{
 "cells": [
  {
   "cell_type": "markdown",
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    "vscode": {
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   "source": [
    "Alignment plots\n",
    "===============\n",
    "\n",
    "Alignment plots are a quick way to visualize how RNAvigate is positionally\n",
    "aligning two data sets. The two sequences will be displayed along the x-axis,\n",
    "with dashes inserted where there are insertions/deletions. A simplified\n",
    "visualization of the alignment appears between the sequences, with grey bars\n",
    "indicating the sequence agreement. The x-axes show the positional alignment\n",
    "used by RNAvigate to compare sequences.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import rnavigate as rnav\n",
    "from rnavigate.examples import rnasep_1, rmrp\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "These two structure models differ only in that one contains structure cassettes\n",
    "on the 5' and 3' ends.\n",
    "\n",
    "This is what a good alignment looks like:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = rnav.plot_alignment(\n",
    "    data1=(rnasep_1, \"ss_ct\"),\n",
    "    data2=(rnasep_1, \"ss_pdb\"),\n",
    ")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "RNAse P and RNAse MRP have structural conservation, but their sequences diverge substantially.\n",
    "\n",
    "Positions will be aligned even though there is very little sequence similarity\n",
    "\n",
    "This is what a bad alignment looks like:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = rnav.plot_alignment(\n",
    "    data1=(rmrp, \"ss\"),\n",
    "    data2=(rnasep_1, \"ss_pdb\"),\n",
    ")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "help(rnav.plot_alignment)"
   ]
  }
 ],
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   "pygments_lexer": "ipython3",
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