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   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "# Heatmap Merged Across Transitions "
   ]
  },
  {
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   "id": "25f013fb-2a84-4c2e-8c9e-08b9aa8b7f19",
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   "source": [
    "    Input: :py:class:`~massdash.structs.FeatureMap`"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "460b7395-8ff7-41cf-92ee-68af77b10605",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "In this plot the signals from all transitions are merged into one heatmap."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5cd87246-e666-4ec1-8767-e2710f21dc98",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "By changing the `type_of_heatmap` in the <link PlotConfig, we can plot different axis against one another. "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "109a0b12-a22f-4b13-8923-08cdb7b8c0be",
   "metadata": {
    "editable": true,
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    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "Options are:\n",
    "\n",
    "1. m/z vs retention time\n",
    "2. m/z vs ion mobility\n",
    "3. retention time vs ion mobility"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "856cd75e-038e-458e-a0fc-b93b4083727a",
   "metadata": {
    "editable": true,
    "nbsphinx": "hidden",
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "%load_ext autoreload \n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c9a89257-de1d-42c4-bc47-089581152abb",
   "metadata": {
    "editable": true,
    "nbsphinx": "hidden",
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "# Please run this before executing any cell\n",
    "import os\n",
    "os.chdir(\"../../test/test_data/\") #### Insert path to data, this is the path to the tutorial data. "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a8a98079-d5f9-4411-8c55-d43b9a6225f5",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "## Load FeatureMap"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "366c87f2-5b42-4d81-be41-6d627cb1b399",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Initializing valid scores for selection\n",
      "[2024-10-10 08:35:00,700] MzMLDataAccess - INFO - Opening mzml/ionMobilityTest.mzML file...: Elapsed 0.0776510238647461 ms\n",
      "[2024-10-10 08:35:00,701] MzMLDataAccess - INFO - There are 50 spectra and 0 chromatograms.\n",
      "[2024-10-10 08:35:00,701] MzMLDataAccess - INFO - There are 25 MS1 spectra and 25 MS2 spectra.\n"
     ]
    }
   ],
   "source": [
    "from massdash.loaders import MzMLDataLoader\n",
    "from massdash.structs import TargetedDIAConfig\n",
    "\n",
    "# Initate TargetedDIAConfig and set parameters\n",
    "extraction_config = TargetedDIAConfig()\n",
    "extraction_config.im_window = 0.2\n",
    "extraction_config.rt_window = 50\n",
    "extraction_config.mz_tol = 20\n",
    "\n",
    "# Initiate loader object\n",
    "loader = MzMLDataLoader(dataFiles=\"mzml/ionMobilityTest.mzML\",\n",
    "                        rsltsFile=\"osw/ionMobilityTest.osw\")\n",
    "\n",
    "# fetch featureMap for target peptide\n",
    "featureMap = loader.loadFeatureMaps(\"AFVDFLSDEIK\", 2, extraction_config)['ionMobilityTest']"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5e9f35c0-eaf7-4173-b5f8-0ea94afddde1",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "## Plot Recipe"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "130f8c86-3dd0-4860-a13e-33539ea6c142",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "For demonstration purposes, `retention time vs ion mobility` is shown but this can be changes by changing to the other config.type_of_heatmap statements."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "a7bab367-86ad-4eb8-9f9f-e0b9b5383cb5",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "outputs": [
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Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    const el = document.getElementById(\"1049\");\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  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"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.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.3.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n          for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\nif (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      const cell = $(document.getElementById(\"1049\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
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       "\n",
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time (s)\",\"coordinates\":null,\"formatter\":{\"id\":\"1056\"},\"group\":null,\"major_label_policy\":{\"id\":\"1057\"},\"ticker\":{\"id\":\"1013\"}},\"id\":\"1012\",\"type\":\"LinearAxis\"},{\"attributes\":{\"overlay\":{\"id\":\"1026\"}},\"id\":\"1022\",\"type\":\"BoxZoomTool\"},{\"attributes\":{\"axis_label\":\"Ion mobility (1/K0)\",\"coordinates\":null,\"formatter\":{\"id\":\"1053\"},\"group\":null,\"major_label_policy\":{\"id\":\"1054\"},\"ticker\":{\"id\":\"1017\"}},\"id\":\"1016\",\"type\":\"LinearAxis\"},{\"attributes\":{\"axis\":{\"id\":\"1012\"},\"coordinates\":null,\"group\":null,\"ticker\":null,\"visible\":false},\"id\":\"1015\",\"type\":\"Grid\"}],\"root_ids\":[\"1003\"]},\"title\":\"Bokeh Application\",\"version\":\"2.4.3\"}};\n",
       "  const render_items = [{\"docid\":\"3d032944-a4fe-4f14-a3f9-1f693f2ce32b\",\"root_ids\":[\"1003\"],\"roots\":{\"1003\":\"96c3ce89-82cc-4a0b-8bc4-5191f9ba1d3d\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    let attempts = 0;\n",
       "    const timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        clearInterval(timer);\n",
       "        embed_document(root);\n",
       "      } else {\n",
       "        attempts++;\n",
       "        if (attempts > 100) {\n",
       "          clearInterval(timer);\n",
       "          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n",
       "        }\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "1003"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "from massdash.plotting import PlotConfig, InteractiveTwoDimensionPlotter\n",
    "\n",
    "config = PlotConfig()\n",
    "config.context = 'jupyter'\n",
    "config.include_ms1 = True\n",
    "config.include_ms2 = True\n",
    "config.aggregate_mslevels = True ## merges heatmaps\n",
    "\n",
    "\n",
    "#config.type_of_heatmap = 'm/z vs retention time'\n",
    "#config.type_of_heatmap = 'm/z vs ion mobility' \n",
    "config.type_of_heatmap = 'retention time vs ion mobility'\n",
    "\n",
    "plotter = InteractiveTwoDimensionPlotter(config)\n",
    "plotter.plot(featureMap)\n",
    "plotter.show()"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
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    "name": "ipython",
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