{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Growth vs. Yield" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Load a few packages." ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [], "source": [ "import pandas\n", "pandas.options.display.max_rows = 12\n", "from cameo import models, phenotypic_phase_plane" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Load a model _E. coli_ central carbon metabolism." ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": true }, "outputs": [], "source": [ "model = models.bigg.e_coli_core.copy()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Compute the phenotypic phase plane for growth and acetate secretion." ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": true }, "outputs": [], "source": [ "result = phenotypic_phase_plane(model,\n", " variables=[model.reactions.BIOMASS_Ecoli_core_w_GAM],\n", " objective=model.reactions.EX_ac_e)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Look at the result in a tabular view." ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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BIOMASS_Ecoli_core_w_GAMobjective_lower_boundobjective_upper_bound
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" ], "text/plain": [ " BIOMASS_Ecoli_core_w_GAM objective_lower_bound objective_upper_bound\n", "0 0.000000 0.0 2.000000e+01\n", "1 0.045996 0.0 1.930093e+01\n", "2 0.091992 0.0 1.860186e+01\n", "3 0.137988 0.0 1.790280e+01\n", "4 0.183983 0.0 1.720373e+01\n", "5 0.229979 0.0 1.650466e+01\n", ".. ... ... ...\n", "14 0.643942 0.0 9.619970e+00\n", "15 0.689938 0.0 7.906992e+00\n", "16 0.735934 0.0 6.021404e+00\n", "17 0.781930 0.0 4.014269e+00\n", "18 0.827926 0.0 2.007135e+00\n", "19 0.873922 0.0 -5.664869e-15\n", "\n", "[20 rows x 3 columns]" ] }, "execution_count": 23, "metadata": {}, "output_type": "execute_result" } ], "source": [ "result.data_frame" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Plot the phenotypic phase plane." ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "\n", "\n", "
\n", "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "result.plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We can also calculate a three dimensional phenotypic phase plane to compare the influence of aerobic and anaerobic environements." ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": true }, "outputs": [], "source": [ "result_3D = phenotypic_phase_plane(model, variables=[model.reactions.EX_ac_e, model.reactions.EX_o2_e], objective=model.reactions.BIOMASS_Ecoli_core_w_GAM, points=50)" ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ " EX_ac_e EX_o2_e objective_lower_bound objective_upper_bound\n", "0 0.0 -6.000000e+01 0.0 -4.842084e-17\n", "1 0.0 -5.877551e+01 0.0 2.801293e-02\n", "2 0.0 -5.755102e+01 0.0 5.602585e-02\n", "3 0.0 -5.632653e+01 0.0 8.403878e-02\n", "4 0.0 -5.510204e+01 0.0 1.120517e-01\n", "5 0.0 -5.387755e+01 0.0 1.400646e-01\n", "... ... ... ... ...\n", "2494 20.0 -6.122449e+00 0.0 0.000000e+00\n", "2495 20.0 -4.897959e+00 0.0 0.000000e+00\n", "2496 20.0 -3.673469e+00 0.0 0.000000e+00\n", "2497 20.0 -2.448980e+00 0.0 0.000000e+00\n", "2498 20.0 -1.224490e+00 0.0 0.000000e+00\n", "2499 20.0 -2.160206e-30 0.0 0.000000e+00\n", "\n", "[2500 rows x 4 columns]" ] }, "execution_count": 26, "metadata": {}, "output_type": "execute_result" } ], "source": [ "result_3D.data_frame" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Unfortunately, 3D plots are not yet supported out of the box." ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "Multi-dimensional plotting is not supported" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "result_3D.plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "So let's quickly write a custom plot (you can use your mouse to rotate the graphic)." ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%matplotlib notebook" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false }, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " this.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width);\n", " canvas.attr('height', height);\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('
')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('