notebooks/xx_graphic_abstract.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Summary\n",
    "\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import random\n",
    "from pathlib import Path\n",
    "\n",
    "import matplotlib as mpl\n",
    "import matplotlib.patches as patches\n",
    "import matplotlib.pyplot as plt\n",
    "import networkx as nx\n",
    "import numpy as np\n",
    "from IPython.display import SVG, set_matplotlib_formats"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "set_matplotlib_formats(\"svg\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "NOTEBOOK_DIR = Path(\"xx_graphic_abstract\")\n",
    "NOTEBOOK_DIR.mkdir(exist_ok=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
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       "      <text id=\"text9507-2-7-3-2-3-7\" style=\"font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.38666677px;line-height:0%;font-family:Arial;-inkscape-font-specification:'Arial, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.28222224px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\" x=\"120.64966\" xml:space=\"preserve\" y=\"330.5365\"><tspan id=\"tspan9609-4\" sodipodi:role=\"line\" style=\"font-size:4.93888903px;line-height:0.5;stroke-width:0.28222224px\" x=\"120.64966\" y=\"330.5365\">V</tspan></text>\n",
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       "      <text id=\"text9507-1-1-7-3-2\" style=\"font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.38666677px;line-height:0%;font-family:Arial;-inkscape-font-specification:'Arial, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;display:inline;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.28222224px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\" x=\"109.18744\" xml:space=\"preserve\" y=\"367.52774\"><tspan id=\"tspan12604\" sodipodi:role=\"line\" style=\"font-size:4.93888903px;line-height:0.5;stroke-width:0.28222224px\" x=\"109.18744\" y=\"367.52774\">F</tspan></text>\n",
       "      <text id=\"text9507-1-1-7-3-2-6\" style=\"font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.38666677px;line-height:0%;font-family:Arial;-inkscape-font-specification:'Arial, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;display:inline;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.28222224px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\" x=\"118.5099\" xml:space=\"preserve\" y=\"370.71286\"><tspan id=\"tspan12624\" sodipodi:role=\"line\" style=\"font-size:4.93888903px;line-height:0.5;stroke-width:0.28222224px\" x=\"118.5099\" y=\"370.71286\">W</tspan></text>\n",
       "      <text id=\"text9507-1-1-7-3-2-6-7\" style=\"font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.38666677px;line-height:0%;font-family:Arial;-inkscape-font-specification:'Arial, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;display:inline;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.28222224px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\" x=\"118.01628\" xml:space=\"preserve\" y=\"340.31348\"><tspan id=\"tspan12644\" sodipodi:role=\"line\" style=\"font-size:4.93888903px;line-height:0.5;stroke-width:0.28222224px\" x=\"118.01628\" y=\"340.31348\">E</tspan></text>\n",
       "      <text id=\"text9507-1-1-7-3-2-6-7-9\" style=\"font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.38666677px;line-height:0%;font-family:Arial;-inkscape-font-specification:'Arial, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;display:inline;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.28222224px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\" x=\"127.91268\" xml:space=\"preserve\" y=\"323.46078\"><tspan id=\"tspan12644-2\" sodipodi:role=\"line\" style=\"font-size:4.93888903px;line-height:0.5;stroke-width:0.28222224px\" x=\"127.91268\" y=\"323.46078\">E</tspan></text>\n",
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       "<IPython.core.display.SVG object>"
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     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "SVG(\"../docs/images/static/introduction/csps-protein-design.svg\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "25\n"
