From 82b3923a762894d1c4ebcb101c90211a5d553063 Mon Sep 17 00:00:00 2001
From: Jesse Bloom <jbloom@fredhutch.org>
Date: Tue, 30 Jan 2024 13:00:13 -0800
Subject: [PATCH] add `mean_abs` and `sum_abs` to `lineplot_and_heatmap` (#183)

Allows display of site statistics reflecting the mean and sum of the absolute values of the mutation values.

Also, update GitHub actions and lint/format with newer versions of `black` and `ruff`.
---
 .github/workflows/test.yaml         |   4 +-
 CHANGELOG.rst                       |   4 +
 notebooks/real_LyCoV1404.ipynb      | 220 ++++++++++++++++++++--------
 notebooks/visualize_RBD.ipynb       | 196 ++++++++++++-------------
 polyclonal/__init__.py              |   2 +-
 polyclonal/plot.py                  |  14 +-
 polyclonal/polyclonal.py            |   2 +
 polyclonal/polyclonal_collection.py |   1 +
 8 files changed, 278 insertions(+), 165 deletions(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 7931d9a4..5cf3657c 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -15,10 +15,10 @@ jobs:
     timeout-minutes: 60
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: install python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index c547f50b..93601ec1 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -6,6 +6,10 @@ All notable changes to this project will be documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_.
 
+6.11
+----
+- In ``lineplot_and_heatmap``, add ``mean_abs`` and ``sum_abs`` as possible site statistics, reflecting the mean and sum of the absolute values of the mutation values.
+
 6.10
 ----
 - In ``lineplot_and_heatmap``, mutations that are hidden are by one slider filtered even if they fail other sliders. Addresses `this issue <https://github.com/dms-vep/dms-vep-pipeline-3/issues/96>`_
diff --git a/notebooks/real_LyCoV1404.ipynb b/notebooks/real_LyCoV1404.ipynb
index 6c7461c6..85c77676 100644
--- a/notebooks/real_LyCoV1404.ipynb
+++ b/notebooks/real_LyCoV1404.ipynb
@@ -17,6 +17,13 @@
    "execution_count": 1,
    "id": "0b46edd2",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:31:05.986024Z",
+     "iopub.status.busy": "2024-01-30T00:31:05.985362Z",
+     "iopub.status.idle": "2024-01-30T00:31:09.251302Z",
+     "shell.execute_reply": "2024-01-30T00:31:09.250503Z",
+     "shell.execute_reply.started": "2024-01-30T00:31:05.985984Z"
+    },
     "tags": []
    },
    "outputs": [],
@@ -45,6 +52,13 @@
    "execution_count": 2,
    "id": "46127941",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:31:09.252784Z",
+     "iopub.status.busy": "2024-01-30T00:31:09.252414Z",
+     "iopub.status.idle": "2024-01-30T00:31:10.120975Z",
+     "shell.execute_reply": "2024-01-30T00:31:10.120248Z",
+     "shell.execute_reply.started": "2024-01-30T00:31:09.252760Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -212,6 +226,13 @@
    "execution_count": 3,
    "id": "ad21ccc1",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:31:10.122151Z",
+     "iopub.status.busy": "2024-01-30T00:31:10.121916Z",
+     "iopub.status.idle": "2024-01-30T00:31:10.262787Z",
+     "shell.execute_reply": "2024-01-30T00:31:10.261975Z",
+     "shell.execute_reply.started": "2024-01-30T00:31:10.122129Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -334,6 +355,13 @@
    "execution_count": 4,
    "id": "2646efb0",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:31:10.265476Z",
+     "iopub.status.busy": "2024-01-30T00:31:10.265178Z",
+     "iopub.status.idle": "2024-01-30T00:31:10.764362Z",
+     "shell.execute_reply": "2024-01-30T00:31:10.763650Z",
+     "shell.execute_reply.started": "2024-01-30T00:31:10.265453Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -342,28 +370,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-e3f62fa563bb488a8ff69c500e6234a8.vega-embed {\n",
+       "  #altair-viz-8786b0e5e4f94e67a0a381bc77c8d9aa.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-e3f62fa563bb488a8ff69c500e6234a8.vega-embed details,\n",
-       "  #altair-viz-e3f62fa563bb488a8ff69c500e6234a8.vega-embed details summary {\n",
+       "  #altair-viz-8786b0e5e4f94e67a0a381bc77c8d9aa.vega-embed details,\n",
+       "  #altair-viz-8786b0e5e4f94e67a0a381bc77c8d9aa.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-e3f62fa563bb488a8ff69c500e6234a8\"></div>\n",
+       "<div id=\"altair-viz-8786b0e5e4f94e67a0a381bc77c8d9aa\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-e3f62fa563bb488a8ff69c500e6234a8\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-e3f62fa563bb488a8ff69c500e6234a8\");\n",
