PyPI - LCNE-patchseq-analysis - Versions diffs - 0.0.2__tar.gz → 0.1.0__tar.gz - Mend

LCNE-patchseq-analysis 0.0.2tar.gz → 0.1.0tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (36) hide show

{lcne_patchseq_analysis-0.0.2 → lcne_patchseq_analysis-0.1.0}/.gitignore RENAMED Viewed

@@ -139,4 +139,5 @@ dmypy.json
 **/.DS_Store
 .vscode
-metadata.yml
+metadata.yml
+data

{lcne_patchseq_analysis-0.0.2 → lcne_patchseq_analysis-0.1.0}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: LCNE-patchseq-analysis
-Version: 0.0.2
+Version: 0.1.0
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 Author-email: Han Hou <han.hou@alleninstitute.org>
@@ -11,6 +11,8 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: pandas
+Requires-Dist: openpyxl
+Requires-Dist: matplotlib
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: coverage; extra == "dev"
@@ -29,14 +31,7 @@ Requires-Dist: furo; extra == "dev"
 ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
 ![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)
-## Usage
- - To use this template, click the green `Use this template` button and `Create new repository`.
- - After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo.
- - To enable the automatic semantic version increments: in the repository go to `Settings` and `Collaborators and teams`. Click the green `Add people` button. Add `svc-aindscicomp` as an admin. Modify the file in `.github/workflows/tag_and_publish.yml` and remove the if statement in line 65. The semantic version will now be incremented every time a code is committed into the main branch.
- - To publish to PyPI, enable semantic versioning and uncomment the publish block in `.github/workflows/tag_and_publish.yml`. The code will now be published to PyPI every time the code is committed into the main branch.
- - The `.github/workflows/test_and_lint.yml` file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the `test_and_lint.yml` can be deleted. The strictness of the code coverage level, etc., can be modified by altering the configurations in the `pyproject.toml` file and the `.flake8` file.
+Library for LCNE-patchseq data analysis
 ## Installation
 To use the software, in the root directory, run

{lcne_patchseq_analysis-0.0.2 → lcne_patchseq_analysis-0.1.0}/README.md RENAMED Viewed

@@ -7,14 +7,7 @@
 ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
 ![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)
-## Usage
- - To use this template, click the green `Use this template` button and `Create new repository`.
- - After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo.
- - To enable the automatic semantic version increments: in the repository go to `Settings` and `Collaborators and teams`. Click the green `Add people` button. Add `svc-aindscicomp` as an admin. Modify the file in `.github/workflows/tag_and_publish.yml` and remove the if statement in line 65. The semantic version will now be incremented every time a code is committed into the main branch.
- - To publish to PyPI, enable semantic versioning and uncomment the publish block in `.github/workflows/tag_and_publish.yml`. The code will now be published to PyPI every time the code is committed into the main branch.
- - The `.github/workflows/test_and_lint.yml` file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the `test_and_lint.yml` can be deleted. The strictness of the code coverage level, etc., can be modified by altering the configurations in the `pyproject.toml` file and the `.flake8` file.
+Library for LCNE-patchseq data analysis
 ## Installation
 To use the software, in the root directory, run

{lcne_patchseq_analysis-0.0.2 → lcne_patchseq_analysis-0.1.0}/environment/Dockerfile RENAMED Viewed

@@ -15,13 +15,5 @@ RUN cd /.code-server \
     && rm code-server.tar.gz \
     && ln -s /.code-server/code-server-4.95.3-linux-amd64/bin/code-server  /usr/bin/code-server
-RUN mkdir -p /.vscode/extensions \
-    && code-server --extensions-dir="/.vscode/extensions" --install-extension REditorSupport.R \
-    && code-server --extensions-dir="/.vscode/extensions" --install-extension continue.continue \
-    && code-server --extensions-dir="/.vscode/extensions" --install-extension ms-python.python \
-    && code-server --extensions-dir="/.vscode/extensions" --install-extension ms-toolsai.jupyter \
-    && code-server --extensions-dir="/.vscode/extensions" --install-extension reageyao.bioSyntax \
-    && code-server --extensions-dir="/.vscode/extensions" --install-extension saoudrizwan.claude-dev
 COPY postInstall /
 RUN /postInstall

{lcne_patchseq_analysis-0.0.2 → lcne_patchseq_analysis-0.1.0}/environment/postInstall RENAMED Viewed