     ]
    }
   ],
   "source": [
    "labels = [\n",
    "    \"A\",\n",
    "    \"P\",\n",
    "    \"G\",\n",
    "    \"N\",\n",
    "    \"A\",\n",
    "    \"Q\",\n",
    "    \"E\",\n",
    "    \"V\",\n",
    "    \"D\",\n",
    "    \"S\",\n",
    "    \"H\",\n",
    "    \"Y\",\n",
    "    \"L\",\n",
    "    \"K\",\n",
    "    \"E\",\n",
    "    \"V\",\n",
    "    \"E\",\n",
    "    \"I\",\n",
    "    \"R\",\n",
    "    \"A\",\n",
    "    \"W\",\n",
    "    \"F\",\n",
    "    \"S\",\n",
    "    \"N\",\n",
    "    \"T\"\n",
    "]\n",
    "print(len(labels))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "G = nx.Graph()\n",
    "G.add_nodes_from(range(25))\n",
    "assert G.number_of_nodes() == 25"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "edges_sequential = np.c_[\n",
    "    list(range(G.number_of_nodes() - 1)), list(range(1, G.number_of_nodes()))\n",
    "].tolist()\n",
    "edges_contacts = [\n",
    "    [22, 0],\n",
    "    [0, 21],\n",
    "    [21, 2],\n",
    "    [2, 20],\n",
    "    [19, 7],\n",
    "    [8, 18],\n",
    "    [10, 18],\n",
    "    [16, 14],\n",
    "    [11, 16],\n",
    "    [16, 20],\n",
    "    [16, 23],\n",
    "    [21, 17],\n",
    "]\n",
    "G.add_edges_from(edges_sequential)\n",
    "G.add_edges_from(edges_contacts)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "angles = [\n",
    "    -20,\n",
    "    -5,\n",
    "    -20,\n",
    "    -25,\n",
    "    -30,\n",
    "    60,\n",
    "    60,\n",
    "    60,\n",
    "    80,\n",
    "    100,\n",
    "    100,\n",
    "    100,\n",
    "    160,\n",
    "    160,\n",
    "    -150,\n",
    "    -90,\n",
    "    -45,\n",
    "    -70,\n",
    "    -90,\n",
    "    -160,\n",
    "    160,\n",
    "    110,\n",
    "    110,\n",
    "    140,\n",
    "]\n",
    "labels = {i: l for i, l in enumerate(labels)}\n",
    "assert len(angles) == G.number_of_nodes() - 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "starting_pos = [0, 2]\n",
    "length = 1\n",
    "\n",
    "positions = [starting_pos]\n",
    "for angle in angles:\n",
    "    dx = np.cos(np.deg2rad(angle)) * length\n",
    "    dy = np.sin(np.deg2rad(angle)) * length\n",
    "    new_pos = [positions[-1][0] + dx, positions[-1][1] + dy]\n",
    "    positions.append(new_pos)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "color_given = \"#3d89ffff\"\n",
    "color_pred = \"#1cff56ff\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
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   "source": [
    "fg, ax = plt.subplots(figsize=(6, 6))\n",
    "ax.axis(\"off\")\n",
    "nx.draw_networkx_nodes(\n",
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    "nx.draw_networkx_edges(\n",
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    "\n",
    "fg.subplots_adjust(0.005, 0.005, 0.995, 0.995)\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"protein-csp-empty.svg\"), transparent=True)\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"protein-csp-empty.pdf\"))\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"protein-csp-empty.png\"), dpi=300)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
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       "      <use xlink:href=\"#DejaVuSans-84\"/>\n",
       "     </g>\n",
       "    </g>\n",
       "   </g>\n",
       "  </g>\n",
       " </g>\n",
       " <defs>\n",
       "  <clipPath id=\"p2b7e0223e9\">\n",
       "   <rect height=\"427.68\" width=\"427.68\" x=\"7.2\" y=\"7.2\"/>\n",
       "  </clipPath>\n",
       " </defs>\n",
       "</svg>\n"
      ],
      "text/plain": [
       "<Figure size 432x432 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "fg, ax = plt.subplots(figsize=(6, 6))\n",
    "ax.axis(\"off\")\n",
    "nx.draw_networkx_nodes(\n",
    "    G,\n",
    "    pos=positions,\n",
    "    node_size=800,\n",
    "    with_labels=True,\n",
    "    #     node_color=\"#3d89ffff\",\n",
    "    node_color=color_pred,\n",
    "    edgecolors=\"k\",\n",
