From fa8ad6fbf2576a3710f6569f4a8e27260dbcae2d Mon Sep 17 00:00:00 2001 From: Maria Marin Date: Wed, 7 Feb 2024 18:36:47 +0000 Subject: [PATCH] Upload New File --- Reposicionamiento /Reposicionamiento.ipynb | 662 +++++++++++++++++++++ 1 file changed, 662 insertions(+) create mode 100644 Reposicionamiento /Reposicionamiento.ipynb diff --git a/Reposicionamiento /Reposicionamiento.ipynb b/Reposicionamiento /Reposicionamiento.ipynb new file mode 100644 index 0000000..1886269 --- /dev/null +++ b/Reposicionamiento /Reposicionamiento.ipynb @@ -0,0 +1,662 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "50a451f7-1809-46d2-973e-74e901d97204", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import numpy as np\n", + "import seaborn as sns\n", + "import matplotlib.pyplot as plt\n", + "import networkx as nx\n", + "from networkx.algorithms import bipartite\n", + "import nxpd\n", + "import funciones_reposicionamiento\n", + "import re" + ] + }, + { + "cell_type": "markdown", + "id": "422cca8f-611e-4e02-8fa5-e90641cb3fb2", + "metadata": {}, + "source": [ + "### Enfermedades estudiadas\n", + "\n", + "
\n", + " \n", + "| Condition | Concept ID |\n", + "|------------------- |------------|\n", + "| Dementia | C0497327 |\n", + "| Bipolar Disorder | C0005586 |\n", + "| Epilepsy | C0014544 |\n", + "| Schizophrenia | C0036341 |\n", + "\n", + "
\n" + ] + }, + { + "cell_type": "markdown", + "id": "62ae066d-075e-45c9-a878-6b971f837d8a", + "metadata": {}, + "source": [ + "### Datos" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "ce71be78-0f8c-4f42-ae9e-e730de08e7fe", + "metadata": {}, + "outputs": [], + "source": [ + "#Cargo los archivos que contienen las matrices de SPL\n", + "spl_enf_dis_gen = pd.read_csv('Data/Matrices SPL/SPL enf en bipartita enf-gen.csv', sep=\",\")\n", + "spl_gen_dis_gen = pd.read_csv('Data/Matrices SPL/SPL genes en bipartita enf-gen.csv', sep=\",\")\n", + "spl_enf_dis_dru = pd.read_csv('Data/Matrices SPL/SPL enf en bipartita enf-dru.csv', sep=\",\")\n", + "spl_dru_dis_dru = pd.read_csv('Data/Matrices SPL/SPL fármacos en bipartita enf-dru.csv', sep=\",\")\n", + "spl_enf_dse_sym = pd.read_csv('Data/Matrices SPL/SPL enf en bipartita enf-sym.csv', sep=\",\")\n", + "spl_sym_dse_sym = pd.read_csv('Data/Matrices SPL/SPL síntomas en bipartita enf-sym.csv', sep=\",\")\n", + "spl_dis_gen_proj = pd.read_csv('Data/Matrices SPL/SPL enf en proyectada enf-gen.csv', sep=\",\")\n", + "spl_dis_dru_proj = pd.read_csv('Data/Matrices SPL/SPL enf en proyectada enf-dru.csv', sep=\",\")\n", + "spl_dse_sym_proj = pd.read_csv('Data/Matrices SPL/SPL enf en proyectada enf-sym.csv', sep=\",\")" + ] + }, + { + "cell_type": "markdown", + "id": "041b026c-bd1b-495d-89c1-2887a43995f5", + "metadata": {}, + "source": [ + "### Fármacos candidatos" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4681667a-28e9-45f2-8792-22280a657c8c", + "metadata": {}, + "outputs": [], + "source": [ + "#cargo el archivo obtenido en la celda anterior\n", + "resultados_proximidad_targets = pd.read_csv('Resultados proximidad y targets en módulo.csv', sep=\",\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5b55709c-6c2b-4225-a0e6-d46c5c29a876", + "metadata": {}, + "outputs": [], + "source": [ + "candidatos_dementia = funciones_reposicionamiento.farmacos_candidatos(resultados_proximidad_targets, \"Demencia\", dis_dru_the)\n", + "candidatos_bipolar = funciones_reposicionamiento.farmacos_candidatos(resultados_proximidad_targets, \"Bipolaridad\", dis_dru_the)\n", + "candidatos_epilepsy = funciones_reposicionamiento.farmacos_candidatos(resultados_proximidad_targets, \"Epilepsia\", dis_dru_the)\n", + "candidatos_schizo = funciones_reposicionamiento.farmacos_candidatos(resultados_proximidad_targets, \"Esquizofrenia\", dis_dru_the)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "222c2ca3-3711-47b2-a1ec-5d72f7dcd652", + "metadata": {}, + "outputs": [], + "source": [ + "enfermedades = ['Demencia', 'Bipolaridad', 'Epilepsia', 'Esquizofrenia']\n", + "\n", + "df_resultados_candidatos = pd.DataFrame()\n", + "\n", + "# Itero sobre las cuatro enfermedades\n", + "for enfermedad in enfermedades:\n", + " # Utilizo la función farmacos_candidatos para cada enfermedad neurológica y concateno los resultados\n", + " resultados_enfermedad = funciones_reposicionamiento.farmacos_candidatos(resultados_proximidad_targets, enfermedad, dis_dru_the)\n", + " df_resultados_candidatos = pd.concat([df_resultados_candidatos, resultados_enfermedad], ignore_index=True)\n", + "\n", + "df_resultados_candidatos.to_csv(\"Fármacos y enfermedades candidatos de reposicionamiento.csv\", index = False)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "fb9495ea-efcc-42c0-97f2-e24d0e231ef1", + "metadata": {}, + "outputs": [], + "source": [ + "#cargo el archivo de fármacos candidatos de reposicionamiento\n", + "candidatos = pd.read_csv('Fármacos y enfermedades candidatos de reposicionamiento.csv', sep=\",\")" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "77745258-518c-4642-8b5a-a825b1750390", + "metadata": {}, + "outputs": [], + "source": [ + "#calculo los SPLs en las tres redes proyectadas entre las enfermedades neurológicas estudiadas y las enfermedades tratadas por los\n", + "#fármacos candidatos de reposicionamiento.\n", + "id_enfermedades = {\n", + " 'Demencia': \"C0497327\",\n", + " 'Bipolaridad': \"C0005586\",\n", + " 'Epilepsia': \"C0014544\",\n", + " 'Esquizofrenia': \"C0036341\"\n", + "}\n", + "\n", + "spls_files = [spl_dis_gen_proj, spl_dis_dru_proj, spl_dse_sym_proj]\n", + "\n", + "spls_enfermedades_candidatas = funciones_reposicionamiento.spl_candidatos(spls_files, id_enfermedades, candidatos)\n", + "spls_enfermedades_candidatas.to_csv(\"SPLs enfermedades candidatas de reposicionamiento.csv\", index = False)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "ad63dea1-2fb0-414d-b461-a40d728154b4", + "metadata": {}, + "outputs": [], + "source": [ + "#cargo el archivo con los resultados de la celda anterior\n", + "spls_enfermedades_candidatas = pd.read_csv(\"SPLs enfermedades candidatas de reposicionamiento.csv\", sep=\",\")" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "19977544-f4b8-4401-9d16-02e4c65a3e64", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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