@@ -10,6 +10,7 @@ if code-server --disable-telemetry --version; then
 			 fi
        code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension ms-python.python
+       code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension ms-toolsai.jupyter
        code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension njpwerner.autodocstring
        code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension KevinRose.vsc-python-indent
        code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension mhutchie.git-graph

lcne_patchseq_analysis-0.1.0/notebook/demo.ipynb ADDED Viewed

@@ -0,0 +1,705 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\n"
+     ]
+    }
+   ],
+   "source": [
+    "!pip install pygwalker --quiet"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from LCNE_patchseq_analysis.data_util.metadata import read_brian_spreadsheet"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df, df_master, df_xyz, df_ephys = read_brian_spreadsheet()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##  Cross tab sanity check"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Check overlapped columns across tabs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 32,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['Annotated structure_master',\n",
+       " 'x_master',\n",
+       " 'y_master',\n",
+       " 'z_master',\n",
+       " 'notes_master',\n",
+       " 'failed_bad_rs_master',\n",
+       " 'failed_electrode_0_master',\n",
+       " 'failed_no_seal_master']"
+      ]
+     },
+     "execution_count": 32,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "duplicate_columns = [col for col in df.columns if 'master' in col]\n",
+    "duplicate_columns"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Search for inconsistent data across the master table and the xyz_running_list"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 34,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Date</th>\n",
+       "      <th>jem-id_cell_specimen</th>\n",
+       "      <th>x_master</th>\n",
+       "      <th>y_master</th>\n",
+       "      <th>z_master</th>\n",
+       "      <th>Annotated structure_master</th>\n",
+       "      <th>x_xyz</th>\n",
+       "      <th>y_xyz</th>\n",
+       "      <th>z_xyz</th>\n",
+       "      <th>Annotated structure_xyz</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>173</th>\n",
+       "      <td>2024-09-13</td>\n",
+       "      <td>Dbh-Cre-KI;Ai65-751021.11.06.03</td>\n",
+       "      <td>10651.381280</td>\n",
+       "      <td>4843.763780</td>\n",
+       "      <td>4673.284468</td>\n",
+       "      <td>MV</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>153</th>\n",
+       "      <td>2024-07-03</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-740851.11.06.01</td>\n",
+       "      <td>10673.417970</td>\n",
+       "      <td>3943.184326</td>\n",
+       "      <td>4822.000000</td>\n",
+       "      <td>PB</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>152</th>\n",
+       "      <td>2024-06-04</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-734082.10.06.02</td>\n",
+       "      <td>10811.337890</td>\n",
+       "      <td>4311.617676</td>\n",
+       "      <td>4976.000000</td>\n",
+       "      <td>PCG</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>151</th>\n",
+       "      <td>2024-06-04</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-734082.10.06.01</td>\n",
+       "      <td>10743.375200</td>\n",
+       "      <td>4243.480758</td>\n",
+       "      <td>4976.000000</td>\n",
+       "      <td>PCG</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>149</th>\n",
+       "      <td>2024-05-24</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-734079.11.06.02</td>\n",
+       "      <td>10508.190430</td>\n",
+       "      <td>3882.932861</td>\n",
+       "      <td>4988.000000</td>\n",
+       "      <td>PCG</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>148</th>\n",
+       "      <td>2024-05-24</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-734079.11.06.01</td>\n",
