Violin expression plot

Make expression plot be violin plot instead of box plot.

import RNApysoforms as RNApy

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


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

## Filter APP gene and keep only top 5 expressed transcripts
app_annotation, app_expression_matrix = RNApy.gene_filtering(annotation=annotation, expression_matrix=expression_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 annotation, notice the `expression_plot_style` parameter set to "violin"
traces = RNApy.make_traces(annotation=app_annotation,  expression_matrix=app_expression_matrix,
                        x_start="rescaled_start", x_end="rescaled_end",
                         y='transcript_id', annotation_hue="transcript_biotype",
                         hover_start="start", hover_end="end",
                         expression_columns=["counts"],
                         expression_fill_color="orange", marker_size=3, arrow_size=7,
                         expression_plot_style="violin")

## Make figure only with RNA isoform expression plots
fig = RNApy.make_plot(traces=traces, subplot_titles=["Counts"],
                   width=1200, height=500, boxgap=0.1, boxgroupgap=0)

## Show figure
fig.show()

Notes:

You can click on the legend items to make figure elements appear and disappear.

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).

The hovering for exons and CDS works best if you hover your mouse over the corners of the CDS/exon boxes.