    "    linewidths=1.5,\n",
    "    ax=ax,\n",
    ")\n",
    "nx.draw_networkx_edges(G, pos=positions, edgelist=edges_sequential, width=2)\n",
    "nx.draw_networkx_edges(\n",
    "    G.to_directed(),\n",
    "    pos=positions,\n",
    "    edgelist=edges_contacts,\n",
    "    #     edgelist=edges_contacts + [[e[1], e[0]] for e in edges_contacts],\n",
    "    arrowstyle=\"<|-|>\",\n",
    "    edge_color=\"#3d89ffff\",\n",
    "    width=2,\n",
    "    style=\"dashed\",\n",
    "    linestyle=\"\",\n",
    "    arrowsize=15,\n",
    "    node_size=1000,\n",
    "    min_source_margin=16,\n",
    "    connectionstyle=\"arc3,rad=0.1\",\n",
    ")\n",
    "nx.draw_networkx_labels(G, pos=positions, labels=labels, font_size=18, verticalalignment=\"center\")\n",
    "\n",
    "fg.subplots_adjust(0.005, 0.005, 0.995, 0.995)\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"protein-csp-filled.svg\"), transparent=True)\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"protein-csp-filled.pdf\"))\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"protein-csp-filled.png\"), dpi=300)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "        <text id=\"text9507-2-7-3-2-3-1-8\" style=\"font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.38666677px;line-height:0%;font-family:Arial;-inkscape-font-specification:'Arial, Normal';text-align:start;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.28222224px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\" x=\"32.440266\" xml:space=\"preserve\" y=\"330.21552\"><tspan id=\"tspan9649\" sodipodi:role=\"line\" style=\"font-size:4.93888903px;line-height:0.5;stroke-width:0.28222224px\" x=\"32.440266\" y=\"330.21552\">L</tspan></text>\n",
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       "<IPython.core.display.SVG object>"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "SVG(\"../docs/images/static/introduction/csps-protein-design.svg\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "def draw_networkx_nodes_ellipses(\n",
    "    G,\n",
    "    pos,\n",
    "    nodelist=None,\n",
    "    node_height=1,\n",
    "    node_width=2,\n",
    "    node_angle=0,\n",
    "    node_color=\"r\",\n",
    "    node_shape=\"o\",\n",
    "    alpha=1.0,\n",
    "    cmap=None,\n",
    "    vmin=None,\n",
    "    vmax=None,\n",
    "    ax=None,\n",
    "    linewidths=None,\n",
    "    label=None,\n",
    "    **kwargs\n",
    "):\n",
    "    \"\"\"Draw the nodes of the graph G.\n",
    "\n",
    "    This draws only the nodes of the graph G.\n",
    "\n",
    "    Parameters\n",
    "    ----------\n",
    "    G : graph\n",
    "       A networkx graph\n",
    "\n",
    "    pos : dictionary\n",
    "       A dictionary with nodes as keys and positions as values.\n",
    "       Positions should be sequences of length 2.\n",
    "\n",
    "    ax : Matplotlib Axes object, optional\n",
    "       Draw the graph in the specified Matplotlib axes.\n",
    "\n",
    "    nodelist : list, optional\n",
    "       Draw only specified nodes (default G.nodes())\n",
    "\n",
    "    node_height : scalar or array\n",
    "       Height of ellipse nodes (default=300).  If an array is specified it must be the\n",
    "       same length as nodelist.\n",
    "       \n",
    "    node_width : scalar or array\n",
    "       Width of ellipse nodes (default=300).  If an array is specified it must be the\n",
    "       same length as nodelist.\n",
    "       \n",
    "    node_width : scalar or array\n",
    "       Angle of major axis of ellipse nodes (default=300).  If an array is specified it must be the\n",
    "       same length as nodelist.\n",
    "       \n",
    "    node_color : color string, or array of floats\n",
    "       Node color. Can be a single color format string (default='r'),\n",
    "       or a  sequence of colors with the same length as nodelist.\n",
    "       If numeric values are specified they will be mapped to\n",
    "       colors using the cmap and vmin,vmax parameters.  See\n",
    "       matplotlib.scatter for more details.\n",
    "\n",