+       "      <td>10447.267580</td>\n",
+       "      <td>3777.822021</td>\n",
+       "      <td>4988.000000</td>\n",
+       "      <td>PCG</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>108</th>\n",
+       "      <td>2023-09-22</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-695527.09.06.01</td>\n",
+       "      <td>10151.019530</td>\n",
+       "      <td>3701.974609</td>\n",
+       "      <td>4824.000000</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>106</th>\n",
+       "      <td>2023-09-01</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-692026.10.10.02</td>\n",
+       "      <td>10534.982420</td>\n",
+       "      <td>4183.531250</td>\n",
+       "      <td>4984.000000</td>\n",
+       "      <td>PAG</td>\n",
+       "      <td>10151.019530</td>\n",
+       "      <td>3701.974609</td>\n",
+       "      <td>4824.0</td>\n",
+       "      <td>PAG</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>101</th>\n",
+       "      <td>2023-08-25</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-692022.09.06.01</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>SCiw</td>\n",
+       "      <td>9531.198242</td>\n",
+       "      <td>2449.594727</td>\n",
+       "      <td>4265.0</td>\n",
+       "      <td>SCiw</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>102</th>\n",
+       "      <td>2023-08-20</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-692023.08.06.01</td>\n",
+       "      <td>10541.875980</td>\n",
+       "      <td>4110.681641</td>\n",
+       "      <td>5034.000000</td>\n",
+       "      <td>PB</td>\n",
+       "      <td>10702.283200</td>\n",
+       "      <td>3840.954834</td>\n",
+       "      <td>4727.0</td>\n",
+       "      <td>PB</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>104</th>\n",
+       "      <td>2023-08-20</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-692023.08.06.03</td>\n",
+       "      <td>10761.001950</td>\n",
+       "      <td>4288.832031</td>\n",
+       "      <td>4727.000000</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>103</th>\n",
+       "      <td>2023-08-20</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-692023.08.06.02</td>\n",
+       "      <td>10702.283200</td>\n",
+       "      <td>3840.954834</td>\n",
+       "      <td>4727.000000</td>\n",
+       "      <td>LC</td>\n",
+       "      <td>10761.001950</td>\n",
+       "      <td>4288.832031</td>\n",
+       "      <td>4727.0</td>\n",
+       "      <td>LC</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>100</th>\n",
+       "      <td>2023-06-02</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-676766.10.06.03</td>\n",
+       "      <td>10521.757810</td>\n",
+       "      <td>4256.657715</td>\n",
+       "      <td>4889.000000</td>\n",
+       "      <td>LDT</td>\n",
+       "      <td>10541.875980</td>\n",
+       "      <td>4110.681641</td>\n",
+       "      <td>5034.0</td>\n",
+       "      <td>LDT</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>67</th>\n",
+       "      <td>2023-03-15</td>\n",
+       "      <td>C57BL6J-665266.11.06.03</td>\n",
+       "      <td>10451.809570</td>\n",
+       "      <td>4402.110352</td>\n",
+       "      <td>4889.000000</td>\n",
+       "      <td>LDT</td>\n",
+       "      <td>10534.982420</td>\n",
+       "      <td>4183.531250</td>\n",
+       "      <td>4984.0</td>\n",
+       "      <td>LDT</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>50</th>\n",
+       "      <td>2023-01-20</td>\n",
+       "      <td>Ndnf-IRES2-dgCre;Ai14-659663.11.06.01</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>LDT</td>\n",
+       "      <td>10391.497070</td>\n",
+       "      <td>4161.165039</td>\n",
+       "      <td>4889.0</td>\n",
+       "      <td>LDT</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>52</th>\n",
+       "      <td>2023-01-20</td>\n",
+       "      <td>Ndnf-IRES2-dgCre;Ai14-659663.11.06.03</td>\n",
+       "      <td>10391.497070</td>\n",
+       "      <td>4161.165039</td>\n",
+       "      <td>4889.000000</td>\n",
+       "      <td>PCG</td>\n",
