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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 03: Expression plot with metadata\n",
    "\n",
    "Create an RNA isoform structure plot with an RNA isoform expression plot with dodged groups beside it"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
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       "        }\n",
       "        </script>\n",
       "        "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import RNApysoforms as RNApy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "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",
    "\n",
    "## Read ENSEMBL gtf and counts matrix with metadata\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)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
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       "│ ---             ┆ ---             ┆ ---       ┆ ---    ┆ ---       ┆ ---    ┆ ---               │\n",
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       "│ ENST00000476106 ┆ ENSG00000142168 ┆ sample_6  ┆ 0.0    ┆ Control   ┆ Female ┆ Control Female    │\n",
       "└─────────────────┴─────────────────┴───────────┴────────┴───────────┴────────┴───────────────────┘"
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     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
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   "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",
    "## Notice how now the counts matrix has the metadata integrated.\n",
    "sod1_counts_matrix.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
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    "\n",
    "## Rescale introns\n",
    "sod1_annotation = RNApy.shorten_gaps(sod1_annotation)\n",
    "\n",
    "\n",
    "\"\"\"\n",
    "Create traces now using the `expression_hue` parameter\n",
    "set to the AD status metadata column that was added to the\n",
    "expression matrix.\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",
    "                         expression_hue=\"AD status\")\n",
    "\n",
    "## Put traces into figure\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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    "### 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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