11: Making expression plot only

Here is one possible way of generating only the expression plot without the RNA isoform annotation

import RNApysoforms as RNApy

## Path to your ENSEMBL GTF file, counts matrix file, and metadata file
ensembl_gtf_path = "../dash_apps/RNApysoforms/tests/test_data/Homo_sapiens_chr21_and_Y.GRCh38.110.gtf"
counts_matrix_path = "../dash_apps/RNApysoforms/tests/test_data/counts_matrix_chr21_and_Y.tsv"
metadata_path = "../dash_apps/RNApysoforms/tests/test_data/sample_metadata.tsv"


## Read ENSEMBL GTF and counts matrix with metadata and normalization
annotation = RNApy.read_ensembl_gtf(ensembl_gtf_path)
counts_matrix = RNApy.read_expression_matrix(expression_matrix_path=counts_matrix_path,
                                          metadata_path=metadata_path,
                                           cpm_normalization=True, relative_abundance=True)


## Filter APP gene and do not filter RNA isoforms by expression
app_annotation, app_expresison_matrix = RNApy.gene_filtering(annotation=annotation, expression_matrix=counts_matrix, target_gene="APP",
                                                        order_by_expression=True, order_by_expression_column="counts",
                                                        keep_top_expressed_transcripts=5)

## Rescale introns
app_annotation = RNApy.shorten_gaps(app_annotation)


## Create traces without annotation
traces = RNApy.make_traces(expression_matrix=app_expresison_matrix,
                        x_start="rescaled_start", x_end="rescaled_end",
                         y='transcript_id', hover_start="start", hover_end="end",
                         expression_columns=["counts", "CPM", "relative_abundance"],
                         expression_hue="AD status", marker_size=3, arrow_size=7)

## Make figure only with RNA isoform expression plots
fig = RNApy.make_plot(traces=traces, subplot_titles=["Counts", "CPM", "Relative Abundance"],
                   width=1200, height=500, boxgap=0.1, boxgroupgap=0.5)

## Show figure
fig.show()