{ "cells": [ { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "data": { "text/html": [ "" ], "text/vnd.plotly.v1+html": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import pickle\n", "import pandas as pd\n", "py.init_notebook_mode(connected=True) " ] }, { "cell_type": "code", "execution_count": 126, "metadata": {}, "outputs": [], "source": [ "(drugmatrix_archive,pubchem_archive,ds1_archive,serotonin_archive) = \\\n", " pickle.load(open('../data/unbalanced_data_results.pkl','rb'))" ] }, { "cell_type": "code", "execution_count": 127, "metadata": {}, "outputs": [], "source": [ "(drugmatrix_archive2,pubchem_archive2,ds1_archive2,serotonin_archive2) = \\\n", " pickle.load(open('../data/unbalanced_data_results.sklearn.pkl','rb'))" ] }, { "cell_type": "code", "execution_count": 128, "metadata": {}, "outputs": [], "source": [ "data = []\n", "# columns: [dataset, name, Kappa_init, ROC, Kappa_final, threshold]\n", "for nm,v in drugmatrix_archive.items():\n", " init,final = v\n", " data.append(['drugmatrix',nm,init[1],init[-1],final[1],final[0]])\n", "for nm,v in pubchem_archive.items():\n", " init,final = v\n", " data.append(['pubchem',nm,init[1],init[-1],final[1],final[0]])\n", "for nm,v in ds1_archive.items():\n", " init,final = v\n", " data.append(['DS1',nm,init[1],init[-1],final[1],final[0]])\n", "for nm,v in serotonin_archive.items():\n", " init,final = v\n", " data.append(['serotonin',nm,init[1],init[-1],final[1],final[0]])\n", "df1 = pd.DataFrame(data,columns=['dataset', 'name', 'kappa_init', 'ROC', 'kappa_final', 'threshold'])" ] }, { "cell_type": "code", "execution_count": 129, "metadata": {}, "outputs": [], "source": [ "data = []\n", "# columns: [dataset, name, Kappa_init, ROC]\n", "for nm,v in drugmatrix_archive2.items():\n", " data.append(['drugmatrix',nm,v[0][1],v[0][-1]])\n", "for nm,v in pubchem_archive2.items():\n", " data.append(['pubchem',nm,v[0][1],v[0][-1]])\n", "for nm,v in ds1_archive2.items():\n", " data.append(['DS1',nm,v[0][1],v[0][-1]])\n", "for nm,v in serotonin_archive2.items():\n", " data.append(['serotonin',nm,v[0][1],v[0][-1]])\n", "df2 = pd.DataFrame(data,columns=['dataset', 'name', 'kappa_BRF', 'ROC_BRF'])" ] }, { "cell_type": "code", "execution_count": 130, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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datasetnamekappa_initROCkappa_finalthresholdkappa_BRFROC_BRF
0drugmatrixCHEMBL19092150.0000000.8298300.4169060.150.2486590.989986
1drugmatrixCHEMBL19092110.3657740.9352240.7513790.250.5513670.990435
2drugmatrixCHEMBL19092100.0000000.9026420.2815300.200.3254290.987178
3drugmatrixCHEMBL19092090.3078500.9205350.6105990.200.4095670.992174
4drugmatrixCHEMBL19092040.0000000.8909000.3849580.100.2562930.985219
\n", "
" ], "text/plain": [ " dataset name kappa_init ROC kappa_final threshold \\\n", "0 drugmatrix CHEMBL1909215 0.000000 0.829830 0.416906 0.15 \n", "1 drugmatrix CHEMBL1909211 0.365774 0.935224 0.751379 0.25 \n", "2 drugmatrix CHEMBL1909210 0.000000 0.902642 0.281530 0.20 \n", "3 drugmatrix CHEMBL1909209 0.307850 0.920535 0.610599 0.20 \n", "4 drugmatrix CHEMBL1909204 0.000000 0.890900 0.384958 0.10 \n", "\n", " kappa_BRF ROC_BRF \n", "0 0.248659 0.989986 \n", "1 0.551367 0.990435 \n", "2 0.325429 0.987178 \n", "3 0.409567 0.992174 \n", "4 0.256293 0.985219 " ] }, "execution_count": 130, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df = df1.merge(df2,on=['dataset','name'])\n", "df.head()" ] }, { "cell_type": "code", "execution_count": 131, "metadata": {}, "outputs": [], "source": [ "df['label'] = [x+\"-\"+y for x,y in zip(df.dataset,df.name)]" ] }, { "cell_type": "code", "execution_count": 132, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", "\n", " if (typeof (root._bokeh_onload_callbacks) === \"undefined\" || force === true) {\n", " root._bokeh_onload_callbacks = [];\n", " root._bokeh_is_loading = undefined;\n", " }\n", "\n", " var JS_MIME_TYPE = 