+       "    if (outputDiv.id !== \"altair-viz-8786b0e5e4f94e67a0a381bc77c8d9aa\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-8786b0e5e4f94e67a0a381bc77c8d9aa\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.15.1?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -399,12 +427,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.15.1\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false}}, \"data\": {\"name\": \"data-3b0145c734c929ff834e40e47fa96f4f\"}, \"mark\": {\"type\": \"line\", \"point\": true, \"size\": 0.5}, \"encoding\": {\"color\": {\"field\": \"n_subs\", \"title\": \"n substitutions\", \"type\": \"nominal\"}, \"column\": {\"field\": \"censored\", \"title\": null, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"antibody_concentration\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"n_subs\", \"type\": \"nominal\"}, {\"field\": \"censored\", \"type\": \"nominal\"}, {\"field\": \"probability escape\", \"format\": \".3g\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"antibody_concentration\", \"type\": \"quantitative\"}, \"y\": {\"field\": \"probability escape\", \"scale\": {\"constant\": 0.05, \"type\": \"symlog\"}, \"type\": \"quantitative\"}}, \"height\": 125, \"width\": 200, \"$schema\": 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+       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false}}, \"data\": {\"name\": \"data-3b0145c734c929ff834e40e47fa96f4f\"}, \"mark\": {\"type\": \"line\", \"point\": true, \"size\": 0.5}, \"encoding\": {\"color\": {\"field\": \"n_subs\", \"title\": \"n substitutions\", \"type\": \"nominal\"}, \"column\": {\"field\": \"censored\", \"title\": null, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"antibody_concentration\", \"format\": \".3g\", \"type\": \"quantitative\"}, {\"field\": \"n_subs\", \"type\": \"nominal\"}, {\"field\": \"censored\", \"type\": \"nominal\"}, {\"field\": \"probability escape\", \"format\": \".3g\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"antibody_concentration\", \"type\": \"quantitative\"}, \"y\": {\"field\": \"probability escape\", \"scale\": {\"constant\": 0.05, \"type\": \"symlog\"}, \"type\": \"quantitative\"}}, \"height\": 125, \"width\": 200, \"$schema\": 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10.46, \"n_subs\": \"3\", \"censored\": \"not censored\", \"probability escape\": 0.03622808548530722}, {\"antibody_concentration\": 10.46, \"n_subs\": \">3\", \"censored\": \"not censored\", \"probability escape\": 0.0548717904383159}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -490,6 +518,13 @@
    "execution_count": 5,
    "id": "9d265060",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:31:10.767460Z",
+     "iopub.status.busy": "2024-01-30T00:31:10.767287Z",
+     "iopub.status.idle": "2024-01-30T00:33:16.269066Z",
+     "shell.execute_reply": "2024-01-30T00:33:16.267817Z",
+     "shell.execute_reply.started": "2024-01-30T00:31:10.767441Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -499,28 +534,28 @@
      "text": [
       "#\n",
       "# Fitting site-level fixed Hill coefficient and non-neutralized frac model.\n",
-      "# Starting optimization of 1248 parameters at Fri Jan 26 11:43:31 2024.\n",
+      "# Starting optimization of 1248 parameters at Mon Jan 29 16:31:23 2024.\n",
       "        step    time_sec        loss    fit_loss  reg_escape  reg_spread reg_spatial reg_uniqueness reg_uniqueness2 reg_activity reg_hill_coefficient reg_non_neutralized_frac\n",
-      "           0    0.036176       37333       37314           0           0           0              0               0       18.641                    0                        0\n",
-      "         100      4.0581        4910        4825      38.903           0           0              0               0       46.113                    0                        0\n",
-      "         187      7.4821      4908.2      4822.4      39.676           0           0              0               0       46.145                    0                        0\n",
-      "# Successfully finished at Fri Jan 26 11:43:39 2024.\n",
+      "           0     0.13355       37333       37314           0           0           0              0               0       18.641                    0                        0\n",
+      "         100      14.986        4910        4825      38.888           0           0              0               0       46.108                    0                        0\n",
+      "         177      26.404      4908.2      4822.5      39.589           0           0              0               0       46.145                    0                        0\n",
+      "# Successfully finished at Mon Jan 29 16:31:49 2024.\n",
       "#\n",
       "# Fitting fixed Hill coefficient and non-neutralized frac model.\n",
-      "# Starting optimization of 8450 parameters at Fri Jan 26 11:43:39 2024.\n",
+      "# Starting optimization of 8450 parameters at Mon Jan 29 16:31:50 2024.\n",
       "        step    time_sec        loss    fit_loss  reg_escape  reg_spread reg_spatial reg_uniqueness reg_uniqueness2 reg_activity reg_hill_coefficient reg_non_neutralized_frac\n",
-      "           0    0.057451      7348.1      7034.8      267.14  2.8796e-31           0              0               0       46.145                    0                        0\n",
