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"## 02: Rescaled introns\n",
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"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",
"\"\"\"\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",
"\n",
"\"\"\"\n",
"Create traces for plotting, make sure to pass x_start and x_end \n",
"as \"rescaled_start\" and \"rescaled_end\" to get shortened introns.\n",
"You can also change hover_start and hover_end to reflext the \n",
"rescaled coordinates, but I find the original genomic coodrinates\n",
"for start and end more informative for the hover display.\n",
"\"\"\"\n",
"traces = RNApy.make_traces(annotation=sod1_annotation, x_start=\"rescaled_start\", x_end=\"rescaled_end\",\n",
" y='transcript_id', annotation_hue=\"transcript_biotype\",\n",
" hover_start=\"start\", hover_end=\"end\")\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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"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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