    "    node_shape :  string\n",
    "       The shape of the node.  Specification is as matplotlib.scatter\n",
    "       marker, one of 'so^>v<dph8' (default='o').\n",
    "\n",
    "    alpha : float\n",
    "       The node transparency (default=1.0)\n",
    "\n",
    "    cmap : Matplotlib colormap\n",
    "       Colormap for mapping intensities of nodes (default=None)\n",
    "\n",
    "    vmin,vmax : floats\n",
    "       Minimum and maximum for node colormap scaling (default=None)\n",
    "\n",
    "    linewidths : [None | scalar | sequence]\n",
    "       Line width of symbol border (default =1.0)\n",
    "\n",
    "    label : [None| string]\n",
    "       Label for legend\n",
    "\n",
    "    Returns\n",
    "    -------\n",
    "    matplotlib.collections.EllipseCollection\n",
    "        `EllipseCollection` of the nodes.\n",
    "    \"\"\"\n",
    "\n",
    "    import collections\n",
    "\n",
    "    try:\n",
    "        import numpy\n",
    "        import matplotlib.pyplot as plt\n",
    "        import matplotlib as mpl\n",
    "\n",
    "    except ImportError:\n",
    "        raise ImportError(\"Matplotlib required for draw()\")\n",
    "    except RuntimeError:\n",
    "        print(\"Matplotlib unable to open display\")\n",
    "        raise\n",
    "\n",
    "    if ax is None:\n",
    "        ax = plt.gca()\n",
    "\n",
    "    if nodelist is None:\n",
    "        nodelist = list(G)\n",
    "\n",
    "    if not nodelist or len(nodelist) == 0:  # empty nodelist, no drawing\n",
    "        return None\n",
    "\n",
    "    try:\n",
    "        xy = numpy.asarray([pos[v] for v in nodelist])\n",
    "    except KeyError as e:\n",
    "        raise nx.NetworkXError(\"Node %s has no position.\" % e)\n",
    "    except ValueError:\n",
    "        raise nx.NetworkXError(\"Bad value in node positions.\")\n",
    "\n",
    "    if isinstance(alpha, collections.Iterable):\n",
    "        node_color = apply_alpha(node_color, alpha, nodelist, cmap, vmin, vmax)\n",
    "        alpha = None\n",
    "\n",
    "    if cmap is not None:\n",
    "        cm = mpl.cm.get_cmap(cmap)\n",
    "        norm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)\n",
    "    else:\n",
    "        cm = None\n",
    "        norm = None\n",
    "\n",
    "    node_collection = mpl.collections.EllipseCollection(\n",
    "        widths=node_width,\n",
    "        heights=node_height,\n",
    "        angles=-45,\n",
    "        offsets=np.array(xy),\n",
    "        cmap=cm,\n",
    "        norm=norm,\n",
    "        transOffset=ax.transData,\n",
    "        linewidths=linewidths,\n",
    "        **kwargs,\n",
    "    )\n",
    "\n",
    "#     node_collection.set_color(node_color)\n",
    "    node_collection.set_label(label)\n",
    "    node_collection.set_zorder(1)\n",
    "    ax.add_collection(node_collection)\n",
    "\n",
    "    return node_collection"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.5235987755982988"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "angle = np.pi / 6\n",
    "angle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "ename": "ValueError",
     "evalue": "'tab20b<' is not a valid value for name; supported values are 'Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap', 'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r', 'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn', 'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2', 'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r', 'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2', 'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r', 'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r', 'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg', 'brg_r', 'bwr', 'bwr_r', 'cividis', 'cividis_r', 'cool', 'cool_r', 'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix', 'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r', 'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar', 'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern', 'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2', 'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv', 