{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 01: Basic usage (quick start)\n",
    "\n",
    "Make a basic RNA transcript structure plot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "        <script type=\"text/javascript\">\n",
       "        window.PlotlyConfig = {MathJaxConfig: 'local'};\n",
       "        if (window.MathJax && window.MathJax.Hub && window.MathJax.Hub.Config) {window.MathJax.Hub.Config({SVG: {font: \"STIX-Web\"}});}\n",
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       "        require.undef(\"plotly\");\n",
       "        requirejs.config({\n",
       "            paths: {\n",
       "                'plotly': ['https://cdn.plot.ly/plotly-2.35.2.min']\n",
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       "        });\n",
       "        require(['plotly'], function(Plotly) {\n",
       "            window._Plotly = Plotly;\n",
       "        });\n",
       "        }\n",
       "        </script>\n",
       "        "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import RNApysoforms as RNApy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div><style>\n",
       ".dataframe > thead > tr,\n",
       ".dataframe > tbody > tr {\n",
       "  text-align: right;\n",
       "  white-space: pre-wrap;\n",
       "}\n",
       "</style>\n",
       "<small>shape: (5, 11)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>gene_id</th><th>gene_name</th><th>transcript_id</th><th>transcript_name</th><th>transcript_biotype</th><th>seqnames</th><th>strand</th><th>type</th><th>start</th><th>end</th><th>exon_number</th></tr><tr><td>str</td><td>str</td><td>str</td><td>str</td><td>str</td><td>str</td><td>str</td><td>str</td><td>i64</td><td>i64</td><td>i64</td></tr></thead><tbody><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000389995&quot;</td><td>&quot;SOD1-202&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;exon&quot;</td><td>31659666</td><td>31659784</td><td>1</td></tr><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000389995&quot;</td><td>&quot;SOD1-202&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;CDS&quot;</td><td>31659770</td><td>31659784</td><td>1</td></tr><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000389995&quot;</td><td>&quot;SOD1-202&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;exon&quot;</td><td>31663790</td><td>31663886</td><td>2</td></tr><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000389995&quot;</td><td>&quot;SOD1-202&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;CDS&quot;</td><td>31663790</td><td>31663886</td><td>2</td></tr><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000389995&quot;</td><td>&quot;SOD1-202&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;exon&quot;</td><td>31666449</td><td>31666518</td><td>3</td></tr></tbody></table></div>"
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      "text/plain": [
       "shape: (5, 11)\n",
       "┌─────────────┬───────────┬─────────────┬────────────┬───┬──────┬──────────┬──────────┬────────────┐\n",
       "│ gene_id     ┆ gene_name ┆ transcript_ ┆ transcript ┆ … ┆ type ┆ start    ┆ end      ┆ exon_numbe │\n",
       "│ ---         ┆ ---       ┆ id          ┆ _name      ┆   ┆ ---  ┆ ---      ┆ ---      ┆ r          │\n",
       "│ str         ┆ str       ┆ ---         ┆ ---        ┆   ┆ str  ┆ i64      ┆ i64      ┆ ---        │\n",
       "│             ┆           ┆ str         ┆ str        ┆   ┆      ┆          ┆          ┆ i64        │\n",
       "╞═════════════╪═══════════╪═════════════╪════════════╪═══╪══════╪══════════╪══════════╪════════════╡\n",
       "│ ENSG0000014 ┆ SOD1      ┆ ENST0000038 ┆ SOD1-202   ┆ … ┆ exon ┆ 31659666 ┆ 31659784 ┆ 1          │\n",
       "│ 2168        ┆           ┆ 9995        ┆            ┆   ┆      ┆          ┆          ┆            │\n",
       "│ ENSG0000014 ┆ SOD1      ┆ ENST0000038 ┆ SOD1-202   ┆ … ┆ CDS  ┆ 31659770 ┆ 31659784 ┆ 1          │\n",
       "│ 2168        ┆           ┆ 9995        ┆            ┆   ┆      ┆          ┆          ┆            │\n",
       "│ ENSG0000014 ┆ SOD1      ┆ ENST0000038 ┆ SOD1-202   ┆ … ┆ exon ┆ 31663790 ┆ 31663886 ┆ 2          │\n",
       "│ 2168        ┆           ┆ 9995        ┆            ┆   ┆      ┆          ┆          ┆            │\n",
       "│ ENSG0000014 ┆ SOD1      ┆ ENST0000038 ┆ SOD1-202   ┆ … ┆ CDS  ┆ 31663790 ┆ 31663886 ┆ 2          │\n",
       "│ 2168        ┆           ┆ 9995        ┆            ┆   ┆      ┆          ┆          ┆            │\n",
       "│ ENSG0000014 ┆ SOD1      ┆ ENST0000038 ┆ SOD1-202   ┆ … ┆ exon ┆ 31666449 ┆ 31666518 ┆ 3          │\n",
       "│ 2168        ┆           ┆ 9995        ┆            ┆   ┆      ┆          ┆          ┆            │\n",
       "└─────────────┴───────────┴─────────────┴────────────┴───┴──────┴──────────┴──────────┴────────────┘"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## Path to your ENSEMBL GTF file\n",
    "ensembl_gtf_path = \"../dash_apps/RNApysoforms/tests/test_data/Homo_sapiens_chr21_and_Y.GRCh38.110.gtf\"\n",
    "\n",
    "\n",
    "## Read ENSEMBL gtf\n",
    "annotation = RNApy.read_ensembl_gtf(ensembl_gtf_path)\n",
    "\n",
    "\n",