-      "         100      6.7995        6863      6706.2      93.396        10.9           0              0               0       52.517                    0                        0\n",
-      "         200      13.405        6855      6701.6      89.267      11.691           0              0               0       52.449                    0                        0\n",
-      "         221      14.788      6854.7      6701.6      88.939      11.715           0              0               0       52.465                    0                        0\n",
-      "# Successfully finished at Fri Jan 26 11:43:54 2024.\n",
+      "           0      2.2456      7347.8      7034.8      266.82  3.6355e-31           0              0               0       46.145                    0                        0\n",
+      "         100      35.417      6864.9      6706.7      95.063      10.674           0              0               0       52.402                    0                        0\n",
+      "         200      65.438      6855.5      6701.8      89.625      11.611           0              0               0       52.473                    0                        0\n",
+      "         265      80.776      6854.7      6701.4      89.038      11.746           0              0               0       52.456                    0                        0\n",
+      "# Successfully finished at Mon Jan 29 16:33:11 2024.\n",
       "#\n",
       "# Fitting model.\n",
-      "# Starting optimization of 8452 parameters at Fri Jan 26 11:43:54 2024.\n",
+      "# Starting optimization of 8452 parameters at Mon Jan 29 16:33:11 2024.\n",
       "        step    time_sec        loss    fit_loss  reg_escape  reg_spread reg_spatial reg_uniqueness reg_uniqueness2 reg_activity reg_hill_coefficient reg_non_neutralized_frac\n",
-      "           0    0.056528      6812.7      6701.6      88.939      11.715           0              0               0       10.493                    0                        0\n",
-      "          15     0.95641      6750.3      6638.2      88.941      11.716           0              0               0       10.443              0.90755                  0.07658\n",
-      "# Successfully finished at Fri Jan 26 11:43:55 2024.\n"
+      "           0     0.23519      6812.7      6701.4      89.038      11.746           0              0               0       10.491                    0                        0\n",
+      "          19      5.2434      6750.3      6638.1      89.041      11.747           0              0               0       10.444              0.90715                 0.076633\n",
+      "# Successfully finished at Mon Jan 29 16:33:16 2024.\n"
      ]
     }
    ],
@@ -558,6 +593,13 @@
    "execution_count": 6,
    "id": "8e887519",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:16.271248Z",
+     "iopub.status.busy": "2024-01-30T00:33:16.270761Z",
+     "iopub.status.idle": "2024-01-30T00:33:16.291062Z",
+     "shell.execute_reply": "2024-01-30T00:33:16.290394Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:16.271214Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -631,6 +673,13 @@
    "execution_count": 7,
    "id": "d7b168a4",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:16.292741Z",
+     "iopub.status.busy": "2024-01-30T00:33:16.292354Z",
+     "iopub.status.idle": "2024-01-30T00:33:16.296224Z",
+     "shell.execute_reply": "2024-01-30T00:33:16.295398Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:16.292714Z"
+    },
     "tags": []
    },
    "outputs": [],
@@ -652,6 +701,13 @@
    "execution_count": 8,
    "id": "f7db9fc1-1a45-403e-b504-6cbc02f68af7",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:16.298068Z",
+     "iopub.status.busy": "2024-01-30T00:33:16.297723Z",
+     "iopub.status.idle": "2024-01-30T00:33:16.403470Z",
+     "shell.execute_reply": "2024-01-30T00:33:16.402824Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:16.298042Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -761,6 +817,13 @@
    "execution_count": 9,
    "id": "1a9d6f5d",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:16.405062Z",
+     "iopub.status.busy": "2024-01-30T00:33:16.404719Z",
+     "iopub.status.idle": "2024-01-30T00:33:22.850549Z",
+     "shell.execute_reply": "2024-01-30T00:33:22.849370Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:16.405039Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -769,28 +832,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-96362a108c804f378035ff6c3c29a700.vega-embed {\n",
+       "  #altair-viz-b1fb2bec0c3b422b900c64b5a119bb33.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-96362a108c804f378035ff6c3c29a700.vega-embed details,\n",
-       "  #altair-viz-96362a108c804f378035ff6c3c29a700.vega-embed details summary {\n",
+       "  #altair-viz-b1fb2bec0c3b422b900c64b5a119bb33.vega-embed details,\n",