'hsv_r', 'inferno', 'inferno_r', 'jet', 'jet_r', 'magma', 'magma_r', 'nipy_spectral', 'nipy_spectral_r', 'ocean', 'ocean_r', 'pink', 'pink_r', 'plasma', 'plasma_r', 'prism', 'prism_r', 'rainbow', 'rainbow_r', 'seismic', 'seismic_r', 'spring', 'spring_r', 'summer', 'summer_r', 'tab10', 'tab10_r', 'tab20', 'tab20_r', 'tab20b', 'tab20b_r', 'tab20c', 'tab20c_r', 'terrain', 'terrain_r', 'twilight', 'twilight_r', 'twilight_shifted', 'twilight_shifted_r', 'viridis', 'viridis_r', 'winter', 'winter_r'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-19-0d60387c4295>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mcmap\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mplt\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_cmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'tab20b<'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/conda/envs/default/lib/python3.7/site-packages/matplotlib/cm.py\u001b[0m in \u001b[0;36mget_cmap\u001b[0;34m(name, lut)\u001b[0m\n\u001b[1;32m    132\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcolors\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mColormap\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    133\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 134\u001b[0;31m     \u001b[0mcbook\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_check_in_list\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msorted\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcmap_d\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    135\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mlut\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    136\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mcmap_d\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/conda/envs/default/lib/python3.7/site-packages/matplotlib/cbook/__init__.py\u001b[0m in \u001b[0;36m_check_in_list\u001b[0;34m(_values, **kwargs)\u001b[0m\n\u001b[1;32m   2143\u001b[0m             raise ValueError(\n\u001b[1;32m   2144\u001b[0m                 \u001b[0;34m\"{!r} is not a valid value for {}; supported values are {}\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2145\u001b[0;31m                 .format(v, k, ', '.join(map(repr, values))))\n\u001b[0m\u001b[1;32m   2146\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   2147\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mValueError\u001b[0m: 'tab20b<' is not a valid value for name; supported values are 'Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap', 'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r', 'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn', 'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2', 'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r', 'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2', 'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r', 'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r', 'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg', 'brg_r', 'bwr', 'bwr_r', 'cividis', 'cividis_r', 'cool', 'cool_r', 'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix', 'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r', 'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar', 'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern', 'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2', 'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv', 'hsv_r', 'inferno', 'inferno_r', 'jet', 'jet_r', 'magma', 'magma_r', 'nipy_spectral', 'nipy_spectral_r', 'ocean', 'ocean_r', 'pink', 'pink_r', 'plasma', 'plasma_r', 'prism', 'prism_r', 'rainbow', 'rainbow_r', 'seismic', 'seismic_r', 'spring', 'spring_r', 'summer', 'summer_r', 'tab10', 'tab10_r', 'tab20', 'tab20_r', 'tab20b', 'tab20b_r', 'tab20c', 'tab20c_r', 'terrain', 'terrain_r', 'twilight', 'twilight_r', 'twilight_shifted', 'twilight_shifted_r', 'viridis', 'viridis_r', 'winter', 'winter_r'"
     ]
    }
   ],
   "source": [
    "cmap = plt.get_cmap('tab20b<')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
