def test_multicore():
an = ANOVA(ic50_test)
results = an.anova_all()
an2 = ANOVA(ic50_test)
results2 = an2.anova_all(multicore=2)
all(results.df.fillna(0) == results2.df.fillna(0))
def test_multicore():
an = ANOVA(ic50_test)
results = an.anova_all()
an2 = ANOVA(ic50_test)
results2 = an2.anova_all(multicore=2)
all(results.df.fillna(0) == results2.df.fillna(0))
def _analyse_all(self, multicore=None):
for gf_filename in sorted(self.gf_filenames):
tcga = gf_filename.split("_")[1].split('.')[0]
print(purple('======================== Analysing %s data' % tcga))
self.mkdir(self.main_directory + os.sep + tcga)
# Computes the ANOVA
try:
self.ic50 = IC50(self.ic50_filename)
except:
print("Clustering IC50 (v18 released data ?)")
self.ic50 = IC50Cluster(self.ic50_filename, verbose=False)
an = ANOVA(self.ic50, gf_filename, self.drug_decode, verbose=False)
if self.test is True:
an.features.df = an.features.df[an.features.df.columns[0:15]]
self.an = an
an.settings = ANOVASettings(**self.settings)
an.settings.analysis_type = tcga
an.init() # This reset the directory
results = an.anova_all(multicore=multicore)
an.settings.directory = self.main_directory + os.sep + tcga
# Store the results
self.results[tcga] = results
print('Analysing %s data and creating images' % tcga)
self.report = ANOVAReport(an)
self.report.settings.savefig = True
self.report.create_html_pages(onweb=False)
def test_anova_all():
an = ANOVA(ic50_test)
# slow, let us cut the features to keep only tenish
# this is a trick but would be nice to have this in the API
features = an.features.df
features = features[features.columns[0:12]]
an = ANOVA(ic50_test, features)
results = an.anova_all()
assert_almost_equal( results.df['ANOVA_FEATURE_FDR'].sum(),
10312.23061065521, 6)
an2 = ANOVA(ic50_test, features, set_media_factor=True)
results = an2.anova_all()
assert_almost_equal( results.df['ANOVA_FEATURE_FDR'].sum(),
10238.529313503008, 6)
def _analyse_all(self, multicore=None):
for gf_filename in sorted(self.gf_filenames):
tcga = gf_filename.split("_")[1].split('.')[0]
print(purple('======================== Analysing %s data' % tcga))
self.mkdir(self.main_directory + os.sep + tcga)
# Computes the ANOVA
try:
self.ic50 = IC50(self.ic50_filename)
except:
print("Clustering IC50 (v18 released data ?)")
self.ic50 = IC50Cluster(self.ic50_filename, verbose=False)
an = ANOVA(self.ic50, gf_filename, self.drug_decode,
verbose=False)
if self.test is True:
an.features.df = an.features.df[an.features.df.columns[0:15]]
self.an = an
an.settings = ANOVASettings(**self.settings)
an.settings.analysis_type = tcga
an.init() # This reset the directory
results = an.anova_all(multicore=multicore)
an.settings.directory = self.main_directory + os.sep + tcga
# Store the results
self.results[tcga] = results
print('Analysing %s data and creating images' % tcga)
self.report = ANOVAReport(an)
self.report.settings.savefig = True
self.report.create_html_pages(onweb=False)
def test_anova_all():
an = ANOVA(ic50_test)
# slow, let us cut the features to keep only tenish
# this is a trick but would be nice to have this in the API
features = an.features.df
features = features[features.columns[0:12]]
an = ANOVA(ic50_test, features)
results = an.anova_all()
assert_almost_equal(results.df['ANOVA_FEATURE_FDR'].sum(),
10312.23061065521, 6)
an2 = ANOVA(ic50_test, features, set_media_factor=True)
results = an2.anova_all()
assert_almost_equal(results.df['ANOVA_FEATURE_FDR'].sum(),
10238.529313503008, 6)
def test_anova_all():
an = ANOVA(ic50_test)
# slow, let us cut the features to keep only ten-ish values
# this is a trick but would be nice to have this in the API
features = an.features.df
features = features[features.columns[0:12]]
an = ANOVA(ic50_test, features)
results = an.anova_all()
results # test __repr__
results.volcano()
results.barplot_effect_size()
assert_almost_equal(results.df["ANOVA_FEATURE_FDR"].sum(), 10312.23061065521, delta=1e-6)
an2 = ANOVA(ic50_test, features, set_media_factor=True)
results = an2.anova_all()
assert_almost_equal(results.df["ANOVA_FEATURE_FDR"].sum(), 10238.529313503008, delta=1e-6)
def test_html():
# same as above, could factorise
an = ANOVA(ic50_test)
features = an.features.df
features = features[features.columns[0:30]]
an = ANOVA(ic50_test, features)
#an.settings.include_media_factor = False
results = an.anova_all()
assert len(results.df) == 302
r = ANOVAReport(gdsc=an, results=results)
assert len(r.get_significant_set()) == 3
# long but should cover everthinh.
try:
r.create_html_pages()
except Exception as err:
raise err
finally:
import shutil
shutil.rmtree('html_gdsc_anova')
def test_html():
# same as above, could factorise
an = ANOVA(ic50_test)
features = an.features.df
features = features[features.columns[0:30]]
an = ANOVA(ic50_test, features)
#an.settings.include_media_factor = False
results = an.anova_all()
assert len(results.df) == 302
r = ANOVAReport(gdsc=an, results=results)
assert len(r.get_significant_set()) == 3
# long but should cover everthinh.
try:
r.create_html_pages()
except Exception as err:
raise err
finally:
import shutil
shutil.rmtree('html_gdsc_anova')
def _analyse_all(self):
for gf_filename in sorted(self.gf_filenames):
tcga = gf_filename.split("_")[1].split('.')[0]
print('================================ Analysing %s data' % tcga)
self.mkdir('ALL' + os.sep + tcga)
# Computes the ANOVA
an = ANOVA(self.ic50_filename, gf_filename, self.drug_decode)
self.an = an
an.settings = ANOVASettings(**self.settings)
an.init() # reset the analysis_type automatically
results = an.anova_all()
# Store the results
self.results[tcga] = results
print('Analysing %s data and creating images' % tcga)
self.report = ANOVAReport(an, self.results[tcga])
self.report.settings.savefig = True
self.report.settings.directory = 'ALL/' + tcga
self.report.settings.analysis_type = tcga
self.report.create_html_pages()
def _analyse_all(self):
for gf_filename in sorted(self.gf_filenames):
tcga = gf_filename.split("_")[1].split('.')[0]
print('================================ Analysing %s data' % tcga)
self.mkdir('ALL' + os.sep + tcga)
# Computes the ANOVA
an = ANOVA(self.ic50_filename, gf_filename, self.drug_decode)
self.an = an
an.settings = ANOVASettings(**self.settings)
an.init() # reset the analysis_type automatically
results = an.anova_all()
# Store the results
self.results[tcga] = results
print('Analysing %s data and creating images' % tcga)
self.report = ANOVAReport(an, self.results[tcga])
self.report.settings.savefig = True
self.report.settings.directory = 'ALL/' + tcga
self.report.settings.analysis_type = tcga
self.report.create_html_pages()