+       "  #altair-viz-b1fb2bec0c3b422b900c64b5a119bb33.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-96362a108c804f378035ff6c3c29a700\"></div>\n",
+       "<div id=\"altair-viz-b1fb2bec0c3b422b900c64b5a119bb33\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-96362a108c804f378035ff6c3c29a700\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-96362a108c804f378035ff6c3c29a700\");\n",
+       "    if (outputDiv.id !== \"altair-viz-b1fb2bec0c3b422b900c64b5a119bb33\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-b1fb2bec0c3b422b900c64b5a119bb33\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.15.1?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -826,12 +889,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.15.1\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false, \"labelOverlap\": \"parity\"}, \"padding\": 10}, \"vconcat\": [{\"data\": {\"name\": \"data-9631765c1c8eedabe994b76062594ede\"}, \"mark\": {\"type\": \"rect\"}, \"encoding\": {\"color\": {\"value\": \"gray\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}}, \"height\": 11, \"name\": \"view_2\", \"title\": \"site zoom bar\", \"width\": 500}, {\"layer\": [{\"mark\": {\"type\": \"line\", \"opacity\": 0.7, \"size\": 1}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": null, \"scale\": {\"domain\": [\"epitope 1\"], \"range\": [\"#0072B2\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"quantitative\"}, {\"field\": \"_stat_site_val\", \"format\": \".3g\", \"title\": \"site escape\", \"type\": 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\"_stat_site_order\": 1211}, {\"site\": 1216, \"wildtype\": \"G\", \"_stat_site_order\": 1212}, {\"site\": 1217, \"wildtype\": \"F\", \"_stat_site_order\": 1213}, {\"site\": 1218, \"wildtype\": \"I\", \"_stat_site_order\": 1214}, {\"site\": 1219, \"wildtype\": \"A\", \"_stat_site_order\": 1215}, {\"site\": 1220, \"wildtype\": \"G\", \"_stat_site_order\": 1216}, {\"site\": 1221, \"wildtype\": \"L\", \"_stat_site_order\": 1217}, {\"site\": 1222, \"wildtype\": \"I\", \"_stat_site_order\": 1218}, {\"site\": 1223, \"wildtype\": \"A\", \"_stat_site_order\": 1219}, {\"site\": 1224, \"wildtype\": \"I\", \"_stat_site_order\": 1220}, {\"site\": 1225, \"wildtype\": \"V\", \"_stat_site_order\": 1221}, {\"site\": 1226, \"wildtype\": \"M\", \"_stat_site_order\": 1222}, {\"site\": 1227, \"wildtype\": \"V\", \"_stat_site_order\": 1223}, {\"site\": 1228, \"wildtype\": \"T\", \"_stat_site_order\": 1224}, {\"site\": 1229, \"wildtype\": \"I\", \"_stat_site_order\": 1225}, {\"site\": 1230, \"wildtype\": \"M\", \"_stat_site_order\": 1226}, {\"site\": 1231, \"wildtype\": \"L\", \"_stat_site_order\": 1227}, {\"site\": 1232, \"wildtype\": \"C\", \"_stat_site_order\": 1228}, {\"site\": 1233, \"wildtype\": \"C\", \"_stat_site_order\": 1229}, {\"site\": 1234, \"wildtype\": \"M\", \"_stat_site_order\": 1230}, {\"site\": 1235, \"wildtype\": \"T\", \"_stat_site_order\": 1231}, {\"site\": 1236, \"wildtype\": \"S\", \"_stat_site_order\": 1232}, {\"site\": 1237, \"wildtype\": \"C\", \"_stat_site_order\": 1233}, {\"site\": 1238, \"wildtype\": \"C\", \"_stat_site_order\": 1234}, {\"site\": 1239, \"wildtype\": \"S\", \"_stat_site_order\": 1235}, {\"site\": 1240, \"wildtype\": \"C\", \"_stat_site_order\": 1236}, {\"site\": 1241, \"wildtype\": \"L\", \"_stat_site_order\": 1237}, {\"site\": 1242, \"wildtype\": \"K\", \"_stat_site_order\": 1238}, {\"site\": 1243, \"wildtype\": \"G\", \"_stat_site_order\": 1239}, {\"site\": 1244, \"wildtype\": \"C\", \"_stat_site_order\": 1240}, {\"site\": 1245, \"wildtype\": \"C\", \"_stat_site_order\": 1241}, {\"site\": 1246, \"wildtype\": \"S\", \"_stat_site_order\": 1242}, {\"site\": 1247, \"wildtype\": \"C\", \"_stat_site_order\": 1243}, {\"site\": 1248, \"wildtype\": \"G\", \"_stat_site_order\": 1244}, {\"site\": 1249, \"wildtype\": \"S\", \"_stat_site_order\": 1245}, {\"site\": 1250, \"wildtype\": \"*\", \"_stat_site_order\": 1246}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -874,6 +937,13 @@
    "execution_count": 10,
    "id": "e06e0259-9ad4-4d3a-81bb-dbf38631d702",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:22.853070Z",
+     "iopub.status.busy": "2024-01-30T00:33:22.852479Z",
+     "iopub.status.idle": "2024-01-30T00:33:37.048502Z",
+     "shell.execute_reply": "2024-01-30T00:33:37.047681Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:22.853022Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -882,28 +952,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-320e7c8f5dee46809fea133128a599d4.vega-embed {\n",
+       "  #altair-viz-4fb60d5413dc4da2ae2f7e4fe801c9e3.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-320e7c8f5dee46809fea133128a599d4.vega-embed details,\n",
-       "  #altair-viz-320e7c8f5dee46809fea133128a599d4.vega-embed details summary {\n",
+       "  #altair-viz-4fb60d5413dc4da2ae2f7e4fe801c9e3.vega-embed details,\n",