+       "      <td>10521.757810</td>\n",
+       "      <td>4256.657715</td>\n",
+       "      <td>4889.0</td>\n",
+       "      <td>PCG</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>53</th>\n",
+       "      <td>2023-01-20</td>\n",
+       "      <td>Ndnf-IRES2-dgCre;Ai14-659663.11.06.04</td>\n",
+       "      <td>9531.198242</td>\n",
+       "      <td>2449.594727</td>\n",
+       "      <td>4265.000000</td>\n",
+       "      <td>PCG</td>\n",
+       "      <td>10451.809570</td>\n",
+       "      <td>4402.110352</td>\n",
+       "      <td>4889.0</td>\n",
+       "      <td>PCG</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "          Date                       jem-id_cell_specimen      x_master  \\\n",
+       "173 2024-09-13            Dbh-Cre-KI;Ai65-751021.11.06.03  10651.381280   \n",
+       "153 2024-07-03  Dbh-Cre_KH212;RCL-H2B-GFP-740851.11.06.01  10673.417970   \n",
+       "152 2024-06-04  Dbh-Cre_KH212;RCL-H2B-GFP-734082.10.06.02  10811.337890   \n",
+       "151 2024-06-04  Dbh-Cre_KH212;RCL-H2B-GFP-734082.10.06.01  10743.375200   \n",
+       "149 2024-05-24  Dbh-Cre_KH212;RCL-H2B-GFP-734079.11.06.02  10508.190430   \n",
+       "148 2024-05-24  Dbh-Cre_KH212;RCL-H2B-GFP-734079.11.06.01  10447.267580   \n",
+       "108 2023-09-22  Dbh-Cre_KH212;RCL-H2B-GFP-695527.09.06.01  10151.019530   \n",
+       "106 2023-09-01  Dbh-Cre_KH212;RCL-H2B-GFP-692026.10.10.02  10534.982420   \n",
+       "101 2023-08-25  Dbh-Cre_KH212;RCL-H2B-GFP-692022.09.06.01           NaN   \n",
+       "102 2023-08-20  Dbh-Cre_KH212;RCL-H2B-GFP-692023.08.06.01  10541.875980   \n",
+       "104 2023-08-20  Dbh-Cre_KH212;RCL-H2B-GFP-692023.08.06.03  10761.001950   \n",
+       "103 2023-08-20  Dbh-Cre_KH212;RCL-H2B-GFP-692023.08.06.02  10702.283200   \n",
+       "100 2023-06-02  Dbh-Cre_KH212;RCL-H2B-GFP-676766.10.06.03  10521.757810   \n",
+       "67  2023-03-15                    C57BL6J-665266.11.06.03  10451.809570   \n",
+       "50  2023-01-20      Ndnf-IRES2-dgCre;Ai14-659663.11.06.01           NaN   \n",
+       "52  2023-01-20      Ndnf-IRES2-dgCre;Ai14-659663.11.06.03  10391.497070   \n",
+       "53  2023-01-20      Ndnf-IRES2-dgCre;Ai14-659663.11.06.04   9531.198242   \n",
+       "\n",
+       "        y_master     z_master Annotated structure_master         x_xyz  \\\n",
+       "173  4843.763780  4673.284468                         MV           NaN   \n",
+       "153  3943.184326  4822.000000                         PB           NaN   \n",
+       "152  4311.617676  4976.000000                        PCG           NaN   \n",
+       "151  4243.480758  4976.000000                        PCG           NaN   \n",
+       "149  3882.932861  4988.000000                        PCG           NaN   \n",
+       "148  3777.822021  4988.000000                        PCG           NaN   \n",
+       "108  3701.974609  4824.000000                        NaN           NaN   \n",
+       "106  4183.531250  4984.000000                        PAG  10151.019530   \n",
+       "101          NaN          NaN                       SCiw   9531.198242   \n",
+       "102  4110.681641  5034.000000                         PB  10702.283200   \n",
+       "104  4288.832031  4727.000000                        NaN           NaN   \n",
+       "103  3840.954834  4727.000000                         LC  10761.001950   \n",
+       "100  4256.657715  4889.000000                        LDT  10541.875980   \n",
+       "67   4402.110352  4889.000000                        LDT  10534.982420   \n",
+       "50           NaN          NaN                        LDT  10391.497070   \n",
+       "52   4161.165039  4889.000000                        PCG  10521.757810   \n",
+       "53   2449.594727  4265.000000                        PCG  10451.809570   \n",
+       "\n",
+       "           y_xyz   z_xyz Annotated structure_xyz  \n",
+       "173          NaN     NaN                     NaN  \n",
+       "153          NaN     NaN                     NaN  \n",
+       "152          NaN     NaN                     NaN  \n",
+       "151          NaN     NaN                     NaN  \n",
