltip=[\n",
    "        c if (c.endswith(\"sample\") or c == \"library\") else alt.Tooltip(c, format=\".3g\")\n",
    "        for c in no_antibody_count_boxplot_df.columns\n",
    "        if c != \"library_sample\"\n",
    "    ],\n",
    ")\n",
    "\n",
    "no_antibody_count_quartile_bars = no_antibody_count_base.encode(\n",
    "    alt.X(\n",
    "        \"percentile_25\",\n",
    "        scale=alt.Scale(type=\"symlog\", constant=20),\n",
    "        title=\"counts for variant\",\n",
    "    ),\n",
    "    alt.X2(\"percentile_75\"),\n",
    ").mark_bar(color=\"blue\")\n",
    "\n",
    "no_antibody_count_range_lines = no_antibody_count_base.encode(\n",
    "    alt.X(\"min\"),\n",
    "    alt.X2(\"max\"),\n",
    ").mark_rule(color=\"blue\", opacity=0.5)\n",
    "\n",
    "no_antibody_count_median_lines = no_antibody_count_base.encode(\n",
    "    alt.X(\"median\"), alt.X2(\"median\")\n",
    ").mark_bar(xOffset=1, x2Offset=-1, color=\"black\")\n",
    "\n",
    "no_antibody_count_threshold = no_antibody_count_base.encode(\n",
    "    alt.X(\"threshold\"), alt.X2(\"threshold\")\n",
    ").mark_bar(xOffset=1, x2Offset=-1, color=\"red\")\n",
    "\n",
    "no_antibody_count_chart = (\n",
    "    no_antibody_count_quartile_bars\n",
    "    + no_antibody_count_range_lines\n",
    "    + no_antibody_count_median_lines\n",
    "    + no_antibody_count_threshold\n",
    ").properties(width=350, height=alt.Step(14))\n",
    "\n",
    "for s in selections:\n",
    "    no_antibody_count_chart = no_antibody_count_chart.add_params(s).transform_filter(s)\n",
    "\n",
    "no_antibody_count_chart"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bb3e5154-8b2f-48b4-9a2e-ac746c2af3c4",
   "metadata": {},
   "source": [
    "Now get just prob escape measurements for variants that exceed pre-selection (no-antibody) count threshold:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "4b411e7f-a13d-461b-992d-da253907e980",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:27.177196Z",
     "iopub.status.busy": "2023-03-19T13:39:27.176916Z",
     "iopub.status.idle": "2023-03-19T13:39:27.229878Z",
     "shell.execute_reply": "2023-03-19T13:39:27.229018Z",
     "shell.execute_reply.started": "2023-03-19T13:39:27.177179Z"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "prob_escape_filtered = prob_escape.merge(\n",
    "    min_no_antibody_count_threshold_df, validate=\"many_to_one\"\n",
    ").query(\"`no-antibody_count` >= threshold\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "01243049-24a8-4afe-8e40-06714b324826",
   "metadata": {},
   "source": [
    "Plot distribution of prob escape values across non-filtered variants.\n",
    "The boxes span 25th to 75th percentile, the black vertical line is at the median, and the thin lines extend from the min to max: "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "518c8e07-a947-4c8d-9585-fd6f06ff30f4",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:27.231069Z",
     "iopub.status.busy": "2023-03-19T13:39:27.230771Z",
     "iopub.status.idle": "2023-03-19T13:39:27.326950Z",
     "shell.execute_reply": "2023-03-19T13:39:27.326166Z",
     "shell.execute_reply.started": "2023-03-19T13:39:27.231050Z"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "prob_escape_boxplot_df = (\n",
    "    prob_escape_filtered.melt(\n",
    "        id_vars=[\"library\", \"antibody_sample\", \"no-antibody_sample\"],\n",
    "        value_vars=[\"prob_escape\", \"prob_escape_uncensored\"],\n",
    "        var_name=\"censored\",\n",
    "        value_name=\"probability escape\",\n",
    "    )\n",
    "    .groupby(\n",
    "        [\"library\", \"antibody_sample\", \"no-antibody_sample\", \"censored\"],\n",
    "        as_index=False,\n",
    "    )\n",
    "    .aggregate(\n",
    "        median=pd.NamedAgg(\"probability escape\", \"median\"),\n",
    "        percentile_25=pd.NamedAgg(\"probability escape\", lambda s: s.quantile(0.25)),\n",
    "        percentile_75=pd.NamedAgg(\"probability escape\", lambda s: s.quantile(0.75)),\n",
    "        min=pd.NamedAgg(\"probability escape\", \"min\"),\n",
    "        max=pd.NamedAgg(\"probability escape\", \"max\"),\n",
    "    )\n",
    "    .assign(\n",
    "        library_sample=lambda x: x[\"library\"] + \" \" + x[\"antibody_sample\"],\n",
    "        censored=lambda x: x[\"censored\"] == \"prob_escape\",\n",
    "    )\n",
    ")\n",
    "assert (\n",
    "    len(prob_escape_boxplot_df)\n",
    "    == 2 * prob_escape_boxplot_df[\"library_sample\"].nunique()\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "ce03ca1a-95a5-4f1d-a204-b658443b4aea",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:27.328092Z",
     "iopub.status.busy": "2023-03-19T13:39:27.327812Z",