+       "  #altair-viz-4fb60d5413dc4da2ae2f7e4fe801c9e3.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-320e7c8f5dee46809fea133128a599d4\"></div>\n",
+       "<div id=\"altair-viz-4fb60d5413dc4da2ae2f7e4fe801c9e3\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-320e7c8f5dee46809fea133128a599d4\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-320e7c8f5dee46809fea133128a599d4\");\n",
+       "    if (outputDiv.id !== \"altair-viz-4fb60d5413dc4da2ae2f7e4fe801c9e3\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-4fb60d5413dc4da2ae2f7e4fe801c9e3\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.15.1?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -939,12 +1009,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.15.1\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
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@@ -982,6 +1052,13 @@
    "execution_count": 11,
    "id": "837eb0ea-e56e-4b5a-badd-94923ceca75d",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:37.049866Z",
+     "iopub.status.busy": "2024-01-30T00:33:37.049556Z",
+     "iopub.status.idle": "2024-01-30T00:33:40.016559Z",
+     "shell.execute_reply": "2024-01-30T00:33:40.015911Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:37.049848Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -990,28 +1067,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-f355df1b852e495abc5e239b1a54635c.vega-embed {\n",
+       "  #altair-viz-0351aa8f4b5c4b1f9ce5da9cddc65857.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-f355df1b852e495abc5e239b1a54635c.vega-embed details,\n",
-       "  #altair-viz-f355df1b852e495abc5e239b1a54635c.vega-embed details summary {\n",
+       "  #altair-viz-0351aa8f4b5c4b1f9ce5da9cddc65857.vega-embed details,\n",
+       "  #altair-viz-0351aa8f4b5c4b1f9ce5da9cddc65857.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-f355df1b852e495abc5e239b1a54635c\"></div>\n",
+       "<div id=\"altair-viz-0351aa8f4b5c4b1f9ce5da9cddc65857\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-f355df1b852e495abc5e239b1a54635c\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-f355df1b852e495abc5e239b1a54635c\");\n",
+       "    if (outputDiv.id !== \"altair-viz-0351aa8f4b5c4b1f9ce5da9cddc65857\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-0351aa8f4b5c4b1f9ce5da9cddc65857\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.15.1?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -1047,12 +1124,12 @@
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        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.15.1\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
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445, \"wildtype\": \"N\", \"_stat_site_order\": 11}, {\"site\": 446, \"wildtype\": \"Y\", \"_stat_site_order\": 12}, {\"site\": 447, \"wildtype\": \"N\", \"_stat_site_order\": 13}, {\"site\": 448, \"wildtype\": \"Y\", \"_stat_site_order\": 14}, {\"site\": 449, \"wildtype\": \"L\", \"_stat_site_order\": 15}, {\"site\": 450, \"wildtype\": \"Y\", \"_stat_site_order\": 16}, {\"site\": 451, \"wildtype\": \"R\", \"_stat_site_order\": 17}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -1090,6 +1167,13 @@
    "execution_count": 12,
    "id": "f9d15bf6-c67b-46aa-9f69-96b97133e701",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:40.019810Z",
+     "iopub.status.busy": "2024-01-30T00:33:40.019413Z",
+     "iopub.status.idle": "2024-01-30T00:33:42.895588Z",
+     "shell.execute_reply": "2024-01-30T00:33:42.894880Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:40.019785Z"
+    },
     "tags": []
    },
    "outputs": [
@@ -1098,28 +1182,28 @@
       "text/html": [
        "\n",
        "<style>\n",
-       "  #altair-viz-08a4af881d4949c29e689458c7ecad1a.vega-embed {\n",
+       "  #altair-viz-b58c24a260054172a692cebf15465f68.vega-embed {\n",
        "    width: 100%;\n",
        "    display: flex;\n",
        "  }\n",
        "\n",
-       "  #altair-viz-08a4af881d4949c29e689458c7ecad1a.vega-embed details,\n",
-       "  #altair-viz-08a4af881d4949c29e689458c7ecad1a.vega-embed details summary {\n",
+       "  #altair-viz-b58c24a260054172a692cebf15465f68.vega-embed details,\n",
+       "  #altair-viz-b58c24a260054172a692cebf15465f68.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-08a4af881d4949c29e689458c7ecad1a\"></div>\n",
+       "<div id=\"altair-viz-b58c24a260054172a692cebf15465f68\"></div>\n",
        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
        "  (function(spec, embedOpt){\n",
        "    let outputDiv = document.currentScript.previousElementSibling;\n",
-       "    if (outputDiv.id !== \"altair-viz-08a4af881d4949c29e689458c7ecad1a\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-08a4af881d4949c29e689458c7ecad1a\");\n",
