{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 02: Expression plot\n",
    "\n",
    "Create an RNA isoform structure plot with an RNA isoform expression plot beside it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Path to your ENSEMBL GTF file and counts matrix file\n",
    "ensembl_gtf_path = \"../dash_apps/RNApysoforms/tests/test_data/Homo_sapiens_chr21_and_Y.GRCh38.110.gtf\"\n",
    "counts_matrix_path = \"../dash_apps/RNApysoforms/tests/test_data/counts_matrix_chr21_and_Y.tsv\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Read ENSEMBL gtf and counts matrix\n",
    "annotation = RNApy.read_ensembl_gtf(ensembl_gtf_path)\n",
    "counts_matrix = RNApy.read_expression_matrix(expression_matrix_path=counts_matrix_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
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       "<small>shape: (5, 4)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>transcript_id</th><th>gene_id</th><th>sample_id</th><th>counts</th></tr><tr><td>str</td><td>str</td><td>str</td><td>f64</td></tr></thead><tbody><tr><td>&quot;ENST00000476106&quot;</td><td>&quot;ENSG00000142168&quot;</td><td>&quot;sample_1&quot;</td><td>0.0</td></tr><tr><td>&quot;ENST00000476106&quot;</td><td>&quot;ENSG00000142168&quot;</td><td>&quot;sample_4&quot;</td><td>0.0</td></tr><tr><td>&quot;ENST00000476106&quot;</td><td>&quot;ENSG00000142168&quot;</td><td>&quot;sample_7&quot;</td><td>0.0</td></tr><tr><td>&quot;ENST00000476106&quot;</td><td>&quot;ENSG00000142168&quot;</td><td>&quot;sample_2&quot;</td><td>0.0</td></tr><tr><td>&quot;ENST00000476106&quot;</td><td>&quot;ENSG00000142168&quot;</td><td>&quot;sample_6&quot;</td><td>0.0</td></tr></tbody></table></div>"
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       "shape: (5, 4)\n",
       "┌─────────────────┬─────────────────┬───────────┬────────┐\n",
       "│ transcript_id   ┆ gene_id         ┆ sample_id ┆ counts │\n",
       "│ ---             ┆ ---             ┆ ---       ┆ ---    │\n",
       "│ str             ┆ str             ┆ str       ┆ f64    │\n",
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       "│ ENST00000476106 ┆ ENSG00000142168 ┆ sample_6  ┆ 0.0    │\n",
       "└─────────────────┴─────────────────┴───────────┴────────┘"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## Filter gene name in annotation and counts matrix.\n",
    "sod1_annotation, sod1_counts_matrix = RNApy.gene_filtering(annotation=annotation, expression_matrix=counts_matrix, target_gene=\"SOD1\")\n",
    "\n",
    "sod1_counts_matrix.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
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       "shape: (5, 13)\n",
       "┌───────────┬───────────┬───────────┬───────────┬───┬──────────┬───────────┬───────────┬───────────┐\n",
       "│ gene_id   ┆ gene_name ┆ transcrip ┆ transcrip ┆ … ┆ end      ┆ exon_numb ┆ rescaled_ ┆ rescaled_ │\n",
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       "│           ┆           ┆ str       ┆ str       ┆   ┆          ┆ i64       ┆ i64       ┆ i64       │\n",
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       "│ ENSG00000 ┆ SOD1      ┆ ENST00000 ┆ SOD1-201  ┆ … ┆ 31659841 ┆ 1         ┆ 29        ┆ 177       │\n",
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       "│ 142168    ┆           ┆ 270142    ┆           ┆   ┆          ┆           ┆           ┆           │\n",
       "└───────────┴───────────┴───────────┴───────────┴───┴──────────┴───────────┴───────────┴───────────┘"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\"\"\"\n",
    "Rescale introns (no need to run function \"to_intron\", shorten_gaps() already does this \n",
    "by default if introns aren't already included in annotation.\n",
    "\"\"\"\n",
    "sod1_annotation = RNApy.shorten_gaps(sod1_annotation)\n",
    "\n",
    "sod1_annotation.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
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    "\"\"\"\n",
    "Create traces for plotting, the expression plot will come out in\n",
    "the order of columns passed on the `expression_columns` parameters.\n",
    "This is important if you are passing multiple expression columns\n",
    "like CPM and relative abundance.\n",
    "\"\"\"\n",
    "traces = RNApy.make_traces(annotation=sod1_annotation,  expression_matrix=sod1_counts_matrix, \n",
    "                        x_start=\"rescaled_start\", x_end=\"rescaled_end\",\n",
    "                         y='transcript_id', annotation_hue=\"transcript_biotype\",\n",
    "                         hover_start=\"start\", hover_end=\"end\",\n",
    "                         expression_columns=[\"counts\"])\n",
    "\n",
    "\"\"\"\n",
    "Put traces into the figure. The order of `subplot_titles` is important.\n",
    "The first plot will always be \"Transcript Structure\" if you passed an annotation\n",
    "to make the traces. After that the order of the expression plots is determined \n",
    "by the `expression_columns` parameter passed to the `make_traces()` function.\n",
    "\"\"\"\n",
    "fig = RNApy.make_plot(traces = traces, subplot_titles = [\"Transcript Structure\", \"Counts\"], width=1200, height=500)\n",
    "\n",
    "## Show figure\n",
    "fig.show()"
   ]
  }
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