     "iopub.status.idle": "2023-03-19T13:39:27.434902Z",
     "shell.execute_reply": "2023-03-19T13:39:27.434145Z",
     "shell.execute_reply.started": "2023-03-19T13:39:27.328075Z"
    },
    "tags": []
   },
   "outputs": [
    {
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       "    function maybeLoadScript(lib, version) {\n",
       "      var key = `${lib.replace(\"-\", \"\")}_version`;\n",
       "      return (VEGA_DEBUG[key] == version) ?\n",
       "        Promise.resolve(paths[lib]) :\n",
       "        new Promise(function(resolve, reject) {\n",
       "          var s = document.createElement('script');\n",
       "          document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
       "          s.async = true;\n",
       "          s.onload = () => {\n",
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       "          s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
       "          s.src = paths[lib];\n",
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       "    function displayChart(vegaEmbed) {\n",
       "      vegaEmbed(outputDiv, spec, embedOpt)\n",
       "        .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
       "    }\n",
       "\n",
       "    if(typeof define === \"function\" && define.amd) {\n",
       "      requirejs.config({paths});\n",
       "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
       "    } else {\n",
       "      maybeLoadScript(\"vega\", \"5\")\n",
       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.6.1\"))\n",
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       "        .catch(showError)\n",
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\"percentile_75\": 0.6535478001584241, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-1_REGN10933_0.037_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.037_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": false, \"median\": 0.41372518608430287, \"percentile_25\": 0.23391423197617786, \"percentile_75\": 0.6535478001584241, \"min\": 0.0, \"max\": 10.871906127994631, \"library_sample\": \"lib1 thaw-1_REGN10933_0.037_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": true, \"median\": 0.407465103365301, \"percentile_25\": 0.25678427472466747, \"percentile_75\": 0.6160948402796893, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-1_REGN10933_0.15_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": false, \"median\": 0.407465103365301, \"percentile_25\": 0.25678427472466747, \"percentile_75\": 0.6160948402796893, \"min\": 0.0, \"max\": 7.039380008029812, \"library_sample\": \"lib1 thaw-1_REGN10933_0.15_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": true, \"median\": 0.21921465904968224, \"percentile_25\": 0.0873576979626129, \"percentile_75\": 0.41109504923582546, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-1_REGN10933_0.15_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": false, \"median\": 0.21921465904968224, \"percentile_25\": 0.0873576979626129, \"percentile_75\": 0.41109504923582546, \"min\": 0.0, \"max\": 7.559235143566167, \"library_sample\": \"lib1 thaw-1_REGN10933_0.15_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": true, \"median\": 0.08459548128531531, \"percentile_25\": 0.0, \"percentile_75\": 0.21643199262178045, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-1_REGN10933_0.59_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": false, \"median\": 0.08459548128531531, \"percentile_25\": 0.0, \"percentile_75\": 0.21643199262178045, \"min\": 0.0, \"max\": 14.174157002871077, \"library_sample\": \"lib1 thaw-1_REGN10933_0.59_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": true, \"median\": 0.12124302487474924, \"percentile_25\": 0.0, \"percentile_75\": 0.3171287033558455, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-1_REGN10933_0.59_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": false, \"median\": 0.12124302487474924, \"percentile_25\": 0.0, \"percentile_75\": 0.3171287033558455, \"min\": 0.0, \"max\": 16.016284184356476, \"library_sample\": \"lib1 thaw-1_REGN10933_0.59_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.00088_1\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_1\", \"censored\": true, \"median\": 0.9287132554938827, \"percentile_25\": 0.5872275054400885, \"percentile_75\": 1.0, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-2_279C_0.00088_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.00088_1\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_1\", \"censored\": false, \"median\": 0.9287132554938827, \"percentile_25\": 0.5872275054400885, \"percentile_75\": 1.3391878774199295, \"min\": 0.0, \"max\": 8.198127551790533, \"library_sample\": \"lib1 thaw-2_279C_0.00088_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.00088_2\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_2\", \"censored\": true, \"median\": 