+       "    if (outputDiv.id !== \"altair-viz-b58c24a260054172a692cebf15465f68\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-b58c24a260054172a692cebf15465f68\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.16.3?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.15.1?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -1155,12 +1239,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.16.3\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.15.1\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
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@@ -1198,6 +1282,13 @@
    "execution_count": 13,
    "id": "aeff75ca",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:42.896845Z",
+     "iopub.status.busy": "2024-01-30T00:33:42.896610Z",
+     "iopub.status.idle": "2024-01-30T00:33:43.017592Z",
+     "shell.execute_reply": "2024-01-30T00:33:43.016901Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:42.896823Z"
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    },
    "outputs": [
@@ -1291,6 +1382,13 @@
    "execution_count": 14,
    "id": "c05b9029-6c4b-4c14-88cd-ed997a32b84a",
    "metadata": {
+    "execution": {
+     "iopub.execute_input": "2024-01-30T00:33:43.019148Z",
+     "iopub.status.busy": "2024-01-30T00:33:43.018903Z",
+     "iopub.status.idle": "2024-01-30T00:33:43.023519Z",
+     "shell.execute_reply": "2024-01-30T00:33:43.022539Z",
+     "shell.execute_reply.started": "2024-01-30T00:33:43.019126Z"
+    },
     "tags": []
    },
    "outputs": [],
@@ -1323,7 +1421,7 @@
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diff --git a/notebooks/visualize_RBD.ipynb b/notebooks/visualize_RBD.ipynb
index bdd1930e..c29a3472 100644
--- a/notebooks/visualize_RBD.ipynb
+++ b/notebooks/visualize_RBD.ipynb
@@ -28,11 +28,11 @@
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@@ -180,11 +180,11 @@
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@@ -264,11 +264,11 @@
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@@ -307,11 +307,11 @@
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@@ -389,11 +389,11 @@
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@@ -562,11 +562,11 @@
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@@ -791,11 +791,11 @@
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@@ -1082,11 +1082,11 @@
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-       "      outputDiv = document.getElementById(\"altair-viz-f5c9bf9dae684e7d9c3674b37a625602\");\n",
+       "    if (outputDiv.id !== \"altair-viz-01d108327b8340cb8387859e37d94a64\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-01d108327b8340cb8387859e37d94a64\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.15.1?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -1261,12 +1261,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.15.1\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false, \"labelOverlap\": \"parity\"}, \"padding\": 10}, \"vconcat\": [{\"data\": {\"name\": \"data-bc219ad30c05bdba170b53124abb8131\"}, \"mark\": {\"type\": \"rect\"}, \"encoding\": {\"color\": {\"value\": \"gray\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}}, \"height\": 11, \"name\": \"view_2\", \"title\": \"site zoom bar\", \"width\": 500}, {\"layer\": [{\"mark\": {\"type\": \"line\", \"opacity\": 0.7, \"size\": 1}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": {\"orient\": \"left\"}, \"scale\": {\"domain\": [\"class 1\", \"class 2\", \"class 3\"], \"range\": [\"#0072B2\", \"#CC79A7\", \"#009E73\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"quantitative\"}, {\"field\": 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-     "shell.execute_reply": "2023-08-18T19:33:55.717268Z",
-     "shell.execute_reply.started": "2023-08-18T19:33:54.103030Z"
+     "iopub.execute_input": "2024-01-30T00:27:19.829053Z",
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+     "iopub.status.idle": "2024-01-30T00:27:23.997242Z",
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@@ -1309,28 +1309,28 @@
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        "\n",
        "<style>\n",
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        "    width: 100%;\n",
        "    display: flex;\n",
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        "\n",
-       "  #altair-viz-c51399f089c1436e86d08ad8355757de.vega-embed details,\n",
-       "  #altair-viz-c51399f089c1436e86d08ad8355757de.vega-embed details summary {\n",
+       "  #altair-viz-f3fca9b4bcd74315869ce6f44a86a7c3.vega-embed details,\n",
+       "  #altair-viz-f3fca9b4bcd74315869ce6f44a86a7c3.vega-embed details summary {\n",
        "    position: relative;\n",
        "  }\n",
        "</style>\n",
-       "<div id=\"altair-viz-c51399f089c1436e86d08ad8355757de\"></div>\n",
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        "<script type=\"text/javascript\">\n",
        "  var VEGA_DEBUG = (typeof VEGA_DEBUG == \"undefined\") ? {} : VEGA_DEBUG;\n",
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-       "    if (outputDiv.id !== \"altair-viz-c51399f089c1436e86d08ad8355757de\") {\n",