'application/javascript';\n", " var HTML_MIME_TYPE = 'text/html';\n", " var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", " var CLASS_NAME = 'output_bokeh rendered_html';\n", "\n", " /**\n", " * Render data to the DOM node\n", " */\n", " function render(props, node) {\n", " var script = document.createElement(\"script\");\n", " node.appendChild(script);\n", " }\n", "\n", " /**\n", " * Handle when an output is cleared or removed\n", " */\n", " function handleClearOutput(event, handle) {\n", " var cell = handle.cell;\n", "\n", " var id = cell.output_area._bokeh_element_id;\n", " var server_id = cell.output_area._bokeh_server_id;\n", " // Clean up Bokeh references\n", " if (id != null && id in Bokeh.index) {\n", " Bokeh.index[id].model.document.clear();\n", " delete Bokeh.index[id];\n", " }\n", "\n", " if (server_id !== undefined) {\n", " // Clean up Bokeh references\n", " var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", " cell.notebook.kernel.execute(cmd, {\n", " iopub: {\n", " output: function(msg) {\n", " var id = msg.content.text.trim();\n", " if (id in Bokeh.index) {\n", " Bokeh.index[id].model.document.clear();\n", " delete Bokeh.index[id];\n", " }\n", " }\n", " }\n", " });\n", " // Destroy server and session\n", " var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", " cell.notebook.kernel.execute(cmd);\n", " }\n", " }\n", "\n", " /**\n", " * Handle when a new output is added\n", " */\n", " function handleAddOutput(event, handle) {\n", " var output_area = handle.output_area;\n", " var output = handle.output;\n", "\n", " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", " if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n", " return\n", " }\n", "\n", " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", "\n", " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", " // store reference to embed id on output_area\n", " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", " }\n", " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", " var bk_div = document.createElement(\"div\");\n", " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", " var script_attrs = bk_div.children[0].attributes;\n", " for (var i = 0; i < script_attrs.length; i++) {\n", " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", " }\n", " // store reference to server id on output_area\n", " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", " }\n", " }\n", "\n", " function register_renderer(events, OutputArea) {\n", "\n", " function append_mime(data, metadata, element) {\n", " // create a DOM node to render to\n", " var toinsert = this.create_output_subarea(\n", " metadata,\n", " CLASS_NAME,\n", " EXEC_MIME_TYPE\n", " );\n", " this.keyboard_manager.register_events(toinsert);\n", " // Render to node\n", " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", " render(props, toinsert[toinsert.length - 1]);\n", " element.append(toinsert);\n", " return toinsert\n", " }\n", "\n", " /* Handle when an output is cleared or removed */\n", " events.on('clear_output.CodeCell', handleClearOutput);\n", " events.on('delete.Cell', handleClearOutput);\n", "\n", " /* Handle when a new output is added */\n", " events.on('output_added.OutputArea', handleAddOutput);\n", "\n", " /**\n", " * Register the mime type and append_mime function with output_area\n", " */\n", " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", " /* Is output safe? */\n", " safe: true,\n", " /* Index of renderer in `output_area.display_order` */\n", " index: 0\n", " });\n", " }\n", "\n", " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", " if (root.Jupyter !== undefined) {\n", " var events = require('base/js/events');\n", " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", "\n", " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", " register_renderer(events, OutputArea);\n", " }\n", " }\n", "\n", " \n", " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " var NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
