Figure 2: Model performance and evaluation using Patchwork (#13)

* update module 4 for patchwork * added patch work notebook * update * reran whole pipeline * updated patch-work figure * Update notebooks/4.visualization/Figure2_model_performance_and_eval.r Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com> * upaded * updated figures and remove f1 score bug * updated module 0 * update * updated patch work figures * update --------- Co-authored-by: Mike Lippincott <58147848+MikeLippincott@users.noreply.github.com>
WayScience · May 23, 2024 · 63ebd6a · 63ebd6a
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diff --git a/data/JUMP_data/download.ipynb b/data/JUMP_data/download.ipynb
@@ -155,6 +155,7 @@
                     "name": "stdout",
                     "output_type": "stream",
                     "text": [
+                        "Shape of Merged dataset (19498, 5805)\n",
                         "NUmber of plates 51\n",
                         "Number of meta features 13\n",
                         "Number of features 5792\n"
@@ -203,7 +204,7 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.12.2"
+            "version": "3.11.8"
         }
     },
     "nbformat": 4,

diff --git a/notebooks/0.feature_selection/0.feature_selection.ipynb b/notebooks/0.feature_selection/0.feature_selection.ipynb
diff --git a/notebooks/0.feature_selection/nbconverted/0.feature_selection.py b/notebooks/0.feature_selection/nbconverted/0.feature_selection.py
@@ -112,6 +112,7 @@
 print("Number of features", len(injury_feats))
 print("Number of plates", len(injured_df["Plate"].unique()))
 print("Number of injuries", len(injured_df["injury_type"].unique()))
+print("Number of treatments", len(injured_df["Compound Name"].unique()))
 print("List of Compounds", injured_df["Compound Name"].unique())
 print("List of Injuries", injured_df["injury_type"].unique())
 injured_df.head()

diff --git a/notebooks/1.data_splits/1.data_splits.ipynb b/notebooks/1.data_splits/1.data_splits.ipynb
diff --git a/notebooks/2.modeling/2.modeling.ipynb b/notebooks/2.modeling/2.modeling.ipynb
@@ -185,7 +185,7 @@
         },
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+            "execution_count": 6,
             "metadata": {},
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@@ -202,7 +202,7 @@
         },
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@@ -224,7 +224,7 @@
         },
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@@ -255,7 +255,7 @@
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@@ -278,7 +278,7 @@
         },
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+            "execution_count": 11,
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@@ -311,7 +311,7 @@
         },
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+            "execution_count": 12,
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@@ -340,7 +340,7 @@
         },
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+            "execution_count": 13,
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@@ -406,7 +406,7 @@
         },
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+            "execution_count": 14,
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@@ -468,7 +468,7 @@
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@@ -501,7 +501,7 @@
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+            "execution_count": 16,
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@@ -534,7 +534,7 @@
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+            "execution_count": 17,
             "metadata": {},
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             "source": [

diff --git a/notebooks/3.jump-analysis/3.jump_analysis.ipynb b/notebooks/3.jump-analysis/3.jump_analysis.ipynb
diff --git a/notebooks/4.visualization/Figure2_model_performance_and_eval.ipynb b/notebooks/4.visualization/Figure2_model_performance_and_eval.ipynb