🎨 better plots (and one typo fix)

Multiomics-Analytics-Group · Feb 21, 2025 · 66cf4a3 · 66cf4a3
1 parent 7a84d40
commit 66cf4a3
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Showing 2 changed files with 38 additions and 17 deletions.
diff --git a/docs/api_examples/enrichment_analysis.ipynb b/docs/api_examples/enrichment_analysis.ipynb
@@ -193,7 +193,7 @@
    "id": "4bbf5dc4",
    "metadata": {},
    "source": [
-    "# ANCOVA: Compute up and downregulated genes\n",
+    "# ANOVA: Compute up and downregulated genes\n",
     "These will be used to find enrichments in the set of both up and downregulated genes."
    ]
   },
@@ -280,13 +280,27 @@
    },
    "outputs": [],
    "source": [
-    "_ = (\n",
-    "    annotations.groupby(\"annotation\")\n",
-    "    .size()\n",
-    "    .value_counts()\n",
-    "    .sort_index()\n",
-    "    .plot(kind=\"bar\")\n",
-    ")"
+    "s_count_pg_per_annotation = (\n",
+    "    annotations.groupby(\"annotation\").size().value_counts().sort_index()\n",
+    ")\n",
+    "_ = s_count_pg_per_annotation.plot(\n",
+    "    kind=\"bar\",\n",
+    "    xlabel=\"Number of protein groups associated with annotation\",\n",
+    "    ylabel=\"Number of annotations\",\n",
+    ")\n",
+    "s_count_pg_per_annotation.to_frame(\"number of annotations\").rename_axis(\n",
+    "    \"N protein groups\"\n",
+    ").T"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e04c98d8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annotations.groupby(\"annotation\").size().value_counts(ascending=False)"
    ]
   },
   {
@@ -577,7 +591,7 @@
     "import plotly.graph_objects as go\n",
     "from vuecore import viz\n",
     "\n",
-    "args = {\"factor\": 1, \"loadings\": 10}\n",
+    "args = {\"factor\": 2, \"loadings\": 1}  # increase number of loadings or scaling factor\n",
     "#! pca_results has three items, but docstring requests only two -> double check\n",
     "figure = viz.get_pca_plot(data=pca_result, identifier=\"PCA enrichment\", args=args)\n",
     "figure = go.Figure(data=figure[\"data\"], layout=figure[\"layout\"])\n",

diff --git a/docs/api_examples/enrichment_analysis.py b/docs/api_examples/enrichment_analysis.py
@@ -92,7 +92,7 @@
 
 
 # %% [markdown]
-# # ANCOVA: Compute up and downregulated genes
+# # ANOVA: Compute up and downregulated genes
 # These will be used to find enrichments in the set of both up and downregulated genes.
 
 # %%
@@ -137,13 +137,20 @@
 # functional annotations are associated only to a single protein group in our dataset.
 
 # %% tags=["hide-input"]
-_ = (
-    annotations.groupby("annotation")
-    .size()
-    .value_counts()
-    .sort_index()
-    .plot(kind="bar")
+s_count_pg_per_annotation = (
+    annotations.groupby("annotation").size().value_counts().sort_index()
 )
+_ = s_count_pg_per_annotation.plot(
+    kind="bar",
+    xlabel="Number of protein groups associated with annotation",
+    ylabel="Number of annotations",
+)
+s_count_pg_per_annotation.to_frame("number of annotations").rename_axis(
+    "N protein groups"
+).T
+
+# %%
+annotations.groupby("annotation").size().value_counts(ascending=False)
 
 # %% [markdown]
 # # Enrichment analysis
@@ -289,7 +296,7 @@
 import plotly.graph_objects as go
 from vuecore import viz
 
-args = {"factor": 1, "loadings": 10}
+args = {"factor": 2, "loadings": 1}  # increase number of loadings or scaling factor
 # #! pca_results has three items, but docstring requests only two -> double check
 figure = viz.get_pca_plot(data=pca_result, identifier="PCA enrichment", args=args)
 figure = go.Figure(data=figure["data"], layout=figure["layout"])