{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 12: Making custom ajustments to figure\n",
    "\n",
    "An example of how to make adjustments to figures after running the `make_plot()` function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "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",
       "        if (typeof require !== 'undefined') {\n",
       "        require.undef(\"plotly\");\n",
       "        requirejs.config({\n",
       "            paths: {\n",
       "                'plotly': ['https://cdn.plot.ly/plotly-2.35.2.min']\n",
       "            }\n",
       "        });\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": 6,
   "metadata": {},
   "outputs": [
    {
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   "source": [
    "## Path to your ENSEMBL GTF file, counts matrix file, and metadata 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\"\n",
    "metadata_path = \"../dash_apps/RNApysoforms/tests/test_data/sample_metadata.tsv\"\n",
    "\n",
    "\n",
    "## Read ENSEMBL GTF and counts matrix with metadata and normalization\n",
    "annotation = RNApy.read_ensembl_gtf(ensembl_gtf_path)\n",
    "counts_matrix = RNApy.read_expression_matrix(expression_matrix_path=counts_matrix_path,\n",
    "                                          metadata_path=metadata_path,\n",
    "                                           cpm_normalization=True, relative_abundance=True)\n",
    "\n",
    "\n",
    "## Filter APP gene and keep only top 5 expressed transcripts\n",
    "app_annotation, app_expresison_matrix = RNApy.gene_filtering(annotation=annotation, expression_matrix=counts_matrix, target_gene=\"APP\",\n",
    "                                                        order_by_expression=True, order_by_expression_column=\"counts\",\n",
    "                                                        keep_top_expressed_transcripts=5)\n",
    "\n",
    "## Rescale introns\n",
    "app_annotation = RNApy.shorten_gaps(app_annotation)\n",
    "\n",
    "\n",
    "## Create traces\n",
    "traces = RNApy.make_traces(annotation=app_annotation,  expression_matrix=app_expresison_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\", \"CPM\", \"relative_abundance\"],\n",
    "                         expression_hue=\"AD status\", marker_size=3, arrow_size=7,\n",
    "                         order_transcripts_by_expression_matrix=False ## Order by annotation order instead of expression matrix\n",
    "                         )\n",
    "\n",
    "## Put traces into figure\n",
    "fig = RNApy.make_plot(traces=traces, subplot_titles=[\"Transcript Structure\", \"Counts\", \"CPM\", \"Relative Abundance\"], \n",
    "                   width=1200, height=500, boxgap=0.1, boxgroupgap=0.5,\n",
    "                   column_widths=[0.4, 0.2, 0.2, 0.2] ## Pass custom column widths to make the Transcript Structure plot bigger\n",
    "                   )\n",
    "\n",
    "\n",
    "## PLOT CUSTOMIZATION, see plotly docs for more ways of customizing it and saving the plot as different file formats\n",
    "\n",
    "# Update figure size and give it a title\n",
    "fig.update_layout(title=dict(text=\"APP RNA isoform expression\", x = 0.5, xanchor=\"center\"),\n",
    "                  width=1250, height=800)\n",
    "\n",
    "## Show figure\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "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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