def _generic_plot(output_dir: str, master: skbio.OrdinationResults,
metadata: qiime2.Metadata,
other_pcoa: skbio.OrdinationResults, plot_name,
custom_axes: str=None):
mf = metadata.to_dataframe()
if other_pcoa is None:
procrustes = None
else:
procrustes = [other_pcoa]
viz = Emperor(master, mf, procrustes=procrustes, remote='.')
if custom_axes is not None:
viz.custom_axes = custom_axes
if other_pcoa:
viz.procrustes_names = ['reference', 'other']
html = viz.make_emperor(standalone=True)
viz.copy_support_files(output_dir)
with open(os.path.join(output_dir, 'emperor.html'), 'w') as fh:
fh.write(html)
index = os.path.join(TEMPLATES, 'index.html')
q2templates.render(index, output_dir, context={'plot_name': plot_name})
def _generic_plot(output_dir: str, master: skbio.OrdinationResults,
metadata: qiime2.Metadata,
other_pcoa: skbio.OrdinationResults, plot_name,
custom_axes: str=None,
feature_metadata: qiime2.Metadata=None):
mf = metadata.to_dataframe()
if feature_metadata is not None:
feature_metadata = feature_metadata.to_dataframe()
if other_pcoa is None:
procrustes = None
else:
procrustes = [other_pcoa]
viz = Emperor(master, mf, feature_mapping_file=feature_metadata,
procrustes=procrustes, remote='.')
if custom_axes is not None:
viz.custom_axes = custom_axes
if other_pcoa:
viz.procrustes_names = ['reference', 'other']
html = viz.make_emperor(standalone=True)
viz.copy_support_files(output_dir)
with open(os.path.join(output_dir, 'emperor.html'), 'w') as fh:
fh.write(html)
index = os.path.join(TEMPLATES, 'index.html')
q2templates.render(index, output_dir, context={'plot_name': plot_name})
def generic_plot(output_dir: str,
master: skbio.OrdinationResults,
metadata: qiime2.Metadata,
other_pcoa: skbio.OrdinationResults,
plot_name: str,
info: str = None,
custom_axes: str = None,
settings: dict = None,
ignore_missing_samples: bool = False,
feature_metadata: qiime2.Metadata = None):
mf = metadata.to_dataframe()
if feature_metadata is not None:
feature_metadata = feature_metadata.to_dataframe()
if other_pcoa is None:
procrustes = None
else:
procrustes = [other_pcoa]
viz = Emperor(master,
mf,
feature_mapping_file=feature_metadata,
ignore_missing_samples=ignore_missing_samples,
procrustes=procrustes,
remote='.')
if custom_axes is not None:
viz.custom_axes = custom_axes
if other_pcoa:
viz.procrustes_names = ['reference', 'other']
viz.info = info
viz.settings = settings
html = viz.make_emperor(standalone=True)
viz.copy_support_files(output_dir)
with open(os.path.join(output_dir, 'emperor.html'), 'w') as fh:
fh.write(html)
index = os.path.join(TEMPLATES, 'index.html')
q2templates.render(index, output_dir, context={'plot_name': plot_name})