gcell.dna.track.Track.plot_tracks_with_genebody#
- Track.plot_tracks_with_genebody(color_dict=None, gene_annot=None, genes_to_highlight=None, beds=None, out_file=None, center=False, protein_coding_only=False, isoforms=False, gene_track_height=1, track_order=None, autoscale=False, group_autoscale=None)[source]#
Plot the tracks with detailed gene structure visualization.
- Parameters:
- color_dict dict, optional
A dictionary mapping track labels to colors. Defaults to None.
- gene_annot Gencode, optional
A Gencode object containing gene annotations. Defaults to None.
- genes_to_highlight list, optional
A list of gene names to highlight. Defaults to None.
- beds list, optional
A list of BED objects containing regions to plot. Defaults to None.
- out_file str, optional
The path to save the output plot. Defaults to None.
- center bool, optional
Whether to center the y-axis around the mean. Defaults to False.
- protein_coding_only bool, optional
Whether to show only protein-coding genes. Defaults to False.
- isoforms bool, optional
Whether to show individual transcript isoforms. Defaults to False.
- gene_track_height float, optional
Height of the gene track relative to signal tracks. Defaults to 1.
- track_order list, optional
List of track labels specifying the order in which to plot the tracks. If not provided, tracks will be plotted in their default order.
- autoscale bool, optional
Whether to normalize each track to its maximum value in the displayed region. Defaults to False.
- group_autoscale dict or list, optional
Groups for autoscaling. If dict, maps group names to lists of track IDs. If list of lists, each sublist contains track IDs for a group. Each group is normalized to the maximum value across group members. Defaults to None.
- Returns:
tuple A tuple containing the matplotlib figure and list of axes.