{ "cells": [ { "cell_type": "markdown", "metadata": { "deletable": true, "editable": true }, "source": [ "# CST Phosphorylation Data Visualization\n", "This notebook will visualize the phosphorylation data before and after normalization and processing. " ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true, "deletable": true, "editable": true }, "outputs": [], "source": [ "from clustergrammer_widget import *\n", "import pandas as pd\n", "import numpy as np\n", "net = Network()" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [ { "data": { "text/plain": [ "(8468, 37)" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "filename = '../lung_cellline_3_1_16/lung_cl_all_ptm/precalc_processed/ptmCCLE_col-iqn.txt'\n", "net.load_file(filename)\n", "net.dat['mat'].shape" ] }, { "cell_type": "markdown", "metadata": { "deletable": true, "editable": true }, "source": [ "## Filter for phosphorylations only" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [], "source": [ "df = net.export_df()\n", "df = df.transpose()\n", "cols = df.columns.tolist()" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "5798\n" ] } ], "source": [ "keep_cols = []\n", "for inst_col in cols:\n", " if '_phospho_' in inst_col:\n", " keep_cols.append(inst_col)\n", " \n", "print(len(keep_cols))" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [ { "data": { "text/plain": [ "(5798, 37)" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df_phos = df[keep_cols]\n", "df_phos = df_phos.transpose()\n", "df_phos.shape" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": true, "deletable": true, "editable": true }, "outputs": [], "source": [ "df_phos.to_csv('../lung_cellline_3_1_16/lung_cl_all_ptm/precalc_processed/phosCCLE_col-iqn.txt', sep='\\t')" ] }, { "cell_type": "markdown", "metadata": { "deletable": true, "editable": true }, "source": [ "## Load Filtered data" ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [], "source": [ "net.load_file('../lung_cellline_3_1_16/lung_cl_all_ptm/precalc_processed/phosCCLE_col-iqn.txt')" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [ { "data": { "text/plain": [ "(5798, 37)" ] }, "execution_count": 25, "metadata": {}, "output_type": "execute_result" } ], "source": [ "net.dat['mat'].shape" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [ { "data": { "text/plain": [ "(5798, 37)" ] }, "execution_count": 26, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# net.filter_N_top('row', 3000, rank_type='var')\n", "net.dat['mat'].shape" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [], "source": [ "net.swap_nan_for_zero()\n", "net.make_clust()" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false, "deletable": true, "editable": true }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "266ec3a23c6a4e81b02e5b0569dfb7ec" } }, "metadata": {}, "output_type": "display_data" } ], "source": [ "clustergrammer_widget(network=net.widget())" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true, "deletable": true, "editable": true }, "outputs": [], "source": [] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python [Root]", "language": "python", "name": "Python [Root]" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.12" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": { "0f844a8de1484b83a055e03e227f8293": { "model_module": "jupyter-js-widgets", "model_module_version": "~2.1.4", "model_name": "LayoutModel", "state": { "_model_module_version": "~2.1.4", "_view_module_version": "~2.1.4" } }, "1063ccc779bf4f06ab8a441e800347df": { "model_module": "jupyter-js-widgets", "model_module_version": "~2.1.4", "model_name": "LayoutModel", "state": { "_model_module_version": "~2.1.4", "_view_module_version": "~2.1.4" } }, "266ec3a23c6a4e81b02e5b0569dfb7ec": { "model_module": "clustergrammer_widget", "model_module_version": "*", "model_name": "hello_model", "state": { "_dom_classes": [], "_model_module_version": "*", "_view_module_version": "*", "layout": "IPY_MODEL_357aa3c021604ece86814055499aede0", "msg_throttle": 1, "network": "{\"row_nodes\": [{\"group\": [3629.0, 1510.0, 538.0, 144.0, 36.