\\n\"+\n", " \"

\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"

\\n\"+\n", " \"\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " var el = document.getElementById(\"9608\");\n", " if (el != null) {\n", " el.textContent = \"BokehJS is loading...\";\n", " }\n", " if (root.Bokeh !== undefined) {\n", " if (el != null) {\n", " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", " }\n", " } else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(display_loaded, 100)\n", " }\n", " }\n", "\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n", " }\n", " finally {\n", " delete root._bokeh_onload_callbacks\n", " }\n", " console.info(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(js_urls, callback) {\n", " root._bokeh_onload_callbacks.push(callback);\n", " if (root._bokeh_is_loading > 0) {\n", " console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " root._bokeh_is_loading = js_urls.length;\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var s = document.createElement('script');\n", " s.src = url;\n", " s.async = false;\n", " s.onreadystatechange = s.onload = function() {\n", " root._bokeh_is_loading--;\n", " if (root._bokeh_is_loading === 0) {\n", " console.log(\"Bokeh: all BokehJS libraries loaded\");\n", " run_callbacks()\n", " }\n", " };\n", " s.onerror = function() {\n", " console.warn(\"failed to load library \" + url);\n", " };\n", " console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.getElementsByTagName(\"head\")[0].appendChild(s);\n", " }\n", " };var element = document.getElementById(\"9608\");\n", " if (element == null) {\n", " console.log(\"Bokeh: ERROR: autoload.js configured with elementid '9608' but no matching script tag was found. \")\n", " return false;\n", " }\n", "\n", " var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-1.0.4.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.0.4.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.0.4.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-1.0.4.min.js\"];\n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " \n", " function(Bokeh) {\n", " \n", " },\n", " function(Bokeh) {\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-1.0.4.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-1.0.4.min.css\");\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.0.4.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.0.4.min.css\");\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-tables-1.0.4.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.0.4.min.css\");\n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " \n", " if ((root.Bokeh !== undefined) || (force === true)) {\n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i].call(root, root.Bokeh);\n", " }if (force === true) {\n", " display_loaded();\n", " }} else if (Date.now() < root._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!root._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " root._bokeh_failed_load = true;\n", " } else if (force !== true) {\n", " var cell = $(document.getElementById(\"9608\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\n", "\n", " }\n", "\n", " if (root._bokeh_is_loading === 0) {\n", " console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(js_urls, function() {\n", " console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(window));" ], "application/vnd.bokehjs_load.v0+json": "\n(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n\n if (typeof (root._bokeh_onload_callbacks) === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n \n\n \n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n var NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded() {\n var el = document.getElementById(\"9608\");\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\n\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n }\n finally {\n delete root._bokeh_onload_callbacks\n }\n