report titers out of bounds of dilution series (#38)

* plots in `serum_titers` notebook indicates titers outside dilution series range * `aggregate_titers` plots titers at bounds * re-run pipeline
jbloomlab · Mar 26, 2024 · 67c6544 · 67c6544
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,8 @@
 - In `process_plate_curvefit_qc` in the YAML configuration, there is a new key called `goodness_of_fit` and now both `min_R2` (the minimum coefficient of determination) and `max_RMSD` (the maximum mean square deviation) for each curve fit are specified as keys under that. The curves are then filtered to retain only those that meet *either* of these criteria (so must fail both to be dropped). Addresses [this issue](https://github.com/jbloomlab/seqneut-pipeline/issues/33) and [this issue](https://github.com/jbloomlab/neutcurve/issues/55#issuecomment-2016975219). Alongside this change, the `rmsd` is now reported in key output files. Also, in the tabulation of failures, `fails_min_R2` now becomes `fails_goodness_of_fit`.
   - This is a **backward-incompatible change** in the configuration YAML. Previously `min_R2` was a standalone key under `process_plate_curvefit_qc`; now `goodness_of_fit` is the required key and `min_R2` and `max_RMSD` are required keys under it.
 
+- Handle titers that are outside the range of the dilutions series by reporting them as upper or lower bounds rather than as interpolated, and marking them appropriately on plots. This change helps with low potency or high potency sera, where there may be no neutralization or high neutralization at all tested concentrations. Addresses [this issue](https://github.com/jbloomlab/seqneut-pipeline/issues/30).
+
 - Added another plate (of H3N2 rather than H1N1) to the `test_example` to test some of the changes introduced in this version.
 
 - Update `seqneut-pipeline` conda environment in `environment.yml`. Update `neutcurve` 2.0.1, also update other packages (`pandas`, `snakemake`, `markdown`, `papermill`) to latest versions.