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"AAAS_phospho_S541\", \"clust\": 3627, \"rank\": 1999, \"ini\": 5798, \"rankvar\": 1166}, {\"group\": [2812.0, 1114.0, 350.0, 90.0, 16.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"AACS_phospho_T659\", \"clust\": 2814, \"rank\": 2470, \"ini\": 5797, \"rankvar\": 186}, {\"group\": [4445.0, 1864.0, 686.0, 189.0, 48.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"AAK1_phospho_S846\", \"clust\": 4450, \"rank\": 1750, \"ini\": 5796, \"rankvar\": 865}, {\"group\": [2210.0, 903.0, 278.0, 67.0, 11.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"AAK1_phospho_T375\", \"clust\": 2209, \"rank\": 2621, \"ini\": 5795, \"rankvar\": 155}, {\"group\": [1552.0, 615.0, 218.0, 60.0, 11.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"AAK1_phospho_T389\", \"clust\": 1552, \"rank\": 4253, \"ini\": 5794, \"rankvar\": 2131}, {\"group\": [3286.0, 1350.0, 462.0, 121.0, 29.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"AAK1_phospho_Y28\", \"clust\": 3290, \"rank\": 4236, \"ini\": 5793, \"rankvar\": 2183}, {\"group\": [4974.0, 2103.0, 778.0, 208.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABCB1_phospho_S675\", \"clust\": 4971, \"rank\": 380, \"ini\": 5792, \"rankvar\": 5607}, {\"group\": [5104.0, 2167.0, 798.0, 211.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABCC2_phospho_S283\", \"clust\": 5094, \"rank\": 947, \"ini\": 5791, \"rankvar\": 5776}, {\"group\": [4036.0, 1677.0, 602.0, 162.0, 42.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABCC2_phospho_S908\", \"clust\": 4019, \"rank\": 2031, \"ini\": 5790, \"rankvar\": 3315}, {\"group\": [4732.0, 1995.0, 743.0, 201.0, 51.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABCC5_phospho_S64\", \"clust\": 4731, \"rank\": 2643, \"ini\": 5789, \"rankvar\": 2922}, {\"group\": [5783.0, 2421.0, 860.0, 219.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABCC5_phospho_S67\", \"clust\": 5780, \"rank\": 2111, \"ini\": 5788, \"rankvar\": 3465}, {\"group\": [2416.0, 1035.0, 331.0, 83.0, 15.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABCF3_phospho_S83\", \"clust\": 2419, \"rank\": 3916, \"ini\": 5787, \"rankvar\": 2367}, {\"group\": [5128.0, 2175.0, 801.0, 211.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABI1_phospho_S222\", \"clust\": 5131, \"rank\": 1325, \"ini\": 5786, \"rankvar\": 2533}, {\"group\": [1040.0, 422.0, 169.0, 52.0, 11.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABI1_phospho_S323\", \"clust\": 1039, \"rank\": 3874, \"ini\": 5785, \"rankvar\": 3559}, {\"group\": [3294.0, 1353.0, 462.0, 121.0, 29.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABI1_phospho_Y198\", \"clust\": 3295, \"rank\": 4157, \"ini\": 5784, \"rankvar\": 3728}, {\"group\": [3254.0, 1340.0, 460.0, 121.0, 29.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABI1_phospho_Y213\", \"clust\": 3254, \"rank\": 3175, \"ini\": 5783, \"rankvar\": 1299}, {\"group\": [665.0, 289.0, 123.0, 39.0, 8.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABI2_phospho_S196\", \"clust\": 672, \"rank\": 4247, \"ini\": 5782, \"rankvar\": 2989}, {\"group\": [4506.0, 1883.0, 694.0, 191.0, 50.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABL1_phospho_Y185\", \"clust\": 4503, \"rank\": 526, \"ini\": 5781, \"rankvar\": 3160}, {\"group\": [1002.0, 402.0, 162.0, 50.0, 10.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABL2_phospho_Y231\", \"clust\": 1001, \"rank\": 4532, \"ini\": 5780, \"rankvar\": 3457}, {\"group\": [491.0, 260.0, 114.0, 37.0, 8.