console.info(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(js_urls, callback) {\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = js_urls.length;\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n var s = document.createElement('script');\n s.src = url;\n s.async = false;\n s.onreadystatechange = s.onload = function() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.log(\"Bokeh: all BokehJS libraries loaded\");\n run_callbacks()\n }\n };\n s.onerror = function() {\n console.warn(\"failed to load library \" + url);\n };\n console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.getElementsByTagName(\"head\")[0].appendChild(s);\n }\n };var element = document.getElementById(\"9608\");\n if (element == null) {\n console.log(\"Bokeh: ERROR: autoload.js configured with elementid '9608' but no matching script tag was found. \")\n return false;\n }\n\n var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-1.0.4.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.0.4.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.0.4.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-1.0.4.min.js\"];\n\n var inline_js = [\n function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\n \n function(Bokeh) {\n \n },\n function(Bokeh) {\n console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-1.0.4.min.css\");\n Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-1.0.4.min.css\");\n console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.0.4.min.css\");\n Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.0.4.min.css\");\n console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-tables-1.0.4.min.css\");\n Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.0.4.min.css\");\n }\n ];\n\n function run_inline_js() {\n \n if ((root.Bokeh !== undefined) || (force === true)) {\n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }if (force === true) {\n display_loaded();\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n var cell = $(document.getElementById(\"9608\")).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n\n }\n\n if (root._bokeh_is_loading === 0) {\n console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(js_urls, function() {\n console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from bokeh.io import output_notebook, show\n", "from bokeh.models import ColumnDataSource, HoverTool, ColorBar\n", "from bokeh.palettes import plasma\n", "from bokeh.plotting import figure\n", "from bokeh.transform import transform, linear_cmap\n", "from bokeh.io import export_png\n", "output_notebook()" ] }, { "cell_type": "code", "execution_count": 143, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "
\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function embed_document(root) {\n", " \n", " var docs_json = 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(\"AUC\", \"(@ROC,@ROC_BRF)\"),\n", " (\"(x,y)\", \"(@kappa_init, @kappa_final)\"),\n", " ('desc', '@label'),\n", "])\n", "mapper = linear_cmap(field_name='ROC',palette=plasma(256), low=min(df.ROC), high=max(df.ROC))\n", "\n", "p = figure(plot_width=600, plot_height=400, tools=[hover], title=\"Kappas\")\n", "cp = p.circle('kappa_init', 'kappa_final', size=7, source=source, color=mapper, line_width=1, line_color='darkgray')\n", "p.line((0,1),(0,1))\n", "# fill_color=transform('y', mapper))\n", "p.xaxis.axis_label='Kappa(init)'\n", "p.yaxis.axis_label='Kappa(shifted)'\n", "color_bar = ColorBar(color_mapper=mapper['transform'], width=8, location=(0,0))\n", "\n", "p.add_layout(color_bar, 'right')\n", "\n", "#output_file('test.html')\n", "show(p)\n", "export_png(p,\"/tmp/p1.png\");" ] }, { "cell_type": "code", "execution_count": 145, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "
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Application\",\"version\":\"1.0.4\"}};\n", " var render_items = [{\"docid\":\"e479a052-3c80-4425-aec3-a76eb663c0d9\",\"roots\":{\"16351\":\"bd1add44-e830-4a0b-95e3-2b47349c40ca\"}}];\n", " root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", "\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " var attempts = 0;\n", " var timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " clearInterval(timer);\n", " }\n", " attempts++;\n", " if (attempts > 100) {\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " clearInterval(timer);\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "16351" } }, "output_type": "display_data" } ], "source": [ "\n", "source = ColumnDataSource(data=df)\n", "hover = HoverTool(tooltips=[\n", " (\"AUC\", \"(@ROC,@ROC_BRF)\"),\n", " (\"(x,y)\", \"(@kappa_final, @kappa_BRF)\"),\n", " ('desc', '@label'),\n", "])\n", "mapper = linear_cmap(field_name='ROC',palette=plasma(256), low=min(df.ROC), high=max(df.ROC))\n", "\n", "p = figure(plot_width=600, plot_height=400, tools=[hover], title=\"Kappas\")\n", "p.circle('kappa_final', 'kappa_BRF', size=7, source=source, color=mapper, line_width=1, line_color='darkgray')\n", "p.line((0,1),(0,1))\n", "# fill_color=transform('y', mapper))\n", "p.xaxis.axis_label='Kappa(shifted)'\n", "p.yaxis.axis_label='Kappa(BRF)'\n", "color_bar = ColorBar(color_mapper=mapper['transform'], width=8, location=(0,0))\n", "\n", "p.add_layout(color_bar, 'right')\n", "\n", "#output_file('test.html')\n", "export_png(p,\"/tmp/p2.png\");\n", "show(p)" ] }, { "cell_type": "code", "execution_count": 146, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "
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(\"AUC\", \"(@ROC,@ROC_BRF)\"),\n", " (\"(x,y)\", \"(@kappa_init, @kappa_BRF)\"),\n", " ('desc', '@label'),\n", "])\n", "mapper = linear_cmap(field_name='ROC',palette=plasma(256), low=min(df.ROC), high=max(df.ROC))\n", "\n", "p = figure(plot_width=600, plot_height=400, tools=[hover], title=\"Kappas\")\n", "p.circle('kappa_init', 'kappa_BRF', size=7, source=source, color=mapper, line_width=1, line_color='darkgray')\n", "p.line((0,1),(0,1))\n", "# fill_color=transform('y', mapper))\n", "p.xaxis.axis_label='Kappa(init)'\n", "p.yaxis.axis_label='Kappa(BRF)'\n", "color_bar = ColorBar(color_mapper=mapper['transform'], width=8, location=(0,0))\n", "\n", "p.add_layout(color_bar, 'right')\n", "\n", "#output_file('test.html')\n", "export_png(p,\"/tmp/p3.png\");\n", "\n", "show(p)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Look at the properties of the datasets" ] }, { "cell_type": "code", "execution_count": 115, "metadata": {}, "outputs": [], "source": [ "data_summary = []\n", "with open('../data/serotonin_data.pkl','rb') as inf:\n", " serotonin_d,assay_lookup = pickle.load(inf)\n", "tpls = sorted([(len(v),k) for k,v in serotonin_d.groupby('target_chembl_id').groups.items()],reverse=True)\n", "for v,k in tpls:\n", " if v<=900:\n", " continue\n", " assay = serotonin_d.loc[serotonin_d['target_chembl_id']==k]\n", " acts = assay.loc[assay['pchembl_value']>9.0]\n", " if len(acts)>=50:\n", " inacts = assay.loc[assay['pchembl_value']<8.5]\n", " else:\n", " # but relax that if we don't end up with a reasonable number of actives:\n", " acts = assay.loc[assay['pchembl_value']>8.0]\n", " inacts = assay.loc[assay['pchembl_value']<7.5]\n", " data_summary.append(['serotonin',k,len(acts),len(inacts)])\n", " \n", "with open('../data/pubchem_data.pkl','rb') as inf:\n", " pubchem_d,pubchem_assay_lookup = pickle.load(inf)\n", "\n", "tpls = sorted([(len(v),k) for k,v in pubchem_d.groupby('assay_chembl_id').groups.items()],reverse=True)\n", "for v,k in tpls:\n", " assay = pubchem_d.loc[pubchem_d['assay_chembl_id']==k]\n", " acts = pd.concat((assay.loc[assay['activity_comment'] == 'Active'], \n", " assay.loc[assay['activity_comment'] == 'active']))\n", " inacts = pd.concat((assay.loc[assay['activity_comment'] == 'inactive'],\n", " assay.loc[assay['activity_comment'] == 'inconclusive'], \n", " assay.loc[assay['activity_comment'] == 'Inconclusive'], \n", " assay.loc[assay['activity_comment'] == 'Not