    "## Filter gene name in annotation and counts matrix\n",
    "sod1_annotation = RNApy.gene_filtering(annotation=annotation, target_gene=\"SOD1\")\n",
    "\n",
    "sod1_annotation.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
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       "}\n",
       "</style>\n",
       "<small>shape: (5, 11)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>gene_id</th><th>gene_name</th><th>transcript_id</th><th>transcript_name</th><th>transcript_biotype</th><th>seqnames</th><th>strand</th><th>type</th><th>start</th><th>end</th><th>exon_number</th></tr><tr><td>str</td><td>str</td><td>str</td><td>str</td><td>str</td><td>str</td><td>str</td><td>str</td><td>i64</td><td>i64</td><td>i64</td></tr></thead><tbody><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000270142&quot;</td><td>&quot;SOD1-201&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;exon&quot;</td><td>31659693</td><td>31659841</td><td>1</td></tr><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000270142&quot;</td><td>&quot;SOD1-201&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;CDS&quot;</td><td>31659770</td><td>31659841</td><td>1</td></tr><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000270142&quot;</td><td>&quot;SOD1-201&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;intron&quot;</td><td>31659841</td><td>31663790</td><td>1</td></tr><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000270142&quot;</td><td>&quot;SOD1-201&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;CDS&quot;</td><td>31663790</td><td>31663886</td><td>2</td></tr><tr><td>&quot;ENSG00000142168&quot;</td><td>&quot;SOD1&quot;</td><td>&quot;ENST00000270142&quot;</td><td>&quot;SOD1-201&quot;</td><td>&quot;protein_coding&quot;</td><td>&quot;21&quot;</td><td>&quot;+&quot;</td><td>&quot;exon&quot;</td><td>31663790</td><td>31663886</td><td>2</td></tr></tbody></table></div>"
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      "text/plain": [
       "shape: (5, 11)\n",
       "┌────────────┬───────────┬────────────┬────────────┬───┬────────┬──────────┬──────────┬────────────┐\n",
       "│ gene_id    ┆ gene_name ┆ transcript ┆ transcript ┆ … ┆ type   ┆ start    ┆ end      ┆ exon_numbe │\n",
       "│ ---        ┆ ---       ┆ _id        ┆ _name      ┆   ┆ ---    ┆ ---      ┆ ---      ┆ r          │\n",
       "│ str        ┆ str       ┆ ---        ┆ ---        ┆   ┆ str    ┆ i64      ┆ i64      ┆ ---        │\n",
       "│            ┆           ┆ str        ┆ str        ┆   ┆        ┆          ┆          ┆ i64        │\n",
       "╞════════════╪═══════════╪════════════╪════════════╪═══╪════════╪══════════╪══════════╪════════════╡\n",
       "│ ENSG000001 ┆ SOD1      ┆ ENST000002 ┆ SOD1-201   ┆ … ┆ exon   ┆ 31659693 ┆ 31659841 ┆ 1          │\n",
       "│ 42168      ┆           ┆ 70142      ┆            ┆   ┆        ┆          ┆          ┆            │\n",
       "│ ENSG000001 ┆ SOD1      ┆ ENST000002 ┆ SOD1-201   ┆ … ┆ CDS    ┆ 31659770 ┆ 31659841 ┆ 1          │\n",
       "│ 42168      ┆           ┆ 70142      ┆            ┆   ┆        ┆          ┆          ┆            │\n",
       "│ ENSG000001 ┆ SOD1      ┆ ENST000002 ┆ SOD1-201   ┆ … ┆ intron ┆ 31659841 ┆ 31663790 ┆ 1          │\n",
       "│ 42168      ┆           ┆ 70142      ┆            ┆   ┆        ┆          ┆          ┆            │\n",
       "│ ENSG000001 ┆ SOD1      ┆ ENST000002 ┆ SOD1-201   ┆ … ┆ CDS    ┆ 31663790 ┆ 31663886 ┆ 2          │\n",
       "│ 42168      ┆           ┆ 70142      ┆            ┆   ┆        ┆          ┆          ┆            │\n",
       "│ ENSG000001 ┆ SOD1      ┆ ENST000002 ┆ SOD1-201   ┆ … ┆ exon   ┆ 31663790 ┆ 31663886 ┆ 2          │\n",
       "│ 42168      ┆           ┆ 70142      ┆            ┆   ┆        ┆          ┆          ┆            │\n",
       "└────────────┴───────────┴────────────┴────────────┴───┴────────┴──────────┴──────────┴────────────┘"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## Make introns\n",
    "sod1_annotation = RNApy.to_intron(sod1_annotation)\n",
    "\n",
    "sod1_annotation.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
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   "source": [
    "## Create traces for plotting\n",
    "traces = RNApy.make_traces(annotation=sod1_annotation, y='transcript_id', annotation_hue=\"transcript_biotype\")\n",
    "\n",
    "## Put traces into figure\n",
    "fig = RNApy.make_plot(traces = traces, subplot_titles = [\"Transcript Structure\"], width=1200, height=500)\n",
    "\n",
    "## Show figure\n",
    "fig.show()\n"
   ]
  },
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   "cell_type": "markdown",
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   "source": [
    "### You can click on the legend items to make figure elements appear and disappear.\n",
    "\n",
    "### The legend title will get grayed out when clicking on the first legend item. I could not find a workaround for that with the current plotly release (version 5).\n",
    "\n",
    "### The hovering for exons and CDS works best if you hover your mouse over the edges of the CDS/exon boxes."
   ]
  }
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