🚧 document ANOVA vs pairwise-ttest results

Multiomics-Analytics-Group · Feb 20, 2025 · 682671e · 682671e
1 parent 995ce24
commit 682671e
Show file tree

Hide file tree

Showing 2 changed files with 154 additions and 30 deletions.
diff --git a/docs/api_examples/ANCOVA_analysis.ipynb b/docs/api_examples/ANCOVA_analysis.ipynb
@@ -160,7 +160,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "For easier inspection we just sample five protein groups. Remove this step in a\n",
+    "For easier inspection we just sample 100 protein groups. Remove this step in a\n",
     "real analysis."
    ]
   },
@@ -171,7 +171,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "omics = omics.sample(5, axis=1, random_state=42)\n",
+    "omics = omics.sample(100, axis=1, random_state=42)\n",
     "omics"
    ]
   },
@@ -403,8 +403,17 @@
    "metadata": {},
    "source": [
     "The first columns contain group averages for each group for the specific\n",
-    "protein group\n",
-    "ancova.iloc[:, :6]"
+    "protein group"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2653ab02",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# ancova.iloc[:, :6]"
    ]
   },
   {
@@ -480,6 +489,34 @@
     "anova"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "89b1ab90",
+   "metadata": {},
+   "source": [
+    "Set subject to None"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "92cc96ee",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "anova = (\n",
+    "    ad.run_anova(\n",
+    "        omics_and_clinic,\n",
+    "        subject=None,\n",
+    "        drop_cols=covariates,\n",
+    "        group=\"AD\",\n",
+    "    )\n",
+    "    .set_index(\"identifier\")\n",
+    "    .sort_values(by=\"padj\")\n",
+    ")\n",
+    "anova"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "28434ecb",
@@ -589,19 +626,7 @@
    "metadata": {},
    "source": [
     "# With three and more groups\n",
-    "Acore make each combinatorial comparison between groups in the group column.\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "33105f5d",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import math\n",
-    "\n",
-    "math.comb(4, 2)"
+    "Acore make each combinatorial comparison between groups in the group column."
    ]
   },
   {
@@ -635,10 +660,10 @@
   {
    "cell_type": "markdown",
    "id": "55a88fd4",
-   "metadata": {
-    "lines_to_next_cell": 0
-   },
-   "source": []
+   "metadata": {},
+   "source": [
+    "Sample five protein groups (for easier inspection) and combine with metadata."
+   ]
   },
   {
    "cell_type": "code",
@@ -647,7 +672,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "omics_and_clinic = omics.join(meta)\n",
+    "omics_and_clinic = omics.sample(5, axis=1, random_state=42).join(meta)\n",
     "omics_and_clinic"
    ]
   },
@@ -664,13 +689,68 @@
     "        subject=\"Sample ID\",\n",
     "        drop_cols=[\"age\", \"gender\"],\n",
     "        group=\"site\",\n",
-    "    )\n",
-    "    .set_index([\"identifier\", \"group1\", \"group2\"])\n",
+    "    ).set_index([\"identifier\", \"group1\", \"group2\"])\n",
     "    # .sort_values(by=\"padj\")\n",
     ")\n",
     "anova"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "ce0bfc17",
+   "metadata": {},
+   "source": [
+    "pairwise t-test results:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "719f895f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cols_pairwise_ttest = [\n",
+    "    # \"group1\",\n",
+    "    # \"group2\",\n",
+    "    \"mean(group1)\",\n",
+    "    \"std(group1)\",\n",
+    "    \"mean(group2)\",\n",
+    "    \"std(group2)\",\n",
+    "    \"posthoc Paired\",\n",
+    "    \"posthoc Parametric\",\n",
+    "    \"posthoc T-Statistics\",\n",
+    "    \"posthoc dof\",\n",
+    "    \"posthoc tail\",\n",
+    "    \"posthoc pvalue\",\n",
+    "    \"posthoc BF10\",\n",
+    "    \"posthoc effsize\",\n",
+    "    # \"identifier\",\n",
+    "    \"log2FC\",\n",
+    "    \"FC\",\n",
+    "    \"efftype\",\n",
+    "]\n",
+    "anova[cols_pairwise_ttest]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d041469a",
+   "metadata": {},
+   "source": [
+    "ANOVA results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "57513226",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "anova.drop(columns=cols_pairwise_ttest)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "c7eed4d2",

diff --git a/docs/api_examples/ANCOVA_analysis.py b/docs/api_examples/ANCOVA_analysis.py
@@ -191,6 +191,8 @@
 # %% [markdown]
 # The first columns contain group averages for each group for the specific
 # protein group
+
+# %%
 # ancova.iloc[:, :6]
 
 # %% [markdown]
@@ -225,6 +227,22 @@
 )
 anova
 
+# %% [markdown]
+# Set subject to None
+
+# %%
+anova = (
+    ad.run_anova(
+        omics_and_clinic,
+        subject=None,
+        drop_cols=covariates,
+        group="AD",
+    )
+    .set_index("identifier")
+    .sort_values(by="padj")
+)
+anova
+
 # %% [markdown]
 # view averages per protein group
 
@@ -265,12 +283,6 @@
 # %% [markdown]
 # # With three and more groups
 # Acore make each combinatorial comparison between groups in the group column.
-#
-
-# %%
-import math
-
-math.comb(4, 2)
 
 # %%
 CLINIC: str = "meta.csv"  # clincial data
@@ -312,6 +324,38 @@
 )
 anova
 
+# %% [markdown]
+# pairwise t-test results:
+
+# %%
+cols_pairwise_ttest = [
+    # "group1",
+    # "group2",
+    "mean(group1)",
+    "std(group1)",
+    "mean(group2)",
+    "std(group2)",
+    "posthoc Paired",
+    "posthoc Parametric",
+    "posthoc T-Statistics",
+    "posthoc dof",
+    "posthoc tail",
+    "posthoc pvalue",
+    "posthoc BF10",
+    "posthoc effsize",
+    # "identifier",
+    "log2FC",
+    "FC",
+    "efftype",
+]
+anova[cols_pairwise_ttest]
+
+# %% [markdown]
+# ANOVA results
+
+# %%
+anova.drop(columns=cols_pairwise_ttest)
+
 # %% [markdown]
 # Test results