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    "Heatmap and contour plots\n",
    "=========================\n",
    "\n",
    "Heatmaps and contour plots are a good way to view inter-nucleotide data when\n",
    "the data are very dense, or when you wish to view inter-nucleotide data\n",
    "density. The x and y axes are nucleotide positions. XY-positions are colored by\n",
    "inter-nucleotide data values or density (heatmap) and overlayed with a contour\n",
    "map. This contour map can show either 3D distance or secondary structure graph\n",
    "path distance (contact distance). These countours will outline areas where\n",
    "nucleotide *X* is close, in 3D space or secondary structure, to nucleotide *Y*."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import rnavigate as rnav\n",
    "from rnavigate.examples import rnasep_1\n",
    "\n",
    "plot = rnav.plot_heatmap(\n",
    "    samples=[rnasep_1],\n",
    "    sequence=\"pdb\",\n",
    "    structure=\"pdb\",\n",
    "    interactions=\"shapejump\",\n",
    "    plot_type=\"kde\",\n",
    ")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "help(rnav.plot_heatmap)\n"
   ]
  }
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