-       "      outputDiv = document.getElementById(\"altair-viz-c51399f089c1436e86d08ad8355757de\");\n",
+       "    if (outputDiv.id !== \"altair-viz-f3fca9b4bcd74315869ce6f44a86a7c3\") {\n",
+       "      outputDiv = document.getElementById(\"altair-viz-f3fca9b4bcd74315869ce6f44a86a7c3\");\n",
        "    }\n",
        "    const paths = {\n",
        "      \"vega\": \"https://cdn.jsdelivr.net/npm/vega@5?noext\",\n",
        "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm/vega-lib?noext\",\n",
-       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.8.0?noext\",\n",
+       "      \"vega-lite\": \"https://cdn.jsdelivr.net/npm/vega-lite@5.15.1?noext\",\n",
        "      \"vega-embed\": \"https://cdn.jsdelivr.net/npm/vega-embed@6?noext\",\n",
        "    };\n",
        "\n",
@@ -1366,12 +1366,12 @@
        "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
        "    } else {\n",
        "      maybeLoadScript(\"vega\", \"5\")\n",
-       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.8.0\"))\n",
+       "        .then(() => maybeLoadScript(\"vega-lite\", \"5.15.1\"))\n",
        "        .then(() => maybeLoadScript(\"vega-embed\", \"6\"))\n",
        "        .catch(showError)\n",
        "        .then(() => displayChart(vegaEmbed));\n",
        "    }\n",
-       "  })({\"config\": {\"view\": {\"continuousWidth\": 300, \"continuousHeight\": 300}, \"axis\": {\"grid\": false, \"labelOverlap\": \"parity\"}, \"padding\": 10}, \"vconcat\": [{\"data\": {\"name\": \"data-bc219ad30c05bdba170b53124abb8131\"}, \"mark\": {\"type\": \"rect\"}, \"encoding\": {\"color\": {\"value\": \"gray\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"quantitative\"}], \"x\": {\"field\": \"site\", \"sort\": {\"field\": \"_stat_site_order\", \"order\": \"ascending\"}, \"type\": \"ordinal\"}}, \"height\": 11, \"name\": \"view_7\", \"title\": \"site zoom bar\", \"width\": 500}, {\"layer\": [{\"mark\": {\"type\": \"line\", \"opacity\": 0.7, \"size\": 1}, \"encoding\": {\"color\": {\"field\": \"epitope\", \"legend\": null, \"scale\": {\"domain\": [\"all\"], \"range\": [\"#0072B2\"]}, \"type\": \"nominal\"}, \"tooltip\": [{\"field\": \"site\", \"type\": \"quantitative\"}, {\"field\": \"_stat_site_val\", \"format\": \".3g\", \"title\": \"site log2 fold change IC90\", 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\"_stat_site_order\": 148}, {\"site\": 505, \"wildtype\": \"Y\", \"_stat_site_order\": 149}, {\"site\": 506, \"wildtype\": \"Q\", \"_stat_site_order\": 150}, {\"site\": 507, \"wildtype\": \"P\", \"_stat_site_order\": 151}, {\"site\": 508, \"wildtype\": \"Y\", \"_stat_site_order\": 152}, {\"site\": 510, \"wildtype\": \"V\", \"_stat_site_order\": 153}, {\"site\": 512, \"wildtype\": \"V\", \"_stat_site_order\": 154}, {\"site\": 513, \"wildtype\": \"L\", \"_stat_site_order\": 155}, {\"site\": 514, \"wildtype\": \"S\", \"_stat_site_order\": 156}, {\"site\": 515, \"wildtype\": \"F\", \"_stat_site_order\": 157}, {\"site\": 516, \"wildtype\": \"E\", \"_stat_site_order\": 158}, {\"site\": 517, \"wildtype\": \"L\", \"_stat_site_order\": 159}, {\"site\": 518, \"wildtype\": \"L\", \"_stat_site_order\": 160}, {\"site\": 519, \"wildtype\": \"H\", \"_stat_site_order\": 161}, {\"site\": 520, \"wildtype\": \"A\", \"_stat_site_order\": 162}, {\"site\": 521, \"wildtype\": \"P\", \"_stat_site_order\": 163}, {\"site\": 522, \"wildtype\": \"A\", \"_stat_site_order\": 164}, {\"site\": 524, \"wildtype\": \"V\", \"_stat_site_order\": 165}, {\"site\": 525, \"wildtype\": \"C\", \"_stat_site_order\": 166}, {\"site\": 526, \"wildtype\": \"G\", \"_stat_site_order\": 167}, {\"site\": 527, \"wildtype\": \"P\", \"_stat_site_order\": 168}, {\"site\": 528, \"wildtype\": \"K\", \"_stat_site_order\": 169}, {\"site\": 529, \"wildtype\": \"K\", \"_stat_site_order\": 170}, {\"site\": 530, \"wildtype\": \"S\", \"_stat_site_order\": 171}, {\"site\": 531, \"wildtype\": \"T\", \"_stat_site_order\": 172}]}}, {\"mode\": \"vega-lite\"});\n",
        "</script>"
       ],
       "text/plain": [
@@ -1403,11 +1403,11 @@
    "execution_count": 12,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-08-18T19:33:55.719096Z",
-     "iopub.status.busy": "2023-08-18T19:33:55.718883Z",
-     "iopub.status.idle": "2023-08-18T19:33:56.183673Z",
-     "shell.execute_reply": "2023-08-18T19:33:56.183052Z",
-     "shell.execute_reply.started": "2023-08-18T19:33:55.719080Z"
+     "iopub.execute_input": "2024-01-30T00:27:23.999385Z",
+     "iopub.status.busy": "2024-01-30T00:27:23.998926Z",
+     "iopub.status.idle": "2024-01-30T00:27:24.960839Z",
+     "shell.execute_reply": "2024-01-30T00:27:24.960114Z",
+     "shell.execute_reply.started": "2024-01-30T00:27:23.999359Z"
     }
    },
    "outputs": [
@@ -1490,11 +1490,11 @@
    "execution_count": 13,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-08-18T19:33:56.185036Z",
-     "iopub.status.busy": "2023-08-18T19:33:56.184722Z",