0.7711911929782914, \"percentile_25\": 0.5031544969922237, \"percentile_75\": 1.0, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-2_279C_0.00088_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.00088_2\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_2\", \"censored\": false, \"median\": 0.7711911929782914, \"percentile_25\": 0.5031544969922237, \"percentile_75\": 1.1029676210382169, \"min\": 0.0, \"max\": 8.0225189242649, \"library_sample\": \"lib1 thaw-2_279C_0.00088_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.0035_1\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_1\", \"censored\": true, \"median\": 0.7043893057330481, \"percentile_25\": 0.4351581526460449, \"percentile_75\": 1.0, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-2_279C_0.0035_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.0035_1\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_1\", \"censored\": false, \"median\": 0.7043893057330481, \"percentile_25\": 0.4351581526460449, \"percentile_75\": 1.080902595984099, \"min\": 0.0, \"max\": 7.9511464831146474, \"library_sample\": \"lib1 thaw-2_279C_0.0035_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.0035_2\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_2\", \"censored\": true, \"median\": 0.5788490075978923, \"percentile_25\": 0.3505870379121079, \"percentile_75\": 0.8727113050883544, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-2_279C_0.0035_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.0035_2\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_2\", \"censored\": false, \"median\": 0.5788490075978923, \"percentile_25\": 0.3505870379121079, \"percentile_75\": 0.8727113050883544, \"min\": 0.0, \"max\": 7.927516596667117, \"library_sample\": \"lib1 thaw-2_279C_0.0035_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.014_1\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_1\", \"censored\": true, \"median\": 0.0014866300502868572, \"percentile_25\": 0.0, \"percentile_75\": 0.13799287061587767, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-2_279C_0.014_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.014_1\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_1\", \"censored\": false, \"median\": 0.0014866300502868572, \"percentile_25\": 0.0, \"percentile_75\": 0.13799287061587767, \"min\": 0.0, \"max\": 7.217018409909195, \"library_sample\": \"lib1 thaw-2_279C_0.014_1\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.014_2\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_2\", \"censored\": true, \"median\": 0.0003206559305228861, \"percentile_25\": 0.0, \"percentile_75\": 0.10574588950380373, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib1 thaw-2_279C_0.014_2\"}, {\"library\": \"lib1\", \"antibody_sample\": \"thaw-2_279C_0.014_2\", \"no-antibody_sample\": \"thaw-2_no-antibody_control_2\", \"censored\": false, \"median\": 0.0003206559305228861, \"percentile_25\": 0.0, \"percentile_75\": 0.10574588950380373, \"min\": 0.0, \"max\": 12.628606282403172, \"library_sample\": \"lib1 thaw-2_279C_0.014_2\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.037_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": true, \"median\": 0.634768740031898, \"percentile_25\": 0.39123538794600365, \"percentile_75\": 0.9278592769876093, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib2 thaw-1_REGN10933_0.037_1\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.037_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": false, \"median\": 0.634768740031898, \"percentile_25\": 0.39123538794600365, \"percentile_75\": 0.9278592769876093, \"min\": 0.0, \"max\": 6.654018583319447, \"library_sample\": \"lib2 thaw-1_REGN10933_0.037_1\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.037_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": true, \"median\": 0.0031816652772293156, \"percentile_25\": 0.0, \"percentile_75\": 0.528914214343192, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib2 thaw-1_REGN10933_0.037_2\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.037_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": false, \"median\": 0.0031816652772293156, \"percentile_25\": 0.0, \"percentile_75\": 0.528914214343192, \"min\": 0.0, \"max\": 8.859130032721582, \"library_sample\": \"lib2 thaw-1_REGN10933_0.037_2\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": true, \"median\": 0.34424427682084724, \"percentile_25\": 0.17634303153609854, \"percentile_75\": 0.5670966221609797, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_1\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": false, \"median\": 0.34424427682084724, \"percentile_25\": 0.17634303153609854, \"percentile_75\": 0.5670966221609797, \"min\": 