Merge pull request #1 from alexwjung/main

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webpage/forest_int.ipynb

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+{"cells":[{"cell_type":"code","execution_count":1,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"IGcSfiuEl2Vo","executionInfo":{"status":"ok","timestamp":1683283387141,"user_tz":-120,"elapsed":7423,"user":{"displayName":"Alexander Jung","userId":"15821513848078905412"}},"outputId":"e0917769-8d32-4089-f7ca-f41178484f31"},"outputs":[{"output_type":"stream","name":"stdout","text":["Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n","Requirement already satisfied: plotly in /usr/local/lib/python3.10/dist-packages (5.13.1)\n","Requirement already satisfied: tenacity>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from plotly) (8.2.2)\n"]}],"source":["!pip3 install plotly"]},{"cell_type":"code","source":["from google.colab import drive\n","drive.mount('/content/drive')"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"6yu1jxDvnf00","executionInfo":{"status":"ok","timestamp":1683283490045,"user_tz":-120,"elapsed":102909,"user":{"displayName":"Alexander Jung","userId":"15821513848078905412"}},"outputId":"e50655f1-7fac-4801-83a7-7f6981e8fbf7"},"execution_count":2,"outputs":[{"output_type":"stream","name":"stdout","text":["Mounted at /content/drive\n"]}]},{"cell_type":"code","source":["## Custom Modules\n","#=======================================================================================================================\n","import sys\n","import os \n","import tqdm\n","import h5py\n","\n","import time\n","import pickle\n","import numpy as np \n","import pandas as pd \n","\n","import plotly.graph_objects as go \n","import plotly.express as px\n","\n","import matplotlib as mpl\n","import matplotlib.pyplot as plt\n","\n","ROOT_DIR = '/content/drive/MyDrive/tmp/plots/'\n","\n","\n","dd_theta = pd.read_csv(ROOT_DIR + 'theta.csv')\n","\n","disease_ref = np.load(ROOT_DIR + 'disease_codes.npy', allow_pickle=True)\n","disease_ref = disease_ref[:, 1]\n","\n","events = ['oesophagus', 'stomach', 'colorectal', 'liver',\n","                'pancreas', 'lung', 'melanoma', 'breast', 'cervix_uteri',\n","                'corpus_uteri', 'ovary', 'prostate', 'testis', 'kidney',\n","                'bladder', 'brain', 'thyroid', 'non_hodgkin_lymphoma', 'multiple_myeloma', 'AML', 'other', 'death']\n","\n","\n","Events = ['Oesophagus', 'Stomach', 'Colorectal', 'Liver',\n","                'Pancreas', 'Lung', 'Melanoma', 'Breast', 'Cervix uteri',\n","                'Corpus Uteri', 'Ovary', 'Prostate', 'Testis', 'Kidney',\n","                'Bladder', 'Brain', 'Thyroid', 'Non Hodgkin Lymphoma', 'Multiple Myeloma', 'AML']\n","\n","gene_names = np.asarray([jj+ii for jj in Events for ii in [' First Degree', ' All', ' Multiple', ' Early']])\n","\n","bth_names = np.asarray(['Alcoholic', 'Smoker', 'High Blood Pressure', 'Low Blood Pressure', 'Height', 'Weight', 'Age at first Birth'])\n","\n","names = np.concatenate((disease_ref, gene_names, bth_names))\n","\n","colormap= np.asarray(['#1E90FF', '#BFEFFF', '#191970', '#87CEFA', '#008B8B', '#946448', '#421a01', '#6e0b3c', \n","                '#9370DB', '#7A378B', '#CD6090', '#006400', '#5ebd70', '#f8d64f', '#EEAD0E', '#f8d6cf',\n","                '#CDCB50', '#CD6600', '#FF8C69', '#8f0000', '#b3b3b3', '#454545'])\n","\n","for cc in range(22):\n","    print(cc, events[cc])\n","\n"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"RZ7h07l2mtzX","executionInfo":{"status":"ok","timestamp":1683283491888,"user_tz":-120,"elapsed":1848,"user":{"displayName":"Alexander Jung","userId":"15821513848078905412"}},"outputId":"21dcda12-62fd-4fdf-bd31-16c82ca95774"},"execution_count":3,"outputs":[{"output_type":"stream","name":"stdout","text":["0 oesophagus\n","1 stomach\n","2 colorectal\n","3 liver\n","4 pancreas\n","5 lung\n","6 melanoma\n","7 breast\n","8 cervix_uteri\n","9 corpus_uteri\n","10 ovary\n","11 prostate\n","12 testis\n","13 kidney\n","14 bladder\n","15 brain\n","16 thyroid\n","17 non_hodgkin_lymphoma\n","18 multiple_myeloma\n","19 AML\n","20 other\n","21 death\n"]}]},{"cell_type":"code","execution_count":4,"metadata":{"tags":[],"id":"QaBBCwxYl2Vs","executionInfo":{"status":"ok","timestamp":1683283538544,"user_tz":-120,"elapsed":2,"user":{"displayName":"Alexander Jung","userId":"15821513848078905412"}}},"outputs":[],"source":["theta = np.exp(np.asarray(dd_theta.iloc[:, np.arange(2, 62, 3)]))\n","theta_lower = np.exp(np.asarray(dd_theta.iloc[:, np.arange(3, 63, 3)]))\n","theta_upper = np.exp(np.asarray(dd_theta.iloc[:, np.arange(4, 64, 3)]))\n","\n","y = np.arange(theta.shape[0])"]},{"cell_type":"code","source":["import plotly.graph_objects as go \n","fig = go.Figure()\n","n=300\n","for cc in range(20):\n","  fig.add_trace(go.Scatter(\n","      x=theta[:, cc],\n","      y=names, \n","      mode=\"markers\",\n","      marker_color=colormap[cc], \n","      name=Events[cc],\n","      customdata=pd.DataFrame({'l': theta_lower[:, cc], \n","              'u': theta_upper[:, cc], \n","              'e': np.repeat(Events[cc], theta.shape[0]) }),\n","      hovertemplate='<b>Cancer: </b>: %{customdata[2]}<br>' + \n","                    '<b>Var: </b>: %{y}<br>' + \n","                    '<b>HR</b>: %{x:.2f} [%{customdata[0]:.2f}, %{customdata[1]:.2f}]<br>' + \n","                    '<extra></extra>'\n","  ))\n","\n","fig.update_xaxes(title_text=\"Hazard Ratio \", type=\"log\", gridcolor='#acacad')\n","fig.update_yaxes(gridcolor='#acacad')\n","\n","\n","fig.update_layout(\n","    paper_bgcolor='rgba(0,0,0,0)',\n","    plot_bgcolor='rgba(0,0,0,0)',\n","    width=1200,\n","    height=950,\n","    \n",")\n","\n","fig.write_html(ROOT_DIR + 'dexp.html')"],"metadata":{"id":"flTGpgBlzTdA","executionInfo":{"status":"ok","timestamp":1683285477768,"user_tz":-120,"elapsed":624,"user":{"displayName":"Alexander Jung","userId":"15821513848078905412"}}},"execution_count":43,"outputs":[]},{"cell_type":"code","execution_count":null,"metadata":{"id":"AW3ySBaml2V0"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"metadata":{"id":"vNykD7Cgl2V1"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"metadata":{"id":"czHbTrItl2V2"},"outputs":[],"source":[]},{"cell_type":"code","execution_count":null,"metadata":{"id":"leMrvnYql2V2"},"outputs":[],"source":[]}],"metadata":{"kernelspec":{"display_name":"Python 3","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":"3.7.3"},"colab":{"provenance":[]}},"nbformat":4,"nbformat_minor":0}