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABL2_phospho_Y668\", \"clust\": 491, \"rank\": 2499, \"ini\": 5779, \"rankvar\": 62}, {\"group\": [5432.0, 2339.0, 838.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_S450\", \"clust\": 5433, \"rank\": 71, \"ini\": 5778, \"rankvar\": 5634}, {\"group\": [5579.0, 2341.0, 838.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_S452\", \"clust\": 5593, \"rank\": 47, \"ini\": 5777, \"rankvar\": 3809}, {\"group\": [5446.0, 2339.0, 838.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_S455\", \"clust\": 5454, \"rank\": 120, \"ini\": 5776, \"rankvar\": 4319}, {\"group\": [5580.0, 2341.0, 838.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_S458\", \"clust\": 5594, \"rank\": 64, \"ini\": 5775, \"rankvar\": 2436}, {\"group\": [5071.0, 2154.0, 795.0, 211.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_S587\", \"clust\": 5074, \"rank\": 335, \"ini\": 5774, \"rankvar\": 5339}, {\"group\": [4514.0, 1891.0, 696.0, 191.0, 50.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_S669\", \"clust\": 4518, \"rank\": 620, \"ini\": 5773, \"rankvar\": 4109}, {\"group\": [5385.0, 2320.0, 838.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_S706\", \"clust\": 5386, \"rank\": 87, \"ini\": 5772, \"rankvar\": 5660}, {\"group\": [5381.0, 2317.0, 838.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_T451\", \"clust\": 5382, \"rank\": 218, \"ini\": 5771, \"rankvar\": 5009}, {\"group\": [4754.0, 2013.0, 751.0, 204.0, 51.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM1_phospho_T670\", \"clust\": 4759, \"rank\": 623, \"ini\": 5770, \"rankvar\": 4231}, {\"group\": [3920.0, 1626.0, 586.0, 159.0, 41.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM3_phospho_S503\", \"clust\": 3917, \"rank\": 1240, \"ini\": 5769, \"rankvar\": 4601}, {\"group\": [5487.0, 2341.0, 838.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM3_phospho_S504\", \"clust\": 5490, \"rank\": 174, \"ini\": 5768, \"rankvar\": 4235}, {\"group\": [3350.0, 1382.0, 474.0, 122.0, 29.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ABLIM3_phospho_Y538\", \"clust\": 3350, \"rank\": 3332, \"ini\": 5767, \"rankvar\": 4665}, {\"group\": [4297.0, 1809.0, 666.0, 185.0, 48.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACACA_phospho_Y1370\", \"clust\": 4297, \"rank\": 2343, \"ini\": 5766, \"rankvar\": 1019}, {\"group\": [1678.0, 693.0, 238.0, 60.0, 11.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACAD9_phospho_Y611\", \"clust\": 1659, \"rank\": 5740, \"ini\": 5765, \"rankvar\": 5774}, {\"group\": [666.0, 289.0, 123.0, 39.0, 8.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACADVL_phospho_T364\", \"clust\": 675, \"rank\": 4235, \"ini\": 5764, \"rankvar\": 2966}, {\"group\": [563.0, 286.0, 123.0, 39.0, 8.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACAT2_phospho_S185\", \"clust\": 557, \"rank\": 3212, \"ini\": 5763, \"rankvar\": 968}, {\"group\": [4643.0, 1942.0, 714.0, 192.0, 50.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACD_phospho_S425\", \"clust\": 4646, \"rank\": 1886, \"ini\": 5762, \"rankvar\": 509}, {\"group\": [1310.0, 508.0, 188.0, 52.0, 11.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACIN1_phospho_S1284\", \"clust\": 1322, \"rank\": 5182, \"ini\": 5761, \"rankvar\": 5514}, {\"group\": [759.0, 321.0, 139.0, 44.0, 9.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACIN1_phospho_S1331\", \"clust\": 759, \"rank\": 3670, \"ini\": 5760, \"rankvar\": 2457}, {\"group\": [3017.0, 1208.0, 400.0, 109.0, 23.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACIN1_phospho_T1332\", \"clust\": 3016, \"rank\": 2379, \"ini\": 5759, \"rankvar\": 168}, {\"group\": [4546.0, 1904.0, 699.0, 191.0, 50.