0.0, \"max\": 4.176747235456095, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_1\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": true, \"median\": 0.303408710529252, \"percentile_25\": 0.18211176331547432, \"percentile_75\": 0.46258335601524225, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.15_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": false, \"median\": 0.303408710529252, \"percentile_25\": 0.18211176331547432, \"percentile_75\": 0.46258335601524225, \"min\": 0.0, \"max\": 4.824573076070082, \"library_sample\": \"lib2 thaw-1_REGN10933_0.15_2\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": true, \"median\": 0.08876356370605121, \"percentile_25\": 0.00043402525333455434, \"percentile_75\": 0.20228926510260703, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_1\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_1\", \"censored\": false, \"median\": 0.08876356370605121, \"percentile_25\": 0.00043402525333455434, \"percentile_75\": 0.20228926510260703, \"min\": 0.0, \"max\": 4.555283749686662, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_1\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": true, \"median\": 0.061318840102064356, \"percentile_25\": 0.0, \"percentile_75\": 0.18980216909961797, \"min\": 0.0, \"max\": 1.0, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\"}, {\"library\": \"lib2\", \"antibody_sample\": \"thaw-1_REGN10933_0.59_2\", \"no-antibody_sample\": \"thaw-1_no-antibody_control_2\", \"censored\": false, \"median\": 0.061318840102064356, \"percentile_25\": 0.0, \"percentile_75\": 0.18980216909961797, \"min\": 0.0, \"max\": 2.7363441687202874, \"library_sample\": \"lib2 thaw-1_REGN10933_0.59_2\"}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.LayerChart(...)"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# NBVAL_SKIP\n",
    "\n",
    "prob_escape_base = alt.Chart(prob_escape_boxplot_df).encode(\n",
    "    y=alt.Y(\"library_sample\", title=None),\n",
    "    tooltip=[\n",
    "        c if (c.endswith(\"sample\") or c == \"library\") else alt.Tooltip(c, format=\".3g\")\n",
    "        for c in prob_escape_boxplot_df.columns\n",
    "        if c != \"library_sample\"\n",
    "    ],\n",
    ")\n",
    "\n",
    "prob_escape_quartile_bars = prob_escape_base.encode(\n",
    "    alt.X(\n",
    "        \"percentile_25\",\n",
    "        scale=alt.Scale(type=\"symlog\", constant=20),\n",
    "        title=\"probability escape\",\n",
    "    ),\n",
    "    alt.X2(\"percentile_75\"),\n",
    ").mark_bar(color=\"blue\")\n",
    "\n",
    "prob_escape_range_lines = prob_escape_base.encode(\n",
    "    alt.X(\"min\"),\n",
    "    alt.X2(\"max\"),\n",
    ").mark_rule(color=\"blue\", opacity=0.5)\n",
    "\n",
    "prob_escape_median_lines = prob_escape_base.encode(\n",
    "    alt.X(\"median\"), alt.X2(\"median\")\n",
    ").mark_bar(xOffset=1, x2Offset=-1, color=\"black\")\n",
    "\n",
    "prob_escape_chart = (\n",
    "    prob_escape_quartile_bars + prob_escape_range_lines + prob_escape_median_lines\n",
    ").properties(width=350, height=alt.Step(14))\n",
    "\n",
    "for s in selections + [censored_selection]:\n",
    "    prob_escape_chart = prob_escape_chart.add_params(s).transform_filter(s)\n",
    "\n",
    "prob_escape_chart"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "919dd46f-b813-421c-a324-3c8bcf7b22b7",
   "metadata": {},
   "source": [
    "## Correlations in variant-level escape probabilitites\n",
    "Analyze correlations between escape probabilities of different variants."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "bc1e5e06-3e9a-4418-bbc9-636218c3c253",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:27.436024Z",
     "iopub.status.busy": "2023-03-19T13:39:27.435746Z",
     "iopub.status.idle": "2023-03-19T13:39:27.851518Z",
     "shell.execute_reply": "2023-03-19T13:39:27.850767Z",
     "shell.execute_reply.started": "2023-03-19T13:39:27.436008Z"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>library</th>\n",
       "      <th>antibody_sample_1</th>\n",
       "      <th>antibody_sample_2</th>\n",
       "      <th>r2</th>\n",
       "      <th>no-antibody_sample_1</th>\n",
       "      <th>antibody_concentration_1</th>\n",
       "      <th>no-antibody_sample_2</th>\n",