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       "<Figure size 216x432 with 1 Axes>"
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   "source": [
    "def standardize(a):\n",
    "    a = a - a.min()\n",
    "    a = a / (a.max() - a.min())\n",
    "    return a\n",
    "\n",
    "\n",
    "def add_padding(a, padding):\n",
    "    range_ = a.max() - a.min()\n",
    "    a = padding + a / range_ * (range_ - padding * 2)\n",
    "    return a\n",
    "\n",
    "\n",
    "def adjust_y_corrd(x, y, angle):\n",
    "    return y + x / np.cos(angle) * np.sin(angle)\n",
    "\n",
    "\n",
    "def adjust_pos(pos, scalex, padding):\n",
    "    x = np.array([v[0] for v in pos.values()])\n",
    "    y = np.array([v[1] for v in pos.values()])\n",
    "    # Put x and y in the 0 to 1 range\n",
    "    x = standardize(x)\n",
    "    y = standardize(y)\n",
    "    #\n",
    "    x = add_padding(x, padding[0])\n",
    "    y = add_padding(y, padding[1])\n",
    "    #\n",
    "    x *= scalex\n",
    "    #\n",
    "    y = adjust_y_corrd(x, y, angle)\n",
    "    #\n",
    "    pos = {k: np.array([x[i], y[i]]) for i, k in enumerate(pos)}\n",
    "    return pos\n",
    "\n",
    "\n",
    "def add_hex_edges(x, y, eps):\n",
    "    x_new = [x[0], x[1], x[1] + eps, x[2] - eps, x[2], x[3], x[3] - eps, x[0] + eps]\n",
    "    y_new = [y[0] + eps, y[1] - eps, y[1], y[2], y[2] - eps, y[3] + eps, y[3], y[0]]\n",
    "    return np.array(x_new), np.array(y_new)\n",
    "\n",
    "\n",
    "cmap = plt.cm.get_cmap(\"tab20c\")\n",
    "\n",
    "scalex = 0.5\n",
    "node_size = 125\n",
    "eps = 0.02\n",
    "\n",
    "x = np.array([0.0, 0.0, 1.0, 1.0]) * scalex\n",
    "y = np.array([0.0, 1.0, 1.0, 0.0])\n",
    "x, y = add_hex_edges(x, y, eps=eps)\n",
    "y = adjust_y_corrd(x, y, angle)\n",
    "\n",
    "pos = np.array(positions)\n",
    "pos = pos - pos.min()\n",
    "node_size = node_size / (pos.max() - pos.min())\n",
    "pos = pos / (pos.max() - pos.min())\n",
    "pos = {i: pos[i] for i in range(len(pos))}\n",
    "pos = adjust_pos(pos, x.max(), padding=(0.1, 0.07))\n",
    "\n",
    "fg, ax = plt.subplots(figsize=(3, 6))\n",
    "\n",
    "ax.add_patch(\n",
    "    patches.Polygon(\n",
    "        xy=list(zip(x, y)),\n",
    "        fill=True,\n",
    "        alpha=0.5,\n",
    "        linewidth=1,\n",
    "                facecolor=cmap(15),\n",
    "#         facecolor=\"lightgrey\",\n",
    "        edgecolor=\"k\",\n",
    "        joinstyle=\"round\",\n",
    "        zorder=0,\n",
    "    )\n",
    ")\n",
    "draw_networkx_nodes_ellipses(\n",
    "    G,\n",
    "    pos,\n",
    "    cmap=cmap,\n",
    "    node_width=node_size * np.cos(angle),\n",
    "    node_height=node_size,\n",
    "    facecolors=\"white\",\n",
    "    edgecolors=\"black\",\n",
    "    linewidths=1.5,\n",
    "    ax=ax,\n",
    ")\n",
    "# edges = nx.draw_networkx_edges(\n",
    "#     G.to_directed(),\n",
    "#     pos=pos,\n",
    "#     edgelist=list(G.edges()),\n",
    "#     arrowstyle=\"<->\",\n",
    "#     width=1,\n",
    "#     style=\"--\",\n",
    "#     linestyle=\"--\",\n",
    "#     arrowsize=10,\n",
    "#     node_size=200,\n",
    "#     min_source_margin=7,\n",
    "#     ax=ax,\n",
    "# )\n",
    "# nx.draw_networkx_edges(G, pos=pos, edgelist=edges_sequential, width=2)\n",
    "nx.draw_networkx_edges(\n",
    "    G.to_directed(),\n",
    "    pos=pos,\n",
    "    edgelist=edges_sequential,\n",
    "    #     edgelist=edges_contacts + [[e[1], e[0]] for e in edges_contacts],\n",
    "    arrowstyle=\"<->\",\n",
    "#     edge_color=\"k\",\n",
    "    edge_color=cmap(12),\n",
    "    width=1.5,\n",
    "    arrowsize=12,\n",
    "    node_size=0,\n",
    "    min_source_margin=0,\n",
    "    connectionstyle=\"arc3,rad=0.1\",\n",
    "    alpha=0.9,\n",
    "    zorder=999,\n",
    ")\n",
    "nx.draw_networkx_edges(\n",
    "    G.to_directed(),\n",
    "    pos=pos,\n",
    "    edgelist=edges_contacts,\n",
    "    #     edgelist=edges_contacts + [[e[1], e[0]] for e in edges_contacts],\n",
