{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Cheetah data analysis report\n", "* Mass Spectrometry data analysis with TX-MS consists of analysing hrMS1, MS2, and DIA data.\n", "* We have structural analysis of the selected XLs here by using nglview.\n", "\n", "#### Authors: Hamed Khakzad, Lars Malmström\n", "* Institut of Computational Science (ICS) and S3IT, University of Zurich\n", "\n", "#### date: 15, January 2019\n", "* version: v0.1\n", "* XL selection and visualization, MS2 data representation.\n", "\n", "##### Inputs needed in the same directory: \n", "\n", "* 1- List of XLs with \"XL\" header\n", "* 2- PDB\n", "* 3- fasta\n", "* 4- ms2 data analysis output (sqlite table)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 1- XL selection and visualization" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "## import section\n", "import nglview as ng\n", "import plotly.plotly as py\n", "#import plotly.figure_factory as ff\n", "from plotly.offline import init_notebook_mode, iplot\n", "import pandas as pd\n", "import ipywidgets as widgets\n", "from ipywidgets import Layout, Button\n", "from string import digits\n", "import qgrid\n", "import sqlite3" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "## initialize section\n", "#init_notebook_mode(connected=True)\n", "\n", "initial_repr = [\n", " {\"type\": \"cartoon\", \"params\": {\n", " \"sele\": \"protein\", \"color\": \"sstruc\"\n", " }}\n", "]" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['-.DLANLTAELDKVK(11)--DEGKASSAK(4).-', '-.EDKQISDASR(3)--PLVEEPQNLIKQNCELFEQLGEYK(11).-', '-.QVEKDLANLTAELDK(4)--DEGKASSAK(4).-', '-.DLANLTAELDKVK(11)--KLVAASQAALG(1).-', '-.DLANLTAELDKVK(11)--KLVAASQAALG(1).-', '-.DLANLTAELDKVK(11)--KLVAASQAALG(1).-', '-.EQLAKQAENGDGNPR(5)--DEGKASSAK(4).-', '-.KQVEK(1)--FPKAEFAEVSK(3).-', '-.EQLAKQAEHK(5)--QNCELFEQLGEYKFQNALLVR(13).-', '-.EQLAKQAEHK(5)--DEGKASSAK(4).-', '-.EAKK(3)--QNCELFEQLGEYKFQNALLVR(13).-', '-.DLANLTAELDKVK(11)--QIKK(3).-', '-.EAKK(3)--QNCELFEQLGEYKFQNALLVR(13).-', '-.AKLEEEK(2)--QNCELFEQLGEYKFQNALLVR(13).-', '-.DLANLTAELDKVK(11)--QIKK(3).-', '-.QVEKALEEANSK(4)--ATKEQLK(3).-', '-.AKLEEEK(2)--QNCELFEQLGEYKFQNALLVR(13).-', '-.LEAEAKALK(6)--QIKK(3).-', '-.LEAEAKALK(6)--ATKEQLK(3).-', '-.EAKK(3)--KYLYEIAR(1).-', '-.VKEDK(2)--ETCFAEEGKK(9).-', '-.EDKQISDASR(3)--EFNAETFTFHADICTLSEKER(19).-', '-.EDKQISDASR(3)--ADDKETCFAEEGK(4).-', '-.EDKQISDASR(3)--ETCFAEEGKK(9).-', '-.LELDQLSSEKEQLTIEK(10)--NLGKVGSK(4).-', '-.EQLAKQAENGDGNPR(5)--VGSKCCK(4).-', '-.AELQAKLEAEAK(6)--QIKK(3).-', '-.VKEEK(2)--VTKCCTESLVNR(3).-', '-.EDKQISDASR(3)--QIKK(3).-', '-.AKLEEEK(2)--ADDKETCFAEEGK(4).-', '-.AKLEEEK(2)--ADDKETCFAEEGK(4).-', '-.AKLEEEK(2)--ADDKETCFAEEGK(4).-', '-.LEAEAKALK(6)--AACLLPKLDELR(7).-', '-.ALKEQLAK(3)--AACLLPKLDELR(7).-', '-.QVEKDLANLTAELDK(4)--YTKK(3).-', '-.QVEKDLANLTAELDK(4)--EQLKAVMDDFAAFVEK(4).-', '-.QVEKDLANLTAELDK(4)--ASSAKQR(5).-', '-.VKEDK(2)--AVMDDFAAFVEKCCK(12).-', '-.EAKK(3)--KLVAASQAALG(1).