+       "149          NaN     NaN                     NaN  \n",
+       "148          NaN     NaN                     NaN  \n",
+       "108          NaN     NaN                     NaN  \n",
+       "106  3701.974609  4824.0                     PAG  \n",
+       "101  2449.594727  4265.0                    SCiw  \n",
+       "102  3840.954834  4727.0                      PB  \n",
+       "104          NaN     NaN                     NaN  \n",
+       "103  4288.832031  4727.0                      LC  \n",
+       "100  4110.681641  5034.0                     LDT  \n",
+       "67   4183.531250  4984.0                     LDT  \n",
+       "50   4161.165039  4889.0                     LDT  \n",
+       "52   4256.657715  4889.0                     PCG  \n",
+       "53   4402.110352  4889.0                     PCG  "
+      ]
+     },
+     "execution_count": 34,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Any rows where the master and xyz columns don't match?\n",
+    "df.loc[\n",
+    "    (\n",
+    "        (\n",
+    "            (df[\"x_master\"] != df[\"x_xyz\"])\n",
+    "            | (df[\"y_master\"] != df[\"y_xyz\"])\n",
+    "            | (df[\"z_master\"] != df[\"z_xyz\"])\n",
+    "            | (df[\"Annotated structure_master\"] != df[\"Annotated structure_xyz\"])\n",
+    "        )\n",
+    "        & ~(df[\"x_master\"].isna() & df[\"x_xyz\"].isna())\n",
+    "    ),\n",
+    "    [\n",
+    "        \"Date\",\n",
+    "        \"jem-id_cell_specimen\",\n",
+    "        \"x_master\",\n",
+    "        \"y_master\",\n",
+    "        \"z_master\",\n",
+    "        \"Annotated structure_master\",\n",
+    "        \"x_xyz\",\n",
+    "        \"y_xyz\",\n",
+    "        \"z_xyz\",\n",
+    "        \"Annotated structure_xyz\",\n",
+    "    ],\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### ❌ Oh no! These inconsistencies must be caused by manually copying and pasting across the tabs!!!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 38,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Date</th>\n",
+       "      <th>jem-id_cell_specimen</th>\n",
+       "      <th>cell_specimen_id</th>\n",
+       "      <th>failed_bad_rs_master</th>\n",
+       "      <th>failed_electrode_0_master</th>\n",
+       "      <th>failed_no_seal_master</th>\n",
+       "      <th>failed_bad_rs_ephys_fx</th>\n",
+       "      <th>failed_electrode_0_ephys_fx</th>\n",
+       "      <th>failed_no_seal_ephys_fx</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>143</th>\n",
+       "      <td>2024-04-03</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-H2B-GFP-724916.11.06.02</td>\n",
+       "      <td>1342558771</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>137</th>\n",
+       "      <td>2024-03-20</td>\n",
+       "      <td>C57BL6J-722426.10.06.01</td>\n",
+       "      <td>1339160242</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>139</th>\n",
+       "      <td>2024-03-20</td>\n",
+       "      <td>C57BL6J-722426.10.06.03</td>\n",
+       "      <td>1339183091</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>83</th>\n",
+       "      <td>2023-04-19</td>\n",
+       "      <td>Slc17a6-IRES-Cre;Ai14-670829.11.06.02</td>\n",
+       "      <td>1265171440</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>27</th>\n",
+       "      <td>2022-11-17</td>\n",
+       "      <td>Slc17a6-IRES-Cre;Ai14-651168.10.06.03</td>\n",
+       "      <td>1226761160</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>24</th>\n",
+       "      <td>2022-11-15</td>\n",
+       "      <td>Dbh-Cre_KH212;RCL-Sun1sfGFP-neo-650884.09.06.05</td>\n",
+       "      <td>1226307625</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>14</th>\n",
+       "      <td>2022-11-02</td>\n",
+       "      <td>Rbp4-Cre_KL100;Ai14-650443.10.06.02</td>\n",
+       "      <td>1223270873</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>10</th>\n",
+       "      <td>2022-10-27</td>\n",
+       "      <td>C57BL6J-647687.09.06.01</td>\n",
