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"## 05: Plot specific transcripts\n",
"\n",
"Hand pick which transcripts to plot and plot them in specific order"
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"C:\\Users\\local_bag222\\Desktop\\dash_apps\\RNApysoforms\\src\\RNApysoforms\\make_traces.py:294: UserWarning:\n",
"\n",
"18 transcript(s) are present in the expression matrix but missing in the annotation. Missing transcripts: ENST00000346798, ENST00000354192, ENST00000357903, ENST00000358918, ENST00000359726, ENST00000415997, ENST00000439274, ENST00000440126, ENST00000448850, ENST00000462267, ENST00000463070, ENST00000464867, ENST00000466453, ENST00000474136, ENST00000491395, ENST00000548570, ENST00000707132, ENST00000707134. Only transcripts present in both will be used for making traces.\n",
"\n"
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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 do not filter RNA isoforms by expression\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",
"\n",
"## Rescale introns\n",
"app_annotation = RNApy.shorten_gaps(app_annotation)\n",
"\n",
"\n",
"\"\"\"\n",
"Filter only the desired transcripts and keep them on in the app_annotation.\n",
"`make_traces()` only plots transcripts present in both the annotationa and the\n",
"expression matrix when both are passed (it does give a warning when that happens),\n",
"so only the transcripts you kept in the annotation will be plotted.\n",
"\"\"\"\n",
"transcript_to_keep = [\"ENST00000348990\", \"ENST00000707133\"]\n",
"app_annotation = app_annotation.filter(pl.col(\"transcript_id\").is_in(transcript_to_keep))\n",
"\n",
"\n",
"## Order transcripts based on `transcripts_to_keep` order\n",
"app_annotation = app_annotation.with_columns(\n",
" pl.col(\"transcript_id\").cast(pl.Categorical).cast(pl.Utf8).replace(\n",
" {k: i for i, k in enumerate(transcript_to_keep)}).alias(\"sort_key\")\n",
" ).sort(\"sort_key\", descending=True).drop(\"sort_key\")\n",
"\n",
"\n",
"\"\"\"\n",
"Create traces for plotting, make sure to set the\n",
"`order_transcripts_by_expression_matrix` to False so\n",
"that the order of the annotation is the one that determines\n",
"the order in which the transcripts are plotted.\n",
"\"\"\"\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",
"\n",
"## Show figure\n",
"fig.show()"
]
}
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