%matplotlib inline
%pylab inline
from gdsctools import anova
matplotlib.rcParams['figure.figsize'] = (10,6)
Populating the interactive namespace from numpy and matplotlib
from gdsctools import *
an = ANOVA(ic50_test)
WARNING: column named 'MEDIA_FACTOR' not found TISSUE FACTOR : included MEDIA FACTOR : NOT included MSI FACTOR : included FEATURE FACTOR : included
results = an.anova_all()
[-----------------100%-----------------] 11 of 11 complete in 3.7 sec
report = ANOVAReport(an, results)
WARNING no drug name or target will be populated You can read one if you wish using read_drug_decode
# This can take a while since it created all HTML and PNG images
# This will be created in a directory called html_gdsc_anova by default
# See settings notebook for details
report.create_html_pages()
Creating main HTML page in directory html_gdsc_anova Creating volcano plots
/home/cokelaer/Work/virtualenv/lib/python2.7/site-packages/matplotlib/collections.py:590: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison if self._edgecolors == str('face'): /home/cokelaer/Work/virtualenv/lib/python2.7/site-packages/mpld3/mplexporter/exporter.py:82: UserWarning: Blended transforms not yet supported. Zoom behavior may not work as expected. warnings.warn("Blended transforms not yet supported. "
openning html_gdsc_anova/index.html Creating individual HTML pages for each drug [-----------------100%-----------------] 11 of 11 complete in 7.3 sec Creating individual HTML pages for each feature [-----------------100%-----------------] 4 of 4 complete in 2.7 sec
/home/cokelaer/Work/virtualenv/lib/python2.7/site-packages/pandas/core/indexing.py:420: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy self.obj[item] = s /home/cokelaer/Work/virtualenv/lib/python2.7/site-packages/pandas/core/index.py:4281: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison return np.sum(name == np.asarray(self.names)) > 1
Creating individual HTML pages for each association [-----------------100%-----------------] 5 of