+       "      <td>1221572804</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>1.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "      <td>0.0</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "          Date                             jem-id_cell_specimen  \\\n",
+       "143 2024-04-03        Dbh-Cre_KH212;RCL-H2B-GFP-724916.11.06.02   \n",
+       "137 2024-03-20                          C57BL6J-722426.10.06.01   \n",
+       "139 2024-03-20                          C57BL6J-722426.10.06.03   \n",
+       "83  2023-04-19            Slc17a6-IRES-Cre;Ai14-670829.11.06.02   \n",
+       "27  2022-11-17            Slc17a6-IRES-Cre;Ai14-651168.10.06.03   \n",
+       "24  2022-11-15  Dbh-Cre_KH212;RCL-Sun1sfGFP-neo-650884.09.06.05   \n",
+       "14  2022-11-02              Rbp4-Cre_KL100;Ai14-650443.10.06.02   \n",
+       "10  2022-10-27                          C57BL6J-647687.09.06.01   \n",
+       "\n",
+       "     cell_specimen_id  failed_bad_rs_master  failed_electrode_0_master  \\\n",
+       "143        1342558771                   0.0                        0.0   \n",
+       "137        1339160242                   1.0                        0.0   \n",
+       "139        1339183091                   1.0                        0.0   \n",
+       "83         1265171440                   0.0                        0.0   \n",
+       "27         1226761160                   0.0                        0.0   \n",
+       "24         1226307625                   0.0                        0.0   \n",
+       "14         1223270873                   0.0                        0.0   \n",
+       "10         1221572804                   0.0                        0.0   \n",
+       "\n",
+       "     failed_no_seal_master  failed_bad_rs_ephys_fx  \\\n",
+       "143                    1.0                     0.0   \n",
+       "137                    0.0                     0.0   \n",
+       "139                    0.0                     0.0   \n",
+       "83                     1.0                     0.0   \n",
+       "27                     1.0                     0.0   \n",
+       "24                     1.0                     0.0   \n",
+       "14                     1.0                     0.0   \n",
+       "10                     1.0                     0.0   \n",
+       "\n",
+       "     failed_electrode_0_ephys_fx  failed_no_seal_ephys_fx  \n",
+       "143                          0.0                      0.0  \n",
+       "137                          0.0                      0.0  \n",
+       "139                          0.0                      0.0  \n",
+       "83                           0.0                      0.0  \n",
+       "27                           0.0                      0.0  \n",
+       "24                           0.0                      0.0  \n",
+       "14                           0.0                      0.0  \n",
+       "10                           0.0                      0.0  "
+      ]
+     },
+     "execution_count": 38,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df.loc[\n",
+    "    (\n",
+    "        (df[\"failed_bad_rs_master\"] != df[\"failed_bad_rs_ephys_fx\"])\n",
+    "        | (df[\"failed_electrode_0_master\"] != df[\"failed_electrode_0_ephys_fx\"])\n",
+    "        | (df[\"failed_no_seal_master\"] != df[\"failed_no_seal_ephys_fx\"])\n",
+    "    ) & ~(df[\"failed_bad_rs_master\"].isna() | df[\"failed_bad_rs_ephys_fx\"].isna()),\n",
+    "    [\n",
+    "        \"Date\",\n",
+    "        \"jem-id_cell_specimen\",\n",
+    "        \"cell_specimen_id\",\n",
+    "        \"failed_bad_rs_master\",\n",
+    "        \"failed_electrode_0_master\",\n",
+    "        \"failed_no_seal_master\",\n",
+    "        \"failed_bad_rs_ephys_fx\",\n",
+    "        \"failed_electrode_0_ephys_fx\",\n",
+    "        \"failed_no_seal_ephys_fx\",\n",
+    "    ],\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Quick overview using pygwalker"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pygwalker as pyg\n",
+    "walker = pyg.walk(df)\n",
+    "walker"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