-     "iopub.status.idle": "2023-08-18T19:33:56.189010Z",
-     "shell.execute_reply": "2023-08-18T19:33:56.188310Z",
-     "shell.execute_reply.started": "2023-08-18T19:33:56.185017Z"
+     "iopub.execute_input": "2024-01-30T00:27:24.962493Z",
+     "iopub.status.busy": "2024-01-30T00:27:24.962168Z",
+     "iopub.status.idle": "2024-01-30T00:27:24.969123Z",
+     "shell.execute_reply": "2024-01-30T00:27:24.968205Z",
+     "shell.execute_reply.started": "2024-01-30T00:27:24.962463Z"
     }
    },
    "outputs": [
@@ -1565,11 +1565,11 @@
    "execution_count": 14,
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2023-08-18T19:33:56.189954Z",
-     "iopub.status.busy": "2023-08-18T19:33:56.189736Z",
-     "iopub.status.idle": "2023-08-18T19:33:56.212175Z",
-     "shell.execute_reply": "2023-08-18T19:33:56.211488Z",
-     "shell.execute_reply.started": "2023-08-18T19:33:56.189936Z"
+     "iopub.execute_input": "2024-01-30T00:27:24.970645Z",
+     "iopub.status.busy": "2024-01-30T00:27:24.970250Z",
+     "iopub.status.idle": "2024-01-30T00:27:25.122190Z",
+     "shell.execute_reply": "2024-01-30T00:27:25.121527Z",
+     "shell.execute_reply.started": "2024-01-30T00:27:24.970615Z"
     },
     "tags": []
    },
@@ -1667,7 +1667,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,
diff --git a/polyclonal/__init__.py b/polyclonal/__init__.py
index 5bba4609..824ee6a7 100644
--- a/polyclonal/__init__.py
+++ b/polyclonal/__init__.py
@@ -31,7 +31,7 @@
 
 __author__ = "`the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_"
 __email__ = "jbloom@fredhutch.org"
-__version__ = "6.10"
+__version__ = "6.11"
 __url__ = "https://github.com/jbloomlab/polyclonal"
 
 from polyclonal.alphabets import AAS
diff --git a/polyclonal/plot.py b/polyclonal/plot.py
index 5f2b3bd9..0a1d735a 100644
--- a/polyclonal/plot.py
+++ b/polyclonal/plot.py
@@ -520,7 +520,7 @@ def lineplot_and_heatmap(
         they fail other filters in `addtl_slider_stats`.
     init_floor_at_zero : bool
         Initial value for option to put floor of zero on value is `stat_col`.
-    init_site_statistic : {'sum', 'mean', 'max', 'min'}
+    init_site_statistic : {'sum', 'mean', 'max', 'min', 'mean_abs', 'sum_abs'}
         Initial value for site statistic in lineplot, calculated from `stat_col`.
     cell_size : float
         Size of cells in heatmap
@@ -594,6 +594,7 @@ def lineplot_and_heatmap(
     -------
     altair.Chart
         Interactive plot.
+
     """
     if addtl_tooltip_stats is None:
         addtl_tooltip_stats = []
@@ -978,7 +979,7 @@ def replace_std(col):
     )
 
     # make the site chart
-    site_statistics = ["sum", "mean", "max", "min"]
+    site_statistics = ["sum", "mean", "max", "min", "sum_abs", "mean_abs"]
     if init_site_statistic not in site_statistics:
         raise ValueError(f"invalid {init_site_statistic=}")
     if set(site_statistics).intersection(req_cols):
@@ -998,8 +999,15 @@ def replace_std(col):
         base_chart.transform_filter(
             (alt.datum.wildtype != alt.datum.mutant) & ~alt.datum["_stat_hide"]
         )
+        .transform_calculate(_stat_abs=alt.expr.abs(alt.datum["_stat"]))
         .transform_aggregate(
-            **{f"_stat_{stat}": f"{stat}(_stat)" for stat in site_statistics},
+            **{
+                f"_stat_{stat}": (
+                    stat.split("_")[0]
+                    + f"({'_stat_abs' if stat.endswith('_abs') else '_stat'})"
+                )
+                for stat in site_statistics
+            },
             groupby=[*site_prop_cols, category_col],
         )
         .transform_fold(
diff --git a/polyclonal/polyclonal.py b/polyclonal/polyclonal.py
index 3b137aa3..1dc6033b 100644
--- a/polyclonal/polyclonal.py
+++ b/polyclonal/polyclonal.py
@@ -2867,6 +2867,7 @@ def filter_variants_by_seen_muts(
         variants_df : pandas.DataFrame
             Copy of input dataframe, with rows of variants
             that have unseen mutations removed.
+
         """
         variants_df = variants_df.copy()
 
@@ -3154,6 +3155,7 @@ def mut_escape_corr(self, ref_poly):
         -------
         corr_df : pandas.DataFrame
             Pairwise epitope correlations for escape.
+
         """
         if self.mut_escape_df is None or ref_poly.mut_escape_df is None:
             raise ValueError("Both objects must have `mut_escape_df` initialized.")
diff --git a/polyclonal/polyclonal_collection.py b/polyclonal/polyclonal_collection.py
index 180a16fe..748bc17a 100644
--- a/polyclonal/polyclonal_collection.py
+++ b/polyclonal/polyclonal_collection.py
@@ -851,6 +851,7 @@ def mut_escape_corr_heatmap(
             Plot squared correlation (eg, :math:`R^2` rather :math:`R`).
         **kwargs
             Keyword args for :func:`polyclonal.plot.corr_heatmap`
+
         """
         corr_label = {"pearson": "r", "kendall": "tau", "spearman": "rho"}[method]
         corr2_label = f"{corr_label}2"