Active']))\n", " data_summary.append(['pubchem',k,len(acts),len(inacts)])\n", "\n", "with open('../data/drugmatrix_data.pkl','rb') as inf:\n", " drugmatrix_d,drugmatrix_assay_lookup = pickle.load(inf)\n", "tpls = sorted([(len(v),k) for k,v in drugmatrix_d.groupby('assay_chembl_id').groups.items()],reverse=True)\n", "for v,k in tpls:\n", " assay = drugmatrix_d.loc[drugmatrix_d['assay_chembl_id']==k]\n", " inact_indices = [x for x,y in enumerate(assay['activity_comment']) if y.find('Not Active')==0]\n", " act_indices = [x for x,y in enumerate(assay['activity_comment']) if y.find('Active')==0]\n", " if len(act_indices)<40:\n", " continue\n", " data_summary.append(['drugbank',k,len(act_indices),len(inact_indices)])\n", " \n", "data_summary = pd.DataFrame(data_summary,columns=['dataset','name','nActive','nInactive']) \n", "data_summary['nPts'] = data_summary.nActive+data_summary.nInactive\n", "data_summary['fracActive'] = data_summary.nActive/data_summary.nPts \n", "data_summary['label'] = [x+\"-\"+y for x,y in zip(data_summary.dataset,data_summary.name)]\n", "data_summary['index'] = [x+1 for x in range(len(data_summary))]" ] }, { "cell_type": "code", "execution_count": 116, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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nActivenInactivenPtsfracActiveindex
count58.00000058.00000058.00000058.00000058.000000
mean295.1896554582.9137934878.1034480.08521629.500000
std929.40208013246.33859013988.7050370.04263116.886879
min3.000000662.000000773.0000000.0004201.000000
25%53.250000768.000000842.0000000.05730415.250000
50%71.500000784.000000842.0000000.07765429.500000
75%103.750000802.000000842.0000000.10481043.750000
max5614.00000078690.00000083178.0000000.22343158.000000
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" ], "text/plain": [ " nActive nInactive nPts fracActive index\n", "count 58.000000 58.000000 58.000000 58.000000 58.000000\n", "mean 295.189655 4582.913793 4878.103448 0.085216 29.500000\n", "std 929.402080 13246.338590 13988.705037 0.042631 16.886879\n", "min 3.000000 662.000000 773.000000 0.000420 1.000000\n", "25% 53.250000 768.000000 842.000000 0.057304 15.250000\n", "50% 71.500000 784.000000 842.000000 0.077654 29.500000\n", "75% 103.750000 802.000000 842.000000 0.104810 43.750000\n", "max 5614.000000 78690.000000 83178.000000 0.223431 58.000000" ] }, "execution_count": 116, "metadata": {}, "output_type": "execute_result" } ], "source": [ "data_summary.describe()" ] }, { "cell_type": "code", "execution_count": 112, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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nActivenInactive...fracActiveindex
countmeanstdmin25%50%75%maxcountmean...75%maxcountmeanstdmin25%50%75%max
dataset
drugbank44.068.00000021.70092740.049.7564.580.00122.044.0774.000...0.0950120.14489344.036.512.84523315.025.7536.547.2558.0
pubchem8.01606.5000002173.7942473.0212.75736.51815.755614.08.027778.125...0.1301250.2043708.010.52.4494907.08.7510.512.2514.0
serotonin6.0212.833333118.29525271.0136.00212.0253.50404.06.01588.000...0.1551430.2234316.03.51.8708291.02.253.54.756.0
\n", "

3 rows × 32 columns

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" ], "text/plain": [ " nActive \\\n", " count mean std min 25% 50% 75% \n", "dataset \n", "drugbank 44.0 68.000000 21.700927 40.0 49.75 64.5 80.00 \n", "pubchem 8.0 1606.500000 2173.794247 3.0 212.75 736.5 1815.75 \n", "serotonin 6.0 212.833333 118.295252 71.0 136.00 212.0 253.50 \n", "\n", " nInactive ... fracActive index \\\n", " max count mean ... 75% max count mean \n", "dataset ... \n", "drugbank 122.0 44.0 774.000 ... 0.095012 0.144893 44.0 36.5 \n", "pubchem 5614.0 8.0 27778.125 ... 0.130125 0.204370 8.0 10.5 \n", "serotonin 404.0 6.0 1588.000 ... 0.155143 0.223431 6.0 3.5 \n", "\n", " \n", " std min 25% 50% 75% max \n", "dataset \n", "drugbank 12.845233 15.0 25.75 36.5 47.25 58.0 \n", "pubchem 2.449490 7.0 8.75 10.5 12.25 14.0 \n", "serotonin 1.870829 1.0 2.25 3.5 4.75 6.0 \n", "\n", "[3 rows x 32 columns]" ] }, "execution_count": 112, "metadata": {}, "output_type": "execute_result" } ], "source": [ "data_summary.groupby('dataset').describe()" ] }, { "cell_type": "code", "execution_count": 124, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "
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root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "8773" } }, "output_type": "display_data" } ], "source": [ "source = ColumnDataSource(data=data_summary)\n", "hover = HoverTool(tooltips=[\n", " (\"(nAct,nInact)\", \"(@nActive, @nInactive)\"),\n", " ('desc', '@label'),\n", "])\n", "\n", "p = figure(plot_width=600, plot_height=400, tools=[hover], title=\"fraction active\")\n", "p.line('index', 'fracActive', source=source)\n", "#p.line((0,1),(0,1))\n", "# fill_color=transform('y', mapper))\n", "#p.xaxis.axis_label=''\n", "p.yaxis.axis_label='frac_active'\n", "\n", "\n", "#output_file('test.html')\n", "show(p)" ] }, { "cell_type": "code", "execution_count": 120, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "
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@nInactive)\"],[\"desc\",\"@label\"]]},\"id\":\"8044\",\"type\":\"HoverTool\"},{\"attributes\":{},\"id\":\"8332\",\"type\":\"BasicTickFormatter\"},{\"attributes\":{},\"id\":\"8052\",\"type\":\"LogScale\"},{\"attributes\":{\"plot\":{\"id\":\"8046\",\"subtype\":\"Figure\",\"type\":\"Plot\"},\"ticker\":{\"id\":\"8057\",\"type\":\"LogTicker\"}},\"id\":\"8060\",\"type\":\"Grid\"},{\"attributes\":{\"ticker\":null},\"id\":\"8330\",\"type\":\"LogTickFormatter\"},{\"attributes\":{\"plot\":null,\"text\":\"fraction active\"},\"id\":\"8045\",\"type\":\"Title\"},{\"attributes\":{},\"id\":\"8054\",\"type\":\"LinearScale\"},{\"attributes\":{\"num_minor_ticks\":10},\"id\":\"8057\",\"type\":\"LogTicker\"},{\"attributes\":{\"axis_label\":\"dataset size\",\"formatter\":{\"id\":\"8330\",\"type\":\"LogTickFormatter\"},\"plot\":{\"id\":\"8046\",\"subtype\":\"Figure\",\"type\":\"Plot\"},\"ticker\":{\"id\":\"8057\",\"type\":\"LogTicker\"}},\"id\":\"8056\",\"type\":\"LogAxis\"}],\"root_ids\":[\"8046\"]},\"title\":\"Bokeh Application\",\"version\":\"1.0.4\"}};\n", " var render_items = [{\"docid\":\"43629058-aabe-47ba-8dce-ea294263b5a8\",\"roots\":{\"8046\":\"30462797-d14f-4633-b695-1a3eac21abae\"}}];\n", " root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n", "\n", " }\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " } else {\n", " var attempts = 0;\n", " var timer = setInterval(function(root) {\n", " if (root.Bokeh !== undefined) {\n", " embed_document(root);\n", " clearInterval(timer);\n", " }\n", " attempts++;\n", " if (attempts > 100) {\n", " console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n", " clearInterval(timer);\n", " }\n", " }, 10, root)\n", " }\n", "})(window);" ], "application/vnd.bokehjs_exec.v0+json": "" }, "metadata": { "application/vnd.bokehjs_exec.v0+json": { "id": "8046" } }, "output_type": "display_data" } ], "source": [ "source = ColumnDataSource(data=data_summary)\n", "hover = HoverTool(tooltips=[\n", " (\"(nAct,nInact)\", \"(@nActive, @nInactive)\"),\n", " ('desc', '@label'),\n", "])\n", "\n", "p = figure(plot_width=600, plot_height=400, tools=[hover], title=\"fraction active\", x_axis_type='log')\n", "p.circle('nPts', 'fracActive', size=7, source=source)\n", "#p.line((0,1),(0,1))\n", "# fill_color=transform('y', mapper))\n", "p.xaxis.axis_label='dataset size'\n", "p.yaxis.axis_label='frac_active'\n", "\n", "\n", "#output_file('test.html')\n", "show(p)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "_draft": { "nbviewer_url": "https://gist.github.com/c82465f2b8eabb9a13ab78e28bc3c275" }, "gist": { "data": { "description": "temp.ipynb", "public": true }, "id": "c82465f2b8eabb9a13ab78e28bc3c275" }, "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": "3.7.2" } }, "nbformat": 4, "nbformat_minor": 2 }