Protein Plots

Visualize transcript structures with protein domain overlays.

API reference

---

ProteinPlots

def ProteinPlots(
    transcript_data:TranscriptData, protein_data:ProteinData, intron_scale:float=0.15, color_offset:int=0,
    kwargs:VAR_KEYWORD
):

Extended TranscriptPlots with protein domain overlay capabilities.

Inherits all transcript plotting functionality from TranscriptPlots and adds methods for overlaying protein domains on transcript structures.

---

ProteinPlots.draw_transcripts_with_protein_domains

def draw_transcripts_with_protein_domains(
    transcript_ids, # Transcript ID(s) to visualize
    provider:str='ensembl', # Domain provider ("ensembl" or "interpro")
Note: InterPro only annotates canonical transcripts
    max_domains:int=12, # Maximum domains to show per transcript
    id_prefixes:Optional[List[str]]=None, # Filter domains by ID prefix (e.g., ["PF"] for Pfam)
    sources:Optional[List[str]]=None, # Filter domains by source database
    fig_width:float=18.0, # Figure width in inches
    palette_name:str='Dark2', # Seaborn color palette name for protein domains
    custom_domains:Optional[Dict[str, List[Dict]]]=None, # Custom domain annotations. Dict mapping transcript_id to list of domain dicts.
Each domain dict should have keys: 'name', 'label', 'start', 'end' (AA coords)
If provided, overrides API fetching for those transcripts.
    show_aa_ticks:bool=True, # Show amino acid position ticks on domain track
): # The generated figure

Draw isoform exon structures + clean domain tracks.

For InterPro provider: domains are only shown on the first (canonical) transcript, since InterPro annotations are only available for canonical isoforms. Other transcripts are still shown for structural comparison.

Examples

Demonstrate protein domain visualization on transcripts.