Merge branch 'tumor-gene-target-screener-winfix'

MaayanLab · Oct 20, 2023 · 8572f20 · 8572f20
2 parents 864e38f + c4b0210
commit 8572f20
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Showing 3 changed files with 8 additions and 5 deletions.
diff --git a/appyters/Tumor_Gene_Target_Screener/Tumor_Gene_Target_Screener.ipynb b/appyters/Tumor_Gene_Target_Screener/Tumor_Gene_Target_Screener.ipynb
@@ -272,6 +272,7 @@
    "outputs": [],
    "source": [
     "%%appyter code_exec\n",
+    "import os\n",
     "import qnorm\n",
     "import numpy as np\n",
     "import pandas as pd\n",
@@ -295,7 +296,7 @@
     "import sys\n",
     "import contextlib\n",
     "@contextlib.contextmanager\n",
-    "def suppress_output(stdout=True, stderr=True, dest='/dev/null'):\n",
+    "def suppress_output(stdout=True, stderr=True, dest=os.devnull):\n",
     "    ''' Usage:\n",
     "    with suppress_output():\n",
     "        print('hi')\n",
@@ -697,6 +698,7 @@
     "%%appyter code_eval\n",
     "\n",
     "with suppress_output():\n",
+    "    df_bg_expr_norm.columns = df_bg_expr_norm.columns.to_flat_index().map(lambda s: ', '.join(s))\n",
     "    dge = limma_voom_differential_expression(\n",
     "        df_bg_expr_norm, df_expr_norm,\n",
     "        voom_design=True,\n",
@@ -845,7 +847,7 @@
    "outputs": [],
    "source": [
     "%%appyter code_exec\n",
-    "dge_final = dge[dge.score >= 1].sort_values(['score', 't'], ascending=False).iloc[:16]\n",
+    "dge_final = dge[dge.score >= 1].sort_values(['score', '-log(adj.P.Val)'], ascending=False).iloc[:16]\n",
     "pd.set_option('display.max_colwidth', None)\n",
     "dge_final['Link'] = dge_final['gene_symbol'].map(lambda g: f\"<a href=\\\"https://cfde-gene-pages.cloud/gene/{g}\\\">{g}</a>\")\n",
     "{% if membrane_screener %}\n",

diff --git a/appyters/Tumor_Gene_Target_Screener/appyter.json b/appyters/Tumor_Gene_Target_Screener/appyter.json
@@ -2,7 +2,7 @@
   "$schema": "https://raw.githubusercontent.com/MaayanLab/appyter-catalog/main/schema/appyter-validator.json",
   "name": "Tumor_Gene_Target_Screener",
   "title": "Tumor Gene Target Screener",
-  "version": "0.3.7",
+  "version": "0.3.9",
   "description": "An appyter for gene target screening of tumors",
   "authors": [
     {

diff --git a/appyters/Tumor_Gene_Target_Screener/requirements.txt b/appyters/Tumor_Gene_Target_Screener/requirements.txt
@@ -1,10 +1,11 @@
 appyter
-maayanlab-bioinformatics @ git+https://github.com/Maayanlab/maayanlab-bioinformatics@v0.5.5
+maayanlab-bioinformatics @ git+https://github.com/Maayanlab/maayanlab-bioinformatics@v0.5.9
 matplotlib
 matplotlib_venn
 numpy
-pandas
+pandas==2.0
 plotly
 qnorm
 rpy2
+s3fs
 scikit-learn