def _debug_dummy_plot(
taxonomy: Taxonomy,
htmlfile: Filename,
scoring: Scoring = Scoring.SHEL,
):
"""
Generate dummy Krona plot via Krona 2.0 XML spec and exit
"""
print(gray(f'Generating dummy Krona plot {htmlfile}...'), end='')
sys.stdout.flush()
samples: List[Sample] = [
Sample('SINGLE'),
]
krona: KronaTree = KronaTree(
samples,
min_score=Score(35),
max_score=Score(100),
scoring=scoring,
)
polytree: MultiTree = MultiTree(samples=samples)
polytree.grow(ontology=taxonomy)
polytree.toxml(ontology=taxonomy, krona=krona)
krona.tohtml(htmlfile, pretty=True)
print(green('OK!'))
def generate_krona():
"""Generate Krona plot with all the results via Krona 2.0 XML spec"""
print(gray('\nBuilding the taxonomy multiple tree... '), end='')
sys.stdout.flush()
krona: KronaTree = KronaTree(
samples,
num_raw_samples=len(raw_samples),
stats=stats,
min_score=Score(
min([
min(scores[sample].values()) for sample in samples
if len(scores[sample])
])),
max_score=Score(
max([
max(scores[sample].values()) for sample in samples
if len(scores[sample])
])),
scoring=scoring,
)
polytree.grow(ontology=ncbi,
abundances=counts,
accs=accs,
scores=scores)
print(green('OK!'))
print(gray('Generating final plot (') + magenta(htmlfile) +
gray(')... '),
end='')
sys.stdout.flush()
polytree.toxml(ontology=ncbi, krona=krona)
krona.tohtml(htmlfile, pretty=False)
print(green('OK!'))