def anova_one_drug_one_feature(anova, options):
"""Analyse the entire data set"""
from gdsctools import anova_report
if options.tissue is not None:
anova.set_cancer_type(options.tissue)
odof = anova_report.Association(anova,
drug=options.drug,
feature=options.feature)
#print(odof.settings)
# for the HTML
#odof.add_dependencies = True
#odof.add_settings = True
df = odof.run()
if df.ix[1]['FEATURE_IC50_effect_size'] is None:
msg = "association %s vs %s not valid for testing (not enough" +\
" MSI or positives for that features ? Try with "+\
" --exclude-msi (you must then set a tissue with "+\
" --tissue"
print(red(msg % (options.drug, options.feature)))
else:
print(df.T)
# HTML report
if options.no_html is True:
return
odof.create_report(onweb=options.onweb)
def anova_one_drug(anova, options):
"""Analyse one specific drug"""
from gdsctools import ANOVAReport
anova.set_cancer_type(options.tissue)
if options.feature:
anova.feature_names = options.features
results = anova.anova_one_drug(options.drug)
print("\nFound %s associations" % len(results))
if len(results)==0:
print(red("\nPlease try with another drug or no --drug option"))
return
# ?? is this required ?
N = len(results)
results.df.insert(0, 'ASSOC_ID', range(1, N+1))
if options.no_html is True:
return
r = ANOVAReport(anova, results=results)
print(darkgreen("\nCreating all figure and html documents in %s" %
r.settings.directory))
r.create_html_pages(onweb=options.onweb)
def anova_one_drug(anova, options):
"""Analyse one specific drug"""
from gdsctools import ANOVAReport
anova.set_cancer_type(options.tissue)
if options.feature:
anova.feature_names = options.features
results = anova.anova_one_drug(options.drug)
print("\nFound %s associations" % len(results))
if len(results) == 0:
print(red("\nPlease try with another drug or no --drug option"))
return
# ?? is this required ?
N = len(results)
results.df.insert(0, 'ASSOC_ID', range(1, N + 1))
if options.no_html is True:
return
r = ANOVAReport(anova, results=results)
print(
darkgreen("\nCreating all figure and html documents in %s" %
r.settings.directory))
r.create_html_pages(onweb=options.onweb)
def anova_one_drug_one_feature(anova, options):
"""Analyse the entire data set"""
from gdsctools import anova_report
if options.tissue is not None:
anova.set_cancer_type(options.tissue)
odof = anova_report.Association(anova,
drug=options.drug,
feature=options.feature)
#print(odof.settings)
# for the HTML
#odof.add_dependencies = True
#odof.add_settings = True
df = odof.run()
if df.ix[1]['FEATURE_IC50_effect_size'] is None:
msg = "association %s vs %s not valid for testing (not enough" +\
" MSI or positives for that features ? Try with "+\
" --exclude-msi (you must then set a tissue with "+\
" --tissue"
print(red(msg % (options.drug, options.feature)))
else:
print(df.T)
# HTML report
if options.no_html is True:
return
odof.create_report(onweb=options.onweb)
def anova_one_drug_one_feature(anova, options):
"""Analyse the entire data set"""
from gdsctools import anova_report
from gdsctools.report import ReportMain
if options.tissue is not None:
anova.set_cancer_type(options.tissue)
# just to create the directory
ReportMain(directory=options.directory)
odof = anova_report.Association(anova,
drug=int(options.drug),
feature=options.feature)
odof.add_href = False
df = odof.run()
if df.loc[1]['FEATURE_IC50_effect_size'] is None:
msg = "association %s vs %s not valid for testing (not enough" +\
" MSI or positives for that features ? Try with "+\
" --exclude-msi (you must then set a tissue with "+\
" --tissue"
print(red(msg % (options.drug, options.feature)))
else:
print(df.T)
# HTML report
if options.no_html is True:
return
odof.create_report(onweb=options.onweb)