{lcne_patchseq_analysis-0.0.2 → lcne_patchseq_analysis-0.1.0}/pyproject.toml RENAMED Viewed

@@ -19,7 +19,9 @@ dynamic = ["version"]
 dependencies = [
     'numpy',
-    'pandas'
+    'pandas',
+    'openpyxl',
+    'matplotlib',
 ]
 [project.optional-dependencies]

lcne_patchseq_analysis-0.1.0/src/LCNE_patchseq_analysis/__init__.py ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ """Init package"""
2	+ __version__ = "0.1.0"

lcne_patchseq_analysis-0.1.0/src/LCNE_patchseq_analysis/data_util/__init__.py ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ """ Utils for accessing data
2	+ """

lcne_patchseq_analysis-0.1.0/src/LCNE_patchseq_analysis/data_util/ephys.py ADDED Viewed

	@@ -0,0 +1 @@
1	+ """Get ephys data"""

lcne_patchseq_analysis-0.1.0/src/LCNE_patchseq_analysis/data_util/metadata.py ADDED Viewed

@@ -0,0 +1,62 @@
+"""Get metadata
+"""
+import pandas as pd
+import os
+file_path = os.path.expanduser("~/capsule/data/IVSCC_LC_summary.xlsx")
+def read_brian_spreadsheet(file_path=file_path):
+    """ Read metadata, cell xyz coordinates, and ephys features from Brian's spreadsheet
+    Assuming IVSCC_LC_summary.xlsx is downloaded at file_path
+    """
+    if not os.path.exists(file_path):
+        raise FileNotFoundError(f"File not found at {file_path}")
+    tab_names = pd.ExcelFile(file_path).sheet_names
+    # Get the master table
+    tab_master = [name for name in tab_names if "updated" in name.lower()][0]
+    df_master = pd.read_excel(file_path, sheet_name=tab_master)
+    # Get xyz coordinates
+    tab_xyz = [name for name in tab_names if "xyz" in name.lower()][0]
+    df_xyz = pd.read_excel(file_path, sheet_name=tab_xyz)
+    # Get ephys features
+    tab_ephys_fx = [name for name in tab_names if "ephys_fx" in name.lower()][0]
+    df_ephys_fx = pd.read_excel(file_path, sheet_name=tab_ephys_fx)
+    # Merge the tables
+    df_all = (
+        df_master.merge(
+            df_xyz.rename(
+                columns={
+                    "specimen_name": "jem-id_cell_specimen",
+                    "structure_acronym": "Annotated structure",
+                }
+            ),
+            on="jem-id_cell_specimen",
+            how="outer",
+            suffixes=("_master", "_xyz"),
+        )
+        .merge(df_ephys_fx.rename(
+                columns={
+                    "failed_seal": "failed_no_seal",
+                    "failed_input_access_resistance": "failed_bad_rs",
+                }
+            ), on="cell_specimen_id", how="outer", suffixes=("_master", "_ephys_fx"))
+        .sort_values("Date", ascending=False)
+    )
+    return df_all, df_master, df_xyz, df_ephys_fx
+if __name__ == "__main__":
+    df_all, df_master, df_xyz, df_ephys_fx = read_brian_spreadsheet()
+    print(df_all.head())
+    print(df_master.head())
+    print(df_xyz.head())
+    print(df_ephys_fx.head())

{lcne_patchseq_analysis-0.0.2 → lcne_patchseq_analysis-0.1.0}/src/LCNE_patchseq_analysis.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: LCNE-patchseq-analysis
-Version: 0.0.2
+Version: 0.1.0
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 Author-email: Han Hou <han.hou@alleninstitute.org>
@@ -11,6 +11,8 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: pandas
+Requires-Dist: openpyxl
+Requires-Dist: matplotlib
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: coverage; extra == "dev"
@@ -29,14 +31,7 @@ Requires-Dist: furo; extra == "dev"
 ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
 ![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)
-## Usage
- - To use this template, click the green `Use this template` button and `Create new repository`.
- - After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo.
- - To enable the automatic semantic version increments: in the repository go to `Settings` and `Collaborators and teams`. Click the green `Add people` button. Add `svc-aindscicomp` as an admin. Modify the file in `.github/workflows/tag_and_publish.yml` and remove the if statement in line 65. The semantic version will now be incremented every time a code is committed into the main branch.
- - To publish to PyPI, enable semantic versioning and uncomment the publish block in `.github/workflows/tag_and_publish.yml`. The code will now be published to PyPI every time the code is committed into the main branch.
- - The `.github/workflows/test_and_lint.yml` file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the `test_and_lint.yml` can be deleted. The strictness of the code coverage level, etc., can be modified by altering the configurations in the `pyproject.toml` file and the `.flake8` file.
+Library for LCNE-patchseq data analysis
 ## Installation
 To use the software, in the root directory, run

{lcne_patchseq_analysis-0.0.2 → lcne_patchseq_analysis-0.1.0}/src/LCNE_patchseq_analysis.egg-info/SOURCES.txt RENAMED Viewed

@@ -19,11 +19,15 @@ docs/source/_static/favicon.ico
 docs/source/_static/light-logo.svg
 environment/Dockerfile
 environment/postInstall
+notebook/demo.ipynb
 src/LCNE_patchseq_analysis/__init__.py
 src/LCNE_patchseq_analysis.egg-info/PKG-INFO
 src/LCNE_patchseq_analysis.egg-info/SOURCES.txt
 src/LCNE_patchseq_analysis.egg-info/dependency_links.txt
 src/LCNE_patchseq_analysis.egg-info/requires.txt
 src/LCNE_patchseq_analysis.egg-info/top_level.txt
+src/LCNE_patchseq_analysis/data_util/__init__.py
+src/LCNE_patchseq_analysis/data_util/ephys.py
+src/LCNE_patchseq_analysis/data_util/metadata.py
 tests/__init__.py
 tests/test_example.py