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACLY_phospho_S442\", \"clust\": 4549, \"rank\": 1637, \"ini\": 5758, \"rankvar\": 840}, {\"group\": [4089.0, 1709.0, 618.0, 168.0, 44.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACLY_phospho_S446\", \"clust\": 4090, \"rank\": 2048, \"ini\": 5757, \"rankvar\": 946}, {\"group\": [4099.0, 1713.0, 619.0, 168.0, 44.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACLY_phospho_S451\", \"clust\": 4080, \"rank\": 760, \"ini\": 5756, \"rankvar\": 4230}, {\"group\": [385.0, 233.0, 103.0, 33.0, 7.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACLY_phospho_S459\", \"clust\": 388, \"rank\": 3459, \"ini\": 5755, \"rankvar\": 1025}, {\"group\": [532.0, 272.0, 118.0, 39.0, 8.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACLY_phospho_T434\", \"clust\": 530, \"rank\": 2787, \"ini\": 5754, \"rankvar\": 1879}, {\"group\": [168.0, 117.0, 55.0, 18.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACLY_phospho_T447\", \"clust\": 164, \"rank\": 4275, \"ini\": 5753, \"rankvar\": 2783}, {\"group\": [3156.0, 1291.0, 440.0, 117.0, 27.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACOT1_phospho_T56\", \"clust\": 3152, \"rank\": 1539, \"ini\": 5752, \"rankvar\": 2274}, {\"group\": [444.0, 242.0, 105.0, 33.0, 7.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACOT7_phospho_Y194\", \"clust\": 436, \"rank\": 4732, \"ini\": 5751, \"rankvar\": 2312}, {\"group\": [5732.0, 2386.0, 846.0, 214.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACOT8_phospho_T301\", \"clust\": 5737, \"rank\": 637, \"ini\": 5750, \"rankvar\": 5191}, {\"group\": [3323.0, 1365.0, 465.0, 121.0, 29.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACSL3_phospho_T688\", \"clust\": 3315, \"rank\": 3348, \"ini\": 5749, \"rankvar\": 1595}, {\"group\": [5208.0, 2208.0, 816.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACTB_phospho_S33\", \"clust\": 5210, \"rank\": 357, \"ini\": 5748, \"rankvar\": 4388}, {\"group\": [3609.0, 1496.0, 532.0, 141.0, 34.0, 2.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACTB_phospho_T162\", \"clust\": 3608, \"rank\": 2578, \"ini\": 5747, \"rankvar\": 20}, {\"group\": [5209.0, 2208.0, 816.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACTB_phospho_T318\", \"clust\": 5211, \"rank\": 614, \"ini\": 5746, \"rankvar\": 3990}, {\"group\": [4379.0, 1856.0, 685.0, 189.0, 48.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACTB_phospho_Y166\", \"clust\": 4381, \"rank\": 2259, \"ini\": 5745, \"rankvar\": 89}, {\"group\": [550.0, 284.0, 123.0, 39.0, 8.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"ACTB_phospho_Y188\", \"clust\": 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1.0], \"name\": \"CACNB1_phospho_S507\", \"clust\": 3907, \"rank\": 943, \"ini\": 5164, \"rankvar\": 3704}, {\"group\": [5184.0, 2192.0, 811.0, 213.0, 52.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"CACNB1_phospho_T499\", \"clust\": 5186, \"rank\": 450, \"ini\": 5163, \"rankvar\": 4481}, {\"group\": [4375.0, 1854.0, 684.0, 189.0, 48.0, 3.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"CACTIN_phospho_S135\", \"clust\": 4374, \"rank\": 1486, \"ini\": 5162, \"rankvar\": 813}, {\"group\": [2322.0, 989.0, 323.0, 82.0, 15.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"CAD_phospho_S1267\", \"clust\": 2322, \"rank\": 3018, \"ini\": 5161, \"rankvar\": 4223}, {\"group\": [2474.0, 1045.0, 331.0, 83.0, 15.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"CAD_phospho_S133\", \"clust\": 2392, \"rank\": 3813, \"ini\": 5160, \"rankvar\": 4882}, {\"group\": [2683.0, 1089.0, 340.0, 85.0, 15.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], \"name\": \"CAD_phospho_S1407\", \"clust\": 2632, \"rank\": 3802, \"ini\": 5159, 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