diff --git a/docs/A23038d0_r32_75K_titers.html b/docs/A23038d0_r32_75K_titers.html
diff --git a/docs/M099d0_titers.html b/docs/M099d0_titers.html
diff --git a/docs/M099d30_titers.html b/docs/M099d30_titers.html
diff --git a/docs/Y044d30_titers.html b/docs/Y044d30_titers.html
diff --git a/docs/Y154d182_titers.html b/docs/Y154d182_titers.html
diff --git a/docs/aggregate_qc_drops.html b/docs/aggregate_qc_drops.html
diff --git a/docs/process_H3N2_plate.html b/docs/process_H3N2_plate.html
diff --git a/docs/process_plate11.html b/docs/process_plate11.html
diff --git a/docs/process_plate2.html b/docs/process_plate2.html
diff --git a/docs/titers.html b/docs/titers.html
diff --git a/notebooks/aggregate_titers.py.ipynb b/notebooks/aggregate_titers.py.ipynb
@@ -111,7 +111,7 @@
     "    toggle=\"true\",\n",
     ")\n",
     "\n",
-    "ncols = 8\n",
+    "ncols = min(8, titers[\"serum\"].nunique())\n",
     "\n",
     "titers_chart = (\n",
     "    alt.Chart(titers)\n",
@@ -144,6 +144,11 @@
     "                title=\"serum (click to select)\",\n",
     "            ),\n",
     "        ),\n",
+    "        alt.Shape(\n",
+    "            \"titer_bound\",\n",
+    "            title=\"titer interpolated or at dilution bounds\",\n",
+    "            legend=alt.Legend(orient=\"bottom\", titleLimit=200),\n",
+    "        ),\n",
     "        color=alt.condition(virus_selection, alt.value(\"red\"), alt.value(\"black\")),\n",
     "        tooltip=[\n",
     "            alt.Tooltip(c, format=\".3g\") if titers[c].dtype == float else c\n",
@@ -152,6 +157,7 @@
     "    )\n",
     "    .mark_line(point=True)\n",
     "    .configure_axis(grid=False)\n",
+    "    .configure_legend(padding=10, labelOffset=2, columnPadding=8, labelLimit=400)\n",
     "    .configure_point(size=45)\n",
     "    .properties(\n",
     "        height=alt.Step(11),\n",
@@ -176,7 +182,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27ff41ab-c967-42a9-adb1-5856810c7f34",
+   "id": "d97b8038-6d77-4786-9955-32b578aba143",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -198,7 +204,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/serum_titers.py.ipynb b/notebooks/serum_titers.py.ipynb
@@ -193,6 +193,7 @@
     "    .encode(\n",
     "        alt.X(\"nt50\", scale=alt.Scale(type=\"log\", nice=False, padding=8)),\n",
     "        alt.Y(\"midpoint\", scale=alt.Scale(type=\"log\", nice=False, padding=8)),\n",
+    "        alt.Color(\"titer_bound\"),\n",
     "        strokeWidth=alt.condition(virus_selection, alt.value(3), alt.value(0)),\n",
     "        size=alt.condition(virus_selection, alt.value(100), alt.value(60)),\n",
     "        tooltip=[\n",
@@ -201,7 +202,7 @@
     "            if c not in {\"serum\", \"titer_as\"}\n",
     "        ],\n",
     "    )\n",
-    "    .mark_circle(stroke=\"red\", fillOpacity=0.45, color=\"black\")\n",
+    "    .mark_circle(stroke=\"black\", fillOpacity=0.45, color=\"black\")\n",
     "    .properties(\n",
     "        width=350,\n",
     "        height=350,\n",
@@ -367,15 +368,15 @@
     "            title=f\"fails {qc_thresholds['min_replicates']=}, {qc_thresholds['max_fold_change_from_median']=}\",\n",
     "            legend=alt.Legend(titleLimit=500),\n",
     "        ),\n",
+    "        alt.Shape(\"titer_bound\"),\n",
     "        strokeWidth=alt.condition(virus_selection, alt.value(2), alt.value(0)),\n",
     "        tooltip=[\n",
     "            alt.Tooltip(c, format=\".3g\") if per_rep_titers_w_fc[c].dtype == float else c\n",
     "            for c in per_rep_titers_w_fc\n",
     "        ],\n",
     "    )\n",
     "    .mark_point(\n",
-    "        shape=\"circle\",\n",
-    "        size=40,\n",
+    "        size=35,\n",
     "        filled=True,\n",
     "        fillOpacity=0.5,\n",
     "        strokeOpacity=1,\n",
@@ -389,14 +390,14 @@
     "        alt.X(\"titer\", scale=alt.Scale(nice=False, padding=5, type=\"log\")),\n",
     "        alt.Y(\"virus\", sort=viruses),\n",
     "        alt.Fill(\"fails_qc\"),\n",
-    "        strokeWidth=alt.condition(virus_selection, alt.value(2), alt.value(0)),\n",
+    "        alt.Shape(\"titer_bound\"),\n",
+    "        strokeWidth=alt.condition(virus_selection, alt.value(2), alt.value(0.5)),\n",
     "        tooltip=[\n",
     "            alt.Tooltip(c, format=\".3g\") if median_titers_noqc[c].dtype == float else c\n",
     "            for c in median_titers_noqc\n",
     "        ],\n",
     "    )\n",
     "    .mark_point(\n",
-    "        shape=\"square\",\n",
     "        size=75,\n",
     "        filled=True,\n",
     "        fillOpacity=0.9,\n",
@@ -411,7 +412,7 @@
     "    .properties(\n",
     "        height=alt.Step(11),\n",
     "        width=250,\n",
-    "        title=f\"{serum} median (square) and per-replicate (small circle) titers\",\n",
+    "        title=f\"{serum} median (large points) and per-replicate (small points) titers\",\n",
     "    )\n",
     "    .configure_axis(grid=False)\n",
     ")\n",
@@ -619,7 +620,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,