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 "cells": [
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 07: Use consistent color maps for making your plots\n",
    "\n",
    "Define color maps for hues used for RNA isoform structure and expression plot so labels are consistently associated with the same colors."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "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\n",
    "import polars as pl"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
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       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
       "            observer.disconnect();\n",
       "        }}\n",
       "}});\n",
       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
       "}}\n",
       "\n",
       "// Listen for the clearing of the current output cell\n",
       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
       "}}\n",
       "\n",
       "                        })                };                });            </script>        </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "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 normalizations\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_counts_matrix = RNApy.gene_filtering(annotation=annotation, expression_matrix=counts_matrix, target_gene=\"APP\",\n",
    "                                                        order_by_expression=True, keep_top_expressed_transcripts=5, \n",
    "                                                        order_by_expression_column=\"counts\")\n",
    "\n",
    "\n",
    "# Rescale introns\n",
    "app_annotation = RNApy.shorten_gaps(app_annotation)\n",
    "\n",
    "\n",
    "# Define a mapping from transcript_biotype to colors\n",
    "biotype_colors = {\n",
    "    'protein_coding': '#F8766D',\n",
    "    'protein_coding_CDS_not_defined': '#00BFC4'\n",
    "}\n",
    "\n",
    "# Define a mapping for \"AD Status\" from expression matrix\n",
    "ad_status_colors = {\n",
    "    'AD': '#7CAE00',\n",
    "    'Control': '#C77CFF',\n",
    "}\n",
    "\n",
    "\n",
    "\n",
    "\"\"\"\n",
    "Create traces, notice the `annotation_color_map` and the\n",
    "`expression_color_map` being passed to define the color maps for the different\n",
    "values contained in the `expression_hue` column from the expression matrix and \n",
    "the `annotation_hue` column from the annotation. This can be applied to ensure\n",
    "that your plot always has the same colors associated with the same\n",
    "`annotation_hue` and `expression_hue` values.\n",
    "\"\"\"\n",
    "traces = RNApy.make_traces(annotation=app_annotation,  expression_matrix=app_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\", \"CPM\", \"relative_abundance\"],\n",
    "                         expression_hue=\"AD status\", marker_size=3, arrow_size=7,\n",
    "                         annotation_color_map=biotype_colors,\n",
    "                         expression_color_map=ad_status_colors)\n",
    "\n",
    "## Put traces into a figure\n",
    "fig = RNApy.make_plot(traces=traces, subplot_titles=[\"Transcript Structure\", \"Counts\", \"CPM\", \"Relative Abundance\"], \n",
    "                   width=1200, height=500)\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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