       "      <th>antibody_concentration_2</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>1.000</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.037</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.037</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.15_1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>0.100</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.150</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.037</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.15_2</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>0.001</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>0.150</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.037</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.59_1</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>0.020</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.590</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.037</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>lib1</td>\n",
       "      <td>thaw-1_REGN10933_0.59_2</td>\n",
       "      <td>thaw-1_REGN10933_0.037_1</td>\n",
       "      <td>0.000</td>\n",
       "      <td>thaw-1_no-antibody_control_2</td>\n",
       "      <td>0.590</td>\n",
       "      <td>thaw-1_no-antibody_control_1</td>\n",
       "      <td>0.037</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  library         antibody_sample_1         antibody_sample_2     r2  \\\n",
       "0    lib1  thaw-1_REGN10933_0.037_1  thaw-1_REGN10933_0.037_1  1.000   \n",
       "1    lib1   thaw-1_REGN10933_0.15_1  thaw-1_REGN10933_0.037_1  0.100   \n",
       "2    lib1   thaw-1_REGN10933_0.15_2  thaw-1_REGN10933_0.037_1  0.001   \n",
       "3    lib1   thaw-1_REGN10933_0.59_1  thaw-1_REGN10933_0.037_1  0.020   \n",
       "4    lib1   thaw-1_REGN10933_0.59_2  thaw-1_REGN10933_0.037_1  0.000   \n",
       "\n",
       "           no-antibody_sample_1  antibody_concentration_1  \\\n",
       "0  thaw-1_no-antibody_control_1                     0.037   \n",
       "1  thaw-1_no-antibody_control_1                     0.150   \n",
       "2  thaw-1_no-antibody_control_2                     0.150   \n",
       "3  thaw-1_no-antibody_control_1                     0.590   \n",
       "4  thaw-1_no-antibody_control_2                     0.590   \n",
       "\n",
       "           no-antibody_sample_2  antibody_concentration_2  \n",
       "0  thaw-1_no-antibody_control_1                     0.037  \n",
       "1  thaw-1_no-antibody_control_1                     0.037  \n",
       "2  thaw-1_no-antibody_control_1                     0.037  \n",
       "3  thaw-1_no-antibody_control_1                     0.037  \n",
       "4  thaw-1_no-antibody_control_1                     0.037  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "assert len(\n",
    "    prob_escape_filtered.groupby([\"library\", \"antibody_sample\", \"no-antibody_sample\"])\n",
    ") == len(prob_escape_filtered.groupby([\"library\", \"antibody_sample\"]))\n",
    "\n",
    "corrs = (\n",
    "    dms_variants.utils.tidy_to_corr(\n",
    "        df=prob_escape_filtered,\n",
    "        sample_col=\"antibody_sample\",\n",
    "        label_col=\"barcode\",\n",
    "        value_col=\"prob_escape\",\n",
    "        group_cols=[\"library\"],\n",
    "    )\n",
    "    .assign(r2=lambda x: x[\"correlation\"] ** 2)\n",
    "    .drop(columns=\"correlation\")\n",
    ")\n",
    "\n",
    "# add other properties\n",
    "suffixes = [\"_1\", \"_2\"]\n",
    "for suffix in suffixes:\n",
    "    corrs = corrs.merge(\n",
    "        selections_df,\n",
    "        left_on=[\"library\", f\"antibody_sample{suffix}\"],\n",
    "        right_on=[\"library\", \"antibody_sample\"],\n",
    "        validate=\"many_to_one\",\n",
    "        suffixes=suffixes,\n",
    "    ).drop(columns=\"antibody_sample\")\n",
    "\n",
    "corrs.round(3).head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "8ae1fae8-f371-46b2-aa14-680f1fc1ded8",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-03-19T13:39:27.852696Z",
     "iopub.status.busy": "2023-03-19T13:39:27.852386Z",
     "iopub.status.idle": "2023-03-19T13:39:27.993352Z",
     "shell.execute_reply": "2023-03-19T13:39:27.992647Z",
     "shell.execute_reply.started": "2023-03-19T13:39:27.852678Z"
    },
    "tags": []
   },
   "outputs": [
    {
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       "    function displayChart(vegaEmbed) {\n",
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       "    }\n",
       "\n",
       "    if(typeof define === \"function\" && define.amd) {\n",
       "      requirejs.config({paths});\n",
       "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
       "    } else {\n",
       "      maybeLoadScript(\"vega\", \"5\")\n",
       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.6.1\"))\n",
       "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
       "        .catch(showError)\n",
