Moved stuff from empkins-d03-macro-analysis

experiments/2022_05_macro/biomarker/Bloodspot_Processing.ipynb

@@ -0,0 +1,184 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "5f638161-775e-4292-977e-0985b9e7533b",
+   "metadata": {},
+   "source": [
+    "# Bloodspot Processing"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6d785b14-abb7-4b01-89c7-93e3f3d754f1",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import json\n",
+    "import re\n",
+    "from pathlib import Path\n",
+    "\n",
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "import pingouin as pg\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "import seaborn as sns\n",
+    "\n",
+    "from fau_colors import cmaps\n",
+    "import biopsykit as bp\n",
+    "from biopsykit.io import biomarker\n",
+    "\n",
+    "from empkins_io.datasets.d03.macro_ap01 import MacroBaseDataset\n",
+    "\n",
+    "%load_ext autoreload\n",
+    "%autoreload 2\n",
+    "%matplotlib widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8eb25a5a-3758-4273-908f-9102fc493a19",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "plt.close(\"all\")\n",
+    "\n",
+    "palette = sns.color_palette(cmaps.faculties)\n",
+    "sns.set_theme(context=\"notebook\", style=\"ticks\", palette=palette)\n",
+    "\n",
+    "plt.rcParams[\"figure.figsize\"] = (10, 5)\n",
+    "plt.rcParams[\"pdf.fonttype\"] = 42\n",
+    "plt.rcParams[\"mathtext.default\"] = \"regular\"\n",
+    "\n",
+    "palette"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1e7feaa7-d152-4ca4-90b8-6b4419331241",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "deploy_type = \"local\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d7016885-ae8c-427a-95a1-df14b934e3f5",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "config_dict = json.load(Path(\"../../../config.json\").open(encoding=\"utf-8\"))\n",
+    "\n",
+    "base_path = Path(config_dict[deploy_type][\"base_path\"])\n",
+    "base_path"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "693236a6-2c6a-4f8f-81ad-bce258555342",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "path_out = base_path.joinpath(\"bloodspots/processed\")\n",
+    "bp.utils.file_handling.mkdirs([path_out])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9e0df28b-6445-45ee-ae14-15174f249f72",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "dataset = MacroBaseDataset(base_path)\n",
+    "dataset"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "50ca0ff0-594f-4026-b216-75d89028a9bd",
+   "metadata": {},
+   "source": [
+    "## CRP"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f741ce0a-6007-49ae-bdfc-502fab7efd39",
+   "metadata": {},
+   "source": [
+    "### Samples"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "79705e08-5eb6-4127-8dd4-14de0c8b2c78",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "crp_data = bp.io.biomarker.load_biomarker_results(\n",
+    "    base_path.joinpath(\"bloodspots/raw/crp_values.xlsx\"), biomarker_type=\"crp\", regex_str=r\"(VP_\\d+)-(T\\w)-(B\\w)\"\n",
+    ")\n",
+    "\n",
+    "crp_data = crp_data.join(dataset.day_condition_map).reset_index()\n",
+    "crp_data = crp_data.drop(columns=\"day\").set_index([\"subject\", \"condition\", \"sample\"])\n",
+    "crp_data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0a8865be-d629-4a0f-b675-5d9001dc65dc",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "crp_data.to_csv(path_out.joinpath(\"crp_samples.csv\"))"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "empkins_d03_macro_analysis",
+   "language": "python",
+   "name": "empkins_d03_macro_analysis"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}