Update gssnng_quick_start.ipynb

removed drop statements
IlyaLab · Aug 8, 2023 · bca4c17 · bca4c17
1 parent 7fedd85
commit bca4c17
Showing 1 changed file with 1 addition and 28 deletions.
diff --git a/notebooks/gssnng_quick_start.ipynb b/notebooks/gssnng_quick_start.ipynb
@@ -146,10 +146,6 @@
     "### RANK BIASED OVERLAP ###\n",
     "### https://dl.acm.org/doi/10.1145/1852102.1852106\n",
     "\n",
-    "# del the previous scores\n",
-    "q.obs.drop(gene_set_names, axis=1, inplace=True)\n",
-    "q.obs.drop('gssnng_groupby', axis=1, inplace=True)\n",
-    "\n",
     "# rescore\n",
     "score_cells.with_gene_sets(\n",
     "        adata=q,\n",
@@ -188,10 +184,6 @@
     "### MEAN Z SCORES COUNTS ###\n",
     "### average of gene-wise Z scores\n",
     "\n",
-    "# del the previous scores\n",
-    "q.obs.drop(gene_set_names, axis=1, inplace=True)\n",
-    "q.obs.drop('gssnng_groupby', axis=1, inplace=True)\n",
-    "\n",
     "# rescore\n",
     "score_cells.with_gene_sets(\n",
     "        adata=q,\n",
@@ -229,10 +221,6 @@
    "source": [
     "### MEDIAN RANKS ###\n",
     "\n",
-    "# del the previous scores\n",
-    "q.obs.drop(gene_set_names, axis=1, inplace=True)\n",
-    "q.obs.drop('gssnng_groupby', axis=1, inplace=True)\n",
-    "\n",
     "# rescore\n",
     "score_cells.with_gene_sets(\n",
     "        adata=q,\n",
@@ -270,10 +258,6 @@
    "source": [
     "# ROBUST STANDARDIZED COUNTS\n",
     "\n",
-    "# del the previous scores\n",
-    "q.obs.drop(gene_set_names, axis=1, inplace=True)\n",
-    "q.obs.drop('gssnng_groupby', axis=1, inplace=True)\n",
-    "\n",
     "# rescore\n",
     "score_cells.with_gene_sets(\n",
     "        adata=q,\n",
@@ -311,10 +295,6 @@
    "source": [
     "### AVERAGE COUNTS ###\n",
     "\n",
-    "# del the previous scores\n",
-    "q.obs.drop(gene_set_names, axis=1, inplace=True)\n",
-    "q.obs.drop('gssnng_groupby', axis=1, inplace=True)\n",
-    "\n",
     "score_cells.with_gene_sets(\n",
     "        adata=q,\n",
     "        gene_set_file=gene_set_file,\n",
@@ -351,10 +331,6 @@
    "source": [
     "### SUMMED UP ###\n",
     "\n",
-    "# del the previous scores\n",
-    "q.obs.drop(gene_set_names, axis=1, inplace=True)\n",
-    "q.obs.drop('gssnng_groupby', axis=1, inplace=True)\n",
-    "\n",
     "# rescore\n",
     "score_cells.with_gene_sets(\n",
     "        adata=q,\n",
@@ -390,10 +366,7 @@
    },
    "outputs": [],
    "source": [
-    "### experimental!! ###\n",
-    "\n",
-    "q.obs.drop(gene_set_names, axis=1, inplace=True)\n",
-    "q.obs.drop('gssnng_groupby', axis=1, inplace=True)\n",
+    "Scoring with ssGSEA\n",
     "\n",
     "# rescore\n",
     "score_cells.with_gene_sets(\n",