def anova_pipeline(args=None):
"""This function is used by the standalone application called
**gdsctools_anova**
Type::
gdsctools_anova --help
to get some help.
"""
msg = "Welcome to GDSCTools standalone"
print_color(msg, purple, underline=True)
# Keep the argument args as None by default to
# allow testing e.g., in nosetests
if args is None:
args = sys.argv[:]
elif len(args) == 1:
args += ['--help']
user_options = ANOVAOptions(prog="gdsctools_anova")
try:
options = user_options.parse_args(args[1:])
except SystemExit:
return
# -----------------------------------------------------------------
# ---------------------------------------- options without analysis
# -----------------------------------------------------------------
if options.version is True:
print("This is version %s of gdsctools_anova" % gdsctools.version)
return
if options.testing is True:
print('Testing mode:')
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
df = an.anova_one_drug_one_feature('Drug_1047_IC50', 'TP53_mut')
assert df.loc[1,'N_FEATURE_pos'] == 554, \
"N_feature_pos must be equal to 554"
print(df.T)
print(darkgreen("\nGDSCTools seems to be installed properly"))
return
if options.save_settings:
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
an.settings.to_json(options.save_settings)
print('Save a default parameter set in %s' % options.save_settings)
return
if options.license is True:
print(gdsctools.license)
return
if options.summary is True:
from gdsctools import anova
an = anova.ANOVA(options.input_ic50, options.input_features)
print(an)
return
if options.print_tissues is True:
from gdsctools import anova
an = anova.ANOVA(options.input_ic50, options.input_features)
tissues = an.tissue_factor
try:
tissues = tissues.sort_values('Tissue Factor').unique()
except:
tissues = tissues.sort(inplace=False).unique()
for name in tissues:
print(name)
return
if options.print_drugs is True:
from gdsctools import anova
gdsc = anova.ANOVA(options.input_ic50, options.input_features)
import textwrap
print("\n".join(textwrap.wrap(" , ".join(gdsc.drugIds))))
return
if options.print_features is True:
from gdsctools import anova
gdsc = anova.ANOVA(options.input_ic50, options.input_features)
import textwrap
print("\n".join(textwrap.wrap(" , ".join(gdsc.feature_names))))
return
# -----------------------------------------------------------------
# --------------------------------------------------- real analysis
# -----------------------------------------------------------------
# dispatcher to the functions according to the user parameters
from gdsctools import ANOVA, ANOVAReport
anova = ANOVA(options.input_ic50, options.input_features,
options.input_drug,
low_memory=not options.fast)
anova = _set_settings(anova, options)
if options.drug and options.drug not in anova.ic50.df.columns:
print(red("Invalid Drug. Try --print-drug-names"))
sys.exit(1)
if options.drug is not None and options.feature is not None:
print_color("ODOF mode", purple)
anova_one_drug_one_feature(anova, options)
elif options.drug is not None:
print_color("ODAF mode", purple)
anova_one_drug(anova, options)
else: # analyse everything
if options.feature is None:
print_color("ADAF mode", purple)
else:
print_color("ADOF mode", purple)
anova_all(anova, options)
if options.onweb is False and options.no_html is False:
msg = "\nNote that a directory {} was created and files saved into it"
print(purple(msg.format(options.directory)))
return
def anova_pipeline(args=None):
"""This function is used by the standalone application called
**gdsctools_anova**
Type::
gdsctools_anova --help
to get some help.
"""
msg = "Welcome to GDSCTools standalone"
print_color(msg, purple, underline=True)
# Keep the argument args as None by default to
# allow testing e.g., in nosetests
if args is None:
args = sys.argv[:]
elif len(args) == 1:
args += ['--help']
user_options = ANOVAOptions(prog="gdsctools_anova")
try:
options = user_options.parse_args(args[1:])
except SystemExit:
return
# -----------------------------------------------------------------
# ---------------------------------------- options without analysis
# -----------------------------------------------------------------
if options.version is True:
print("This is version %s of gdsctools_anova" % gdsctools.version)
return
if options.testing is True:
print('Testing mode:')
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
df = an.anova_one_drug_one_feature('Drug_1047_IC50', 'TP53_mut')
assert df.loc[1,'N_FEATURE_pos'] == 554, \
"N_feature_pos must be equal to 554"
print(df.T)
print(darkgreen("\nGDSCTools seems to be installed properly"))
return
if options.save_settings:
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
an.settings.to_json(options.save_settings)
print('Save a default parameter set in %s' % options.save_settings)
return
if options.license is True:
print(gdsctools.license)
return
if options.summary is True:
from gdsctools import anova
an = anova.ANOVA(options.input_ic50, options.input_features)
print(an)
return
if options.print_tissues is True:
from gdsctools import anova
an = anova.ANOVA(options.input_ic50, options.input_features)
tissues = an.tissue_factor
try:
tissues = tissues.sort_values('Tissue Factor').unique()
except:
tissues = tissues.sort(inplace=False).unique()
for name in tissues:
print(name)
return
if options.print_drugs is True:
from gdsctools import anova
gdsc = anova.ANOVA(options.input_ic50, options.input_features)
import textwrap
print("\n".join(textwrap.wrap(" , ".join(gdsc.drugIds))))
return
if options.print_features is True:
from gdsctools import anova
gdsc = anova.ANOVA(options.input_ic50, options.input_features)
import textwrap
print("\n".join(textwrap.wrap(" , ".join(gdsc.feature_names))))
return
# -----------------------------------------------------------------
# --------------------------------------------------- real analysis
# -----------------------------------------------------------------
# dispatcher to the functions according to the user parameters
from gdsctools import ANOVA, ANOVAReport
anova = ANOVA(options.input_ic50,
options.input_features,
options.input_drug,
low_memory=not options.fast)
anova = _set_settings(anova, options)
if options.drug and options.drug not in anova.ic50.df.columns:
print(red("Invalid Drug. Try --print-drug-names"))
sys.exit(1)
if options.drug is not None and options.feature is not None:
print_color("ODOF mode", purple)
anova_one_drug_one_feature(anova, options)
elif options.drug is not None:
print_color("ODAF mode", purple)
anova_one_drug(anova, options)
else: # analyse everything
if options.feature is None:
print_color("ADAF mode", purple)
else:
print_color("ADOF mode", purple)
anova_all(anova, options)
if options.onweb is False and options.no_html is False:
msg = "\nNote that a directory {} was created and files saved into it"
print(purple(msg.format(options.directory)))
return
"""
Association between a Drug and a Feature
=========================================
Boxplot association
"""
#####################################################
#
from gdsctools import ANOVA, ic50_test
gdsc = ANOVA(ic50_test)
gdsc.set_cancer_type('breast')
df = gdsc.anova_one_drug_one_feature(1047, 'TP53_mut', show=True)
"""
Association between a Drug and a Feature
=========================================
Boxplot association
"""
#####################################################
#
from gdsctools import ANOVA, ic50_test
gdsc = ANOVA(ic50_test)
gdsc.set_cancer_type('breast')
df = gdsc.anova_one_drug_one_feature(1047, 'TP53_mut', show=True)
