plot curves with draw_in_bounds so line does not go past points (#43)

Draw neutralization curves using `draw_in_bounds=True` with `neutcurve` to avoid lines extrapolating beyond data. Addresses [this issue](jbloomlab/neutcurve#59).
jbloomlab · Apr 11, 2024 · 3c762ad · 3c762ad
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,8 @@
   - `altair` to 5.3
   - `python` to 3.12
 
+- Draw neutralization curves using `draw_in_bounds=True` with `neutcurve` to avoid lines extrapolating beyond data. Addresses [this issue](https://github.com/jbloomlab/neutcurve/issues/59).
+
 ## version 3.0.0
 - In `curvefit_params` in the YAML configuration, now `fixslope` should be specified in addition `fixtop` and `fixbottom`. In addition, all three of these can be set to constraint ranges rather than just totally free or to fixed values. Alongside this change, the slope of curve fits are now reported in key output files. Addresses [this issue](https://github.com/jbloomlab/neutcurve/issues/53) and [this issue](https://github.com/jbloomlab/seqneut-pipeline/issues/32).
   - This is a **backward-incompatible change** in the configuration YAML, now you must specify `fixslope` under `curvefit_params`.

diff --git a/docs/aggregate_qc_drops.html b/docs/aggregate_qc_drops.html
diff --git a/docs/pilot_A23038d0_r32_75K_titers.html b/docs/pilot_A23038d0_r32_75K_titers.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/serum_M099d0_titers.html b/docs/serum_M099d0_titers.html
diff --git a/docs/serum_M099d30_titers.html b/docs/serum_M099d30_titers.html
diff --git a/docs/serum_Y044d30_titers.html b/docs/serum_Y044d30_titers.html
diff --git a/docs/serum_Y154d182_titers.html b/docs/serum_Y154d182_titers.html
diff --git a/funcs.smk b/funcs.smk
@@ -60,7 +60,7 @@ def process_plate(plate, plate_params):
     plate_d = copy.deepcopy(plate_params)
     plate_d["group"] = str(plate_d["group"])
     plate_d["date"] = str(plate_d["date"])
-    if not re.fullmatch("\d{4}\-\d{2}\-\d{2}", str(plate_d["date"])):
+    if not re.fullmatch(r"\d{4}\-\d{2}\-\d{2}", str(plate_d["date"])):
         raise ValueError(f"{plate =} {plate_d['date'] =} not in YYYY-MM-DD format")
 
     # Process samples_csv to create the sample data frame

diff --git a/notebooks/group_serum_titers.py.ipynb b/notebooks/group_serum_titers.py.ipynb
@@ -451,6 +451,7 @@
     "        heightscale=1.2,\n",
     "        widthscale=1.2,\n",
     "        subplot_titles=\"{virus}\",\n",
+    "        draw_in_bounds=True,\n",
     "    )\n",
     "    _ = fig.suptitle(\n",
     "        f\"neutralization curves for viruses failing QC for {group} {serum}\",\n",
@@ -532,6 +533,7 @@
     "    widthscale=1.2,\n",
     "    subplot_titles=\"{virus}\",\n",
     "    viruses=[v for v in viruses if v not in viruses_to_drop],\n",
+    "    draw_in_bounds=True,\n",
     ")\n",
     "_ = fig.suptitle(\n",
     "    f\"neutralization curves for retained viruses for {group} {serum}\",\n",

diff --git a/notebooks/process_plate.py.ipynb b/notebooks/process_plate.py.ipynb
@@ -1313,6 +1313,7 @@
     "        titlesize=10,\n",
     "        ticksize=10,\n",
     "        ncol=6,\n",
+    "        draw_in_bounds=True,\n",
     "    )\n",
     "    display(fig)\n",
     "    plt.close(fig)\n",
@@ -1417,6 +1418,7 @@
     "        titlesize=10,\n",
     "        ticksize=10,\n",
     "        ncol=6,\n",
+    "        draw_in_bounds=True,\n",
     "    )\n",
     "else:\n",
     "    print(\"No sera passed QC.\")"