{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Arc plots\n",
    "=========\n",
    "\n",
    "Arc plots are a flexible plot type for comparing multiple layers of RNA data\n",
    "simultaneously. Sequence annotations, per-nucleotide data, inter-nucleotide\n",
    "data, and secondary structures can all be displayed on arc plots.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import rnavigate as rnav\n",
    "from rnavigate.examples import tpp\n",
    "\n",
    "plot = rnav.plot_arcs(\n",
    "    samples=[tpp],\n",
    "    sequence=\"ss\",\n",
    "    structure=\"ss\",\n",
    "    profile=\"dmsmap\",\n",
    "    profile_scale_factor=5,\n",
    ")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "help(rnav.plot_arcs)"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "RNAvigate",
   "language": "python",
   "name": "python3"
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    "name": "ipython",
    "version": 3
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   "name": "python",
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   "pygments_lexer": "ipython3",
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