🎨 change heading level and prepare to make it easier to read

Multiomics-Analytics-Group · Feb 21, 2025 · 289dcf1 · 289dcf1
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Showing 2 changed files with 18 additions and 14 deletions.
diff --git a/docs/api_examples/ANCOVA_analysis.ipynb b/docs/api_examples/ANCOVA_analysis.ipynb
@@ -73,7 +73,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Load data.\n",
+    "# Data for recipe\n",
     "Clinical data:"
    ]
   },
@@ -225,7 +225,7 @@
    "id": "ac633c36",
    "metadata": {},
    "source": [
-    "### Checking missing data\n",
+    "## Checking missing data\n",
     "... between two AD groups (after previous filtering)"
    ]
   },
@@ -264,7 +264,9 @@
    },
    "outputs": [],
    "source": [
-    "data_completeness.T.sort_values(0).plot(style=\".\", ylim=(0, 1.05), alpha=0.5, rot=45)"
+    "ax = data_completeness.T.sort_values(0).plot(\n",
+    "    style=\".\", ylim=(0, 1.05), alpha=0.5, rot=45\n",
+    ")"
    ]
   },
   {
@@ -312,7 +314,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Running ANCOVA analysis\n",
+    "# ANCOVA analysis for two groups\n",
     "Use combined dataset for ANCOVA analysis."
    ]
   },
@@ -413,7 +415,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# ancova.iloc[:, :6]"
+    "ancova.iloc[:, :6]"
    ]
   },
   {
@@ -465,7 +467,7 @@
    "id": "50d10e85",
    "metadata": {},
    "source": [
-    "## ANOVA analysis\n",
+    "# ANOVA analysis for two groups\n",
     "not controlling for covariates\n",
     "> To check: pvalues for proteins with missing mean values? some merging issue?"
    ]
@@ -592,7 +594,7 @@
    "id": "69771096",
    "metadata": {},
    "source": [
-    "## Comparing ANOVA and ANCOVA results\n",
+    "# Comparing ANOVA and ANCOVA results for two groups\n",
     "Cross tabulated results after FDR correction for both ANOVA and ANCOVA"
    ]
   },

diff --git a/docs/api_examples/ANCOVA_analysis.py b/docs/api_examples/ANCOVA_analysis.py
@@ -46,7 +46,7 @@
 )
 
 # %% [markdown]
-# ## Load data.
+# # Data for recipe
 # Clinical data:
 
 # %% tags=["hide-input"]
@@ -108,7 +108,7 @@
 
 
 # %% [markdown]
-# ### Checking missing data
+# ## Checking missing data
 # ... between two AD groups (after previous filtering)
 
 # %% tags=["hide-input"]
@@ -122,7 +122,9 @@
 # in non-Alzheimer disease group
 
 # %% tags=["hide-input"]
-data_completeness.T.sort_values(0).plot(style=".", ylim=(0, 1.05), alpha=0.5, rot=45)
+ax = data_completeness.T.sort_values(0).plot(
+    style=".", ylim=(0, 1.05), alpha=0.5, rot=45
+)
 
 # %% [markdown]
 # Plot 20 protein groups with biggest difference in missing values between groups
@@ -150,7 +152,7 @@
 )
 
 # %% [markdown]
-# ## Running ANCOVA analysis
+# # ANCOVA analysis for two groups
 # Use combined dataset for ANCOVA analysis.
 
 # %% tags=["hide-input"]
@@ -193,7 +195,7 @@
 # protein group
 
 # %%
-# ancova.iloc[:, :6]
+ancova.iloc[:, :6]
 
 # %% [markdown]
 # The others contain the test results (based on a linear model) for each protein group
@@ -210,7 +212,7 @@
 ancova.iloc[:, 6:].filter(regex=f"^(?!.*({regex_filter})).*$")
 
 # %% [markdown]
-# ## ANOVA analysis
+# # ANOVA analysis for two groups
 # not controlling for covariates
 # > To check: pvalues for proteins with missing mean values? some merging issue?
 
@@ -267,7 +269,7 @@
 anova.drop(columns=viewed_cols)
 
 # %% [markdown]
-# ## Comparing ANOVA and ANCOVA results
+# # Comparing ANOVA and ANCOVA results for two groups
 # Cross tabulated results after FDR correction for both ANOVA and ANCOVA
 
 # %% tags=["hide-input"]