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\"antibody_concentration_2\": 0.037}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.037_1\", \"r2\": 0.0009316475807050236, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.037}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.037_2\", \"r2\": 0.0016704228973551426, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.037}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.037_2\", \"r2\": 1.0, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.037}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.037_2\", \"r2\": 0.001129041335630099, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.037}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.037_2\", \"r2\": 0.012907111959176194, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.037}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.037_2\", \"r2\": 0.0035651215846707962, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.037}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.037_2\", \"r2\": 0.00472318566166516, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.037}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_1\", \"r2\": 0.09758399679523468, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_1\", \"r2\": 0.001129041335630099, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_1\", \"r2\": 1.0, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_1\", \"r2\": 0.019030508968818523, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_1\", \"r2\": 0.07044554757985061, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_1\", \"r2\": 0.019062445655725062, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_2\", \"r2\": 0.0035660060127626516, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_2\", \"r2\": 0.012907111959176194, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_2\", \"r2\": 0.019030508968818523, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_2\", \"r2\": 1.0, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_2\", \"r2\": 0.033758356850870676, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.15_2\", \"r2\": 0.07806292912782932, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.15}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_1\", \"r2\": 0.03324097724378673, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_1\", \"r2\": 0.0035651215846707962, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_1\", \"r2\": 0.07044554757985061, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_1\", \"r2\": 0.033758356850870676, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_1\", \"r2\": 1.0, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_1\", \"r2\": 0.08667426819195391, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_2\", \"r2\": 0.0009316475807050236, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.037_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_2\", \"r2\": 0.00472318566166516, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.037, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_2\", \"r2\": 0.019062445655725062, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.15_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_2\", \"r2\": 0.07806292912782932, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.15, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_1\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_2\", \"r2\": 0.08667426819195391, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_1\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.59}, {\"library\": \"lib2\", \"antibody_sample_1\": \"thaw-1_REGN10933_0.59_2\", \"antibody_sample_2\": \"thaw-1_REGN10933_0.59_2\", \"r2\": 1.0, \"no-antibody_sample_1\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_1\": 0.59, \"no-antibody_sample_2\": \"thaw-1_no-antibody_control_2\", \"antibody_concentration_2\": 0.59}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.Chart(...)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# NBVAL_SKIP\n",
    "\n",
    "for library, library_corr in corrs.groupby(\"library\"):\n",
    "    corr_chart = (\n",
    "        alt.Chart(library_corr)\n",
    "        .encode(\n",
    "            alt.X(\"antibody_sample_1\", title=None),\n",
    "            alt.Y(\"antibody_sample_2\", title=None),\n",
    "            color=alt.Color(\"r2\", scale=alt.Scale(zero=True)),\n",
    "            tooltip=[\n",
    "                (\n",
    "                    alt.Tooltip(c, format=\".3g\")\n",
    "                    if c == \"r2\" or c.startswith(\"antibody_concentration\")\n",
    "                    else c\n",
    "                )\n",
    "                for c in library_corr.columns\n",
    "            ],\n",
    "        )\n",
    "        .mark_rect(stroke=\"black\")\n",
    "        .properties(width=alt.Step(15), height=alt.Step(15), title=library)\n",
    "        .configure_axis(labelLimit=500)\n",
    "    )\n",
    "    display(corr_chart)"
   ]
  }
 ],
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    "name": "ipython",
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