-', '-.AKLEEEK(2)--ADLAKYICENQDSISSK(5).-', '-.LEEEKQISDASR(5)--FPKAEFAEVSK(3).-', '-.EDKQISDASR(3)--NLGKVGSK(4).-', '-.QVEKDLANLTAELDK(4)--YTKK(3).-', '-.QVEKDLANLTAELDK(4)--EQLKAVMDDFAAFVEK(4).-', '-.EAKK(3)--KLVAASQAALG(1).-', '-.EAKK(3)--KLVAASQAALG(1).-', '-.LTEKEK(4)--ETCFAEEGKK(9).-', '-.ALKEQLAK(3)--ETCFAEEGKK(9).-', '-.EQLAKQAENGDGNPR(5)--EQLKAVMDDFAAFVEK(4).-', '-.ELEESKK(6)--KLVAASQAALG(1).-', '-.ALKEQLAK(3)--YKAAFTECCQAADK(2).-', '-.EQLAKQAEHK(5)--PEVDVMCTAFHDNEETFLKK(19).-', '-.EQLAKQAEHK(5)--YKAAFTECCQAADK(2).-', '-.EQLAKQAEHK(5)--AAFTECCQAADKAACLLPK(12).-', '-.EQLAKQAEHK(5)--QTALVELVKHK(9).-', '-.EQLAKQAEHK(5)--AVMDDFAAFVEKCCK(12).-', '-.EEKQISDASR(3)--PKATK(2).-', '-.QVEKDLANLTAELDK(4)--PLLEKSHCIAEVENDEMPADLPSLAADFVESK(5).-', '-.EDKQISDASR(3)--KQTALVELVK(1).-', '-.EAKK(3)--KLVAASQAALG(1).-', '-.VKEDK(2)--TYETTLEKCCAAADPHECYAK(8).-', '-.EQLTIEKAK(7)--KQTALVELVK(1).-', '-.EAKK(3)--KLVAASQAALG(1).-', '-.VKEEK(2)--AVMDDFAAFVEKCCK(12).-', '-.EEKQISDASR(3)--KQTALVELVK(1).-', '-.EEKQISDASR(3)--PKATK(2).-', '-.EEKQISDASR(3)--ETCFAEEGKK(9).-', '-.QVEKALEEANSK(4)--PKATK(2).-', '-.EQLTIEKAK(7)--KQTALVELVK(1).-', '-.AKLEEEK(2)--KVPQVSTPTLVEVSR(1).-', '-.EAKK(3)--KLVAASQAALG(1).-', '-.LEAEAKALK(6)--CCKADDK(3).-', '-.LEAEAKALK(6)--ADDKETCFAEEGK(4).-', '-.EQLAKQAENGDGNPR(5)--QTALVELVKHK(9).-', '-.EQLAKQAENGDGNPR(5)--CCKADDK(3).-', '-.EQLAKQAENGDGNPR(5)--CCKADDK(3).-', '-.EQLAKQAENGDGNPR(5)--CCKADDK(3).-', '-.EQLAKQAENGDGNPR(5)--ETCFAEEGKK(9).-', '-.EQLAKQAEHK(5)--MPCAEDYLSVVLNQLCVLHEKTPVSDR(21).-', '-.EQLAKQAEHK(5)--KQTALVELVK(1).-', '-.EQLAKQAEHK(5)--KLVAASQAALG(1).-', '-.KQVEK(1)--YTKK(3).-', '-.KQVEK(1)--KVPQVSTPTLVEVSR(1).-', '-.QVEKDLANLTAELDK(4)--ATKEQLK(3).-', '-.EEKQISDASR(3)--HKPK(2).-', '-.QVEKDLANLTAELDK(4)--NLGKVGSK(4).-', '-.EAKK(3)--DEGKASSAK(4).-', '-.EAKK(3)--YICENQDSISSKLK(12).-', '-.KQVEK(1)--KYLYEIAR(1).-', '-.KQVEK(1)--LKECCEK(2).-', '-.QVEKDLANLTAELDK(4)--NLGKVGSK(4).-', '-.QVEKDLANLTAELDK(4)--VGSKCCK(4).-', '-.VKEDK(2)--AACLLPKLDELR(7).-', '-.EDKQISDASR(3)--QNCELFEQLGEYKFQNALLVR(13).-', '-.EDKQISDASR(3)--QIKK(3).-', '-.KQVEK(1)--ETCFAEEGKK(9).-', '-.EQLTIEKAK(7)--ADDKETCFAEEGK(4).-', '-.LEEEKQISDASR(5)--KVPQVSTPTLVEVSR(1).-', '-.LEEEKQISDASR(5)--QTALVELVKHK(9).-', '-.LEEEKQISDASR(5)--PKATK(2).-', '-.KQVEK(1)--YTKK(3).-', '-.KQVEK(1)--KVPQVSTPTLVEVSR(1).-', '-.QVEKDLANLTAELDK(4)--VFDEFKPLVEEPQNLIK(6).-', '-.QVEKDLANLTAELDK(4)--NLGKVGSK(4).-', '-.QVEKDLANLTAELDK(4)--VGSKCCK(4).-', '-.QVEKDLANLTAELDK(4)--ATKEQLK(3).-', '-.VKEDK(2)--HPEAKR(5).-', '-.VKEDK(2)--HPEAKR(5).-', '-.LEEEKQISDASR(5)--YTKK(3).-', '-.KQVEK(1)--ETCFAEEGKK(9).-', '-.EEKQISDASR(3)--HKPK(2).-', '-.EEKQISDASR(3)--ATKEQLK(3).-', '-.KQVEK(1)--YTKK(3).-', '-.KQVEK(1)--KVPQVSTPTLVEVSR(1).-', '-.LELDQLSSEKEQLTIEK(10)--EFNAETFTFHADICTLSEKER(19).-', '-.EQLTIEKAK(7)--NLGKVGSK(4).-', '-.EQLTIEKAK(7)--NLGKVGSK(4).-', '-.EQLTIEKAK(7)--ADDKETCFAEEGK(4).-', '-.LEEEKQISDASR(5)--YTKK(3).-', '-.LEEEKQISDASR(5)--KVPQVSTPTLVEVSR(1).