notebook adjustments

angelolab · Jul 7, 2023 · 79cf261 · 79cf261
1 parent c52fce9
commit 79cf261
Showing 1 changed file with 9 additions and 7 deletions.
diff --git a/templates/6_tma_batch_qc_metrics.ipynb b/templates/6_tma_batch_qc_metrics.ipynb
@@ -123,7 +123,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "qc_tma_metrics_dir: str = os.path.join(cohort_image_dir, \"qc_tma_metrics\", cohort_name)\n",
+    "qc_tma_metrics_dir: str = os.path.join(cohort_path, \"qc_tma_metrics\")\n",
     "\n",
     "if not os.path.exists(qc_tma_metrics_dir):\n",
     "    os.makedirs(qc_tma_metrics_dir)"
@@ -192,7 +192,9 @@
    "outputs": [],
    "source": [
     "qc_tmas = qc_comp.QCTMA(\n",
-    "    cohort_path=cohort_path, qc_tma_metrics_dir=qc_tma_metrics_dir, qc_metrics=qc_metrics\n",
+    "    qc_metrics=qc_metrics,\n",
+    "    cohort_path=cohort_path,\n",
+    "    metrics_dir=qc_tma_metrics_dir,\n",
     ")\n",
     "\n",
     "qc_tmas.compute_qc_tma_metrics(tmas=tmas)"
@@ -360,10 +362,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "qc_batch_effect_metrics_dir: str = os.path.join(cohort_image_dir, \"qc_batch_effects\", cohort_name)\n",
+    "qc_batch_effect_metrics_dir: str = os.path.join(cohort_path, \"qc_batch_effects\")\n",
     "\n",
-    "if not os.path.exists(qc_tma_metrics_dir):\n",
-    "    os.makedirs(qc_tma_metrics_dir)"
+    "if not os.path.exists(qc_batch_effect_metrics_dir):\n",
+    "    os.makedirs(qc_batch_effect_metrics_dir)"
    ]
   },
   {
@@ -496,7 +498,7 @@
     "\n",
     "The QC metrics used to generate this heatmap are normalized by dividing each value by the average of each row, then taking the `log2` of it. Therefore, a value of 1 would be interpreted as be 2 times greater than the row average, and a value of -1 would be 2 times less than the row average.\n",
     "\n",
-    "These plots get saved in a `figures` subfolder within `qc_cohort_metrics_dir`."
+    "These plots get saved in a `figures` subfolder within `qc_batch_effect_metrics_dir`."
    ]
   },
   {
@@ -515,7 +517,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "qc_metrics_plots.qc_batch_effect_heatmap(qc_batch, tissues=tissues, save_figure=True)"
+    "qc_metrics_plots.qc_batch_effect_heatmap(qc_batch, batch_name=batch_name, save_figure=True)"
    ]
   }
  ],