.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "examples/gallery/sequence/annotation/plasmid_map_custom.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_examples_gallery_sequence_annotation_plasmid_map_custom.py: Visualization of a custom plasmid ================================= .. currentmodule:: biotite.sequence This script shows how :class:`Feature` objects are displayed in a plasmid map by using a custom 'toy' :class:`Annotation`. .. GENERATED FROM PYTHON SOURCE LINES 10-109 .. image-sg:: /examples/gallery/sequence/annotation/images/sphx_glr_plasmid_map_custom_001.png :alt: plasmid map custom :srcset: /examples/gallery/sequence/annotation/images/sphx_glr_plasmid_map_custom_001.png :class: sphx-glr-single-img .. code-block:: Python # Code source: Patrick Kunzmann # License: BSD 3 clause import matplotlib.pyplot as plt import biotite.sequence as seq import biotite.sequence.graphics as graphics annotation = seq.Annotation( [ seq.Feature( "source", [seq.Location(0, 1500)], {"organism": "Escherichia coli"} ), # Ori seq.Feature( "rep_origin", [seq.Location(600, 700, seq.Location.Strand.REVERSE)], {"regulatory_class": "promoter", "note": "MyProm"}, ), # Promoter seq.Feature( "regulatory", [seq.Location(1000, 1060)], {"regulatory_class": "promoter", "note": "MyProm"}, ), seq.Feature("protein_bind", [seq.Location(1025, 1045)], {"note": "repr"}), # Gene A seq.Feature( "regulatory", [seq.Location(1070, 1080)], {"regulatory_class": "ribosome_binding_site"}, ), seq.Feature("CDS", [seq.Location(1091, 1150)], {"product": "geneA"}), # Gene B seq.Feature( "regulatory", [seq.Location(1180, 1190)], {"regulatory_class": "ribosome_binding_site"}, ), seq.Feature("CDS", [seq.Location(1201, 1350)], {"product": "geneB"}), seq.Feature( "regulatory", [seq.Location(1220, 1230)], {"regulatory_class": "ribosome_binding_site"}, ), seq.Feature("CDS", [seq.Location(1240, 1350)], {"product": "geneB2"}), # Gene C seq.Feature( "regulatory", [seq.Location(1380, 1390)], {"regulatory_class": "ribosome_binding_site"}, ), seq.Feature( "CDS", # CDS extends over periodic boundary -> two locations [seq.Location(1, 300), seq.Location(1402, 1500)], {"product": "geneC"}, ), # Terminator seq.Feature( "regulatory", [seq.Location(310, 350)], {"regulatory_class": "terminator", "note": "MyTerm"}, ), # Primers # The labels will be too long to be displayed on the map # If you want to display them nevertheless, set the # 'omit_oversized_labels' to False seq.Feature("primer_bind", [seq.Location(1385, 1405)], {"note": "geneC"}), seq.Feature( "primer_bind", [seq.Location(345, 365, seq.Location.Strand.REVERSE)], {"note": "geneC_R"}, ), # Terminator seq.Feature( "regulatory", [seq.Location(310, 350)], {"regulatory_class": "terminator", "note": "MyTerm"}, ), ] ) fig = plt.figure(figsize=(8.0, 8.0)) ax = fig.add_subplot(111, projection="polar") graphics.plot_plasmid_map( ax, annotation, plasmid_size=1500, label="My plasmid", label_properties={"fontsize": 8}, ) ticks = ax.get_xticks() labels = ax.get_xticklabels() fig.tight_layout() plt.show() .. _sphx_glr_download_examples_gallery_sequence_annotation_plasmid_map_custom.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plasmid_map_custom.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plasmid_map_custom.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plasmid_map_custom.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_