    "    arrowstyle=\"<->\",\n",
    "#     edge_color=\"k\",\n",
    "    edge_color=cmap(12),\n",
    "    width=1.5,\n",
    "    arrowsize=9,\n",
    "    node_size=400,\n",
    "    min_source_margin=11,\n",
    "    connectionstyle=\"arc3,rad=0.1\",\n",
    "    alpha=0.7,\n",
    "    zorder=999,\n",
    ")\n",
    "\n",
    "\n",
    "# offset = 0.55\n",
    "# x += offset\n",
    "# pos = {k: np.array([v[0] + offset, v[1]]) for k, v in pos.items()}\n",
    "\n",
    "# for loc in pos.values():\n",
    "#     ax.arrow(loc[0] - 0.05, loc[1], 0.01, 0, width=0.005, alpha=0.5, zorder=3, fill=False)\n",
    "# #     center_y = adjust_y_corrd(center_x, 0, angle)\n",
    "# #     ax.arrow(0.3, center_y, 0.2, 0, width=0.02, alpha=0.5, zorder=3, fill=False)\n",
    "\n",
    "\n",
    "# ax.add_patch(\n",
    "#     patches.Polygon(\n",
    "#         xy=list(zip(x, y)), fill=True, alpha=0.5, linewidth=1, facecolor=cmap(3), edgecolor=\"k\",\n",
    "#     )\n",
    "# )\n",
    "# draw_networkx_nodes_ellipses(\n",
    "#     G,\n",
    "#     pos,\n",
    "#     cmap=cmap,\n",
    "#     node_color=cmap(0),\n",
    "#     node_width=node_size * np.cos(angle),\n",
    "#     node_height=node_size,\n",
    "#     ax=ax,\n",
    "# )\n",
    "# # edges = nx.draw_networkx_edges(\n",
    "# #     G.to_directed(),\n",
    "# #     pos=pos,\n",
    "# #     edgelist=list(G.edges()),\n",
    "# #     arrowstyle=\"<->\",\n",
    "# #     width=1,\n",
    "# #     style=\"--\",\n",
    "# #     linestyle=\"--\",\n",
    "# #     arrowsize=10,\n",
    "# #     node_size=200,\n",
    "# #     min_source_margin=7,\n",
    "# #     ax=ax,\n",
    "# # )\n",
    "# nx.draw_networkx_edges(G, pos=positions, edgelist=edges_sequential, width=2)\n",
    "# out = nx.draw_networkx_edges(\n",
    "#     G.to_directed(),\n",
    "#     pos=positions,\n",
    "#     edgelist=edges_contacts,\n",
    "#     #     edgelist=edges_contacts + [[e[1], e[0]] for e in edges_contacts],\n",
    "#     arrowstyle=\"<|-|>\",\n",
    "#     edge_color=\"#3d89ffff\",\n",
    "#     width=2,\n",
    "#     style=\"dashed\",\n",
    "#     linestyle=\"\",\n",
    "#     arrowsize=15,\n",
    "#     node_size=1000,\n",
    "#     min_source_margin=16,\n",
    "#     connectionstyle=\"arc3,rad=0.1\",\n",
    "# )\n",
    "\n",
    "ax.set_xlim(-0.005, 0.505)\n",
    "ax.set_ylim(y.min(), y.max())\n",
    "ax.axis(\"off\")\n",
    "\n",
    "fg.subplots_adjust(0.005, 0.005, 0.995, 0.995)\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"graph-conv-layer.svg\"), transparent=True)\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"graph-conv-layer.pdf\"))\n",
    "fg.savefig(NOTEBOOK_DIR.joinpath(\"graph-conv-layer.png\"), dpi=300)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(0.12156862745098039, 0.4666666666666667, 0.7058823529411765, 1.0)"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cmap(0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'p' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-18-b1bae578b96d>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mpos\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpos\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mpos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mpos\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpos\u001b[0m \u001b[0;34m/\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mpos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmax\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mpos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m: name 'p' is not defined"
     ]
    }
   ],
   "source": [
    "pos = np.array(positions)\n",
    "pos = pos - pos.min()\n",
    "pos = pos / (pos.max() - pos.min())\n",
    "p"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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    "name": "ipython",
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   "file_extension": ".py",
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   "name": "python",
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