def plot_cm(ecs, output_file=None):
"""
Simple wrapper for contact map plotting
"""
with misc.plot_context("Arial"):
fig = plt.figure(figsize=(8, 8))
if kwargs["scale_sizes"]:
ecs = ecs.copy()
ecs.loc[:, "size"] = ecs.cn.values / ecs.cn.max()
pairs.plot_contact_map(
ecs,
d_intra,
d_multimer,
distance_cutoff=kwargs["distance_cutoff"],
show_secstruct=kwargs["draw_secondary_structure"],
margin=5,
boundaries=kwargs["boundaries"])
plt.suptitle("{} evolutionary couplings".format(len(ecs)),
fontsize=14)
if output_file is not None:
plt.savefig(output_file, bbox_inches="tight")
plt.close(fig)
def plot_cm(ecs, output_file=None):
"""
Simple wrapper for contact map plotting
"""
with misc.plot_context("Arial"):
fig = plt.figure(figsize=(10, 10))
if kwargs["scale_sizes"]:
ecs = ecs.copy()
ecs.loc[:, "size"] = ecs.score.values / ecs.score.max()
# avoid negative sizes
ecs.loc[ecs["size"] < 0, "size"] = 0
# draw PDB structure and alignment/EC coverage information on contact map if selected
# (for now, not a required parameter, default to True)
if kwargs.get("draw_coverage", True):
additional_plot_kwargs = {
"show_structure_coverage": True,
"margin": 0,
"ec_coverage": ec_table,
}
else:
additional_plot_kwargs = {
"show_structure_coverage": False,
"margin": 5,
"ec_coverage": None,
}
pairs.plot_contact_map(
ecs,
d_intra,
d_multimer,
distance_cutoff=kwargs["distance_cutoff"],
show_secstruct=kwargs["draw_secondary_structure"],
boundaries=kwargs["boundaries"],
**additional_plot_kwargs)
# print PDB information if selected as parameter
# (for now, not a required parameter, default to True)
if kwargs.get("print_pdb_information",
True) and sifts_map is not None and len(
sifts_map.hits) > 0:
print_pdb_structure_info(
sifts_map,
ax=plt.gca(),
header_text="PDB structures:",
)
plt.suptitle("{} evolutionary couplings".format(len(ecs)),
fontsize=14)
if output_file is not None:
plt.savefig(output_file, bbox_inches="tight")
plt.close(fig)