-', '-.LEEEKQISDASR(5)--QTALVELVKHK(9).-', '-.LEEEKQISDASR(5)--PKATK(2).-']\n" ] } ], "source": [ "## MS2 SQLite table should be ready in the same directory\n", "ms2_table = \"MS2_results.db\"\n", "conn0 = sqlite3.connect(ms2_table)\n", "c0 = conn0.cursor()\n", "c0.execute(\"SELECT * from MS2Data ORDER BY count desc\")\n", "table0 = c0.fetchall()\n", "\n", "ms2_xl_list = []\n", "for row in table0:\n", " ms2_xl_list.append(str(row[0]))\n", "print (ms2_xl_list)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "## All inputs here\n", "filename = \"LR_models/lr_model_2_0.pdb\"\n", "top_XL_file = filename[:-5]+\"XLs.txt\"\n", "with open (top_XL_file,'r') as ms1_file:\n", " ms1_xl = ms1_file.read().splitlines()\n", "\n", "top_XL_list = list(set(ms2_xl_list).intersection(ms1_xl))\n", "\n", "df = df = pd.DataFrame({'col':top_XL_list})\n", "\n", "seq_file1 = \"m1.txt\"\n", "seq_file2 = \"alb.txt\"" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "scrolled": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/usr/local/lib/python3.5/dist-packages/pandas/core/computation/check.py:17: UserWarning:\n", "\n", "The installed version of numexpr 2.4.3 is not supported in pandas and will be not be used\n", "The minimum supported version is 2.4.6\n", "\n", "\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "70b4c99cb3604d0cacafc0ef50e37533", "version_major": 2, "version_minor": 0 }, "text/plain": [ "A Jupyter Widget" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "#qgrid.enable()\n", "qgrid_widget = qgrid.QgridWidget(df=df, show_toolbar=True)\n", "qgrid_widget" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['-.VKEDK(2)--AACLLPKLDELR(7).-', '-.QVEKDLANLTAELDK(4)--VGSKCCK(4).-', '-.EDKQISDASR(3)--NLGKVGSK(4).-', '-.EDKQISDASR(3)--QIKK(3).-', '-.KQVEK(1)--KYLYEIAR(1).-', '-.EDKQISDASR(3)--KQTALVELVK(1).-', '-.EDKQISDASR(3)--ETCFAEEGKK(9).-', '-.KQVEK(1)--ETCFAEEGKK(9).-', '-.EAKK(3)--DEGKASSAK(4).-', '-.EDKQISDASR(3)--ADDKETCFAEEGK(4).-', '-.EAKK(3)--KYLYEIAR(1).-', '-.DLANLTAELDKVK(11)--QIKK(3).-', '-.VKEDK(2)--AVMDDFAAFVEKCCK(12).-', '-.EAKK(3)--YICENQDSISSKLK(12).-', '-.QVEKDLANLTAELDK(4)--ASSAKQR(5).-', '-.DLANLTAELDKVK(11)--DEGKASSAK(4).-', '-.VKEDK(2)--ETCFAEEGKK(9).-', '-.EDKQISDASR(3)--QNCELFEQLGEYKFQNALLVR(13).-', '-.EAKK(3)--KLVAASQAALG(1).-', '-.QVEKDLANLTAELDK(4)--DEGKASSAK(4).-', '-.EDKQISDASR(3)--EFNAETFTFHADICTLSEKER(19).-', '-.DLANLTAELDKVK(11)--KLVAASQAALG(1).-', '-.AKLEEEK(2)--ADLAKYICENQDSISSK(5).-', '-.EAKK(3)--QNCELFEQLGEYKFQNALLVR(13).-', '-.KQVEK(1)--LKECCEK(2).-', '-.QVEKDLANLTAELDK(4)--PLLEKSHCIAEVENDEMPADLPSLAADFVESK(5).-', '-.KQVEK(1)--FPKAEFAEVSK(3).-', '-.LEEEKQISDASR(5)--FPKAEFAEVSK(3).-', '-.QVEKDLANLTAELDK(4)--NLGKVGSK(4).