{
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "FragMapper\n",
    "==========\n",
    "\n",
    "Maintained by Seth Veenbaas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import rnavigate as rnav\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Import data to RNAvigate and run Fragmapper analysis\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rnavigate.examples import quinaxoline, linezolid, methyl\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The above import statement is equivalent to running the following code from\n",
    "inside `/path/to/RNAvigate/rnavigate/examples/rrna_fragmap/`.\n",
    "\n",
    "```python\n",
    "# Reference structure data is shared between samples\n",
    "common_data = rnav.Sample(\n",
    "    sample='6HA1 - LSU',\n",
    "    sequence='6HA1_LSU.fasta',\n",
    "    pdb={'pdb': '6HA1_LSU.pdb',\n",
    "         'sequence': 'sequence',\n",
    "         'chain': 'A'},\n",
    "    ss='6HA1_LSU.json'\n",
    ")\n",
    "# Flip structure diagram along x and y axes\n",
    "common_data.data['ss'].data[\"X_coordinate\"] *= -1\n",
    "common_data.data['ss'].data[\"Y_coordinate\"] *= -1\n",
    "# Quinaxoline test sample\n",
    "quinoxiline = rnav.Sample(\n",
    "    'B. sub rRNA FragMaP: quinoxiline',\n",
    "    inherit=common_data,\n",
    "    shapemap='2_QN_DMSO_subtracted_LSU_profile.txt'\n",
    ")\n",
    "# Linezolid test sample\n",
    "lnz = rnav.Sample(\n",
    "    'B. sub rRNA FragMaP: linezolid',\n",
    "    inherit=common_data,\n",
    "    shapemap='2_ZLD_DMSO_subtracted_LSU_profile.txt'\n",
    ")\n",
    "# Methyl control sample\n",
    "met = rnav.Sample(\n",
    "    'B. sub rRNA FragMaP: methyl',\n",
    "    inherit=common_data,\n",
    "    shapemap='2_Methyl_DMSO_subtracted_LSU_profile.txt'\n",
    ")\n",
    "```\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Run Fragmapper analysis and saving a FragMaP profile object\n",
    "# NOTE: Fragmapper requires 1 test sample and 1 control sample\n",
    "qn_fm = rnav.analysis.Fragmapper(quinaxoline, methyl)\n",
    "lnz_fm = rnav.analysis.Fragmapper(linezolid, methyl)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## FragMaP scatter plots"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Scatter plot with FragMaP profiles"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# FragMapper.plot_scatter()\n",
    "print(lnz_fm.get_data(\"fragmap\").data.columns)\n",
    "fig, ax = lnz_fm.plot_scatter()\n",
    "fig, ax = qn_fm.plot_scatter()\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Scatter plot with raw mutation rates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# FragMaP_profile_object.plot_scatter()\n",
    "fig1, ax1 = lnz_fm.plot_scatter()\n",
    "fig2, ax2 = qn_fm.plot_scatter()\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## View FragMaP profile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = rnav.plot_profile(\n",
    "    samples=[lnz_fm],\n",
    "    profile=\"fragmap\",\n",
    "    region=[2000, 2700],\n",
    "    sequence='shapemap',\n",
    "    plot_error=False\n",
    "    )\n",
    "ax = plot.axes[0, 0]\n",
    "ax.set(ylim=[-2, 10])\n",
    "ax.legend(['ZLD FragMaP Profile']);\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## View raw sample data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plot = rnav.plot_skyline(\n",
    "    samples=[lnz_fm],\n",
    "    profile=\"fragmap\",\n",
    "    columns=[\"Modified_rate_1\", \"Modified_rate_2\", \"Delta_rate\"],\n",
    "    sequence=\"shapemap\",\n",
    "    region=[2000, 2700],\n",
    "    annotations=[\"fragmap_sites\"],\n",
    "    annotations_mode='bar',\n",
    "    plot_kwargs={\"subplot_kw\": {\"ylim\": (-0.01, 0.2)}},\n",
    "    )\n",
    "\n",
    "plot.axes[0, 0].legend(\n",
    "    [\"ZLD mutation rate\", \"methyl mutation rate\", \"delta rate\"]\n",
    "    );\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## View FragMaP site annotation in secondary structure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "with rnav.styles.Settings({'ss': {'structure': {'linewidth': 2}}}):\n",
    "    plot = rnav.plot_ss(\n",
    "        [lnz_fm],\n",
    "        profile='fragmap',\n",
    "        structure='ss',\n",
    "        colors={'structure': 'sequence',\n",
    "                'nucleotides': 'none',},\n",
    "        bp_style='conventional',\n",
    "        annotations=['fragmap_sites'],\n",
    "        nt_ticks=100\n",
    "        )\n"
   ]
  }
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