-']\n" ] } ], "source": [ "tmp_list = []\n", "x = qgrid_widget._df.values\n", "for item in x:\n", " tmp_list.append(item[1])\n", "\n", "with open(seq_file1,'r') as seqfile1:\n", " sequence1 = seqfile1.read()\n", "\n", "with open(seq_file2,'r') as seqfile2:\n", " sequence2 = seqfile2.read()\n", "\n", "sequence = sequence1 + sequence2 \n", "\n", "selected_XL = tmp_list\n", "print (selected_XL)" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "cb069496446d4009b167a4cc64bde9b7", "version_major": 2, "version_minor": 0 }, "text/plain": [ "A Jupyter Widget" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "view = ng.NGLWidget(representation=initial_repr)\n", "view.add_component(filename)\n", "\n", "for num_xl,xl in enumerate(selected_XL):\n", " temp = []\n", " temp1 = []\n", " temp2 = []\n", " #print num_xl, xl\n", "\n", " K_pos_P1 = 0\n", " K_pos_P2 = 0\n", "\n", " xl_without_digit = ''.join([i for i in xl if not i.isdigit()])\n", " # xl_without_digit = xl.translate(None, digits) (python 2)\n", " peptide1 = xl_without_digit.split('--')[0].replace(\"-\",\"\").replace(\".\",\"\")[:-2]\n", " peptide2 = xl_without_digit.split('--')[1].replace(\"-\",\"\")[:-3]\n", "\n", " # print (peptide1)\n", " # print (peptide2)\n", " \n", " K_pos_P1 = peptide1.find('K')\n", " K_pos_P2 = peptide2.find('K')\n", " \n", " seq_pos_p1_k = sequence.find(peptide1) + K_pos_P1\n", " seq_pos_p2_k = sequence.find(peptide2) + K_pos_P2\n", " #print seq_pos_p1_k, seq_pos_p2_k\n", " \n", " position_1 = str(seq_pos_p1_k) + \".CA\"\n", " position_2 = str(seq_pos_p2_k) + \".CA\"\n", " \n", " view.add_surface(position_1,opacity=0.7, color=\"red\")\n", " view.add_surface(position_2,opacity=0.7, color=\"blue\")\n", " \n", " view.add_representation( \"label\", position_1, color=\"black\" )\n", " view.add_representation( \"label\", position_2, color=\"black\" )\n", " \n", " view.add_representation(\"distance\", selection= 'all', atomPair= [ [ position_1, position_2 ] ], color= \"black\", labelColor= \"black\")\n", "\n", "view" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 2- MS2 data analysis and visualization" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "xl = selected_XL[0]\n", "\n", "## MS2 SQLite table should be ready in the same directory\n", "ms2_table = \"MS2_results.db\"\n", "conn0 = sqlite3.connect(ms2_table)\n", "c0 = conn0.cursor()\n", "c0.execute(\"SELECT * from MS2Data where XL='\"+xl+\"' ORDER BY count desc\")\n", "table0 = c0.fetchall()\n", "\n", "#print table0\n", "\n", "if table0 == []:\n", " print (\"XL is not in the table!\")\n", "else:\n", " main_spectra = [float(i) for i in table0[0][12].strip('{}').split(',')]\n", " main_intensity = [float(i) for i in table0[0][13].strip('{}').split(',')]\n", " covered_Frags = [str(i) for i in table0[0][9].strip('{}').split(',')]\n", " covered_mz = [float(i) for i in table0[0][10].strip('{}').split(',')]\n", " covered_int = [float(i) for i in table0[0][11].strip('{}').split(',')]\n", " #peptide1 = 0\n", " #peptide2 = 0\n", " num_mgf = table0[0][2]\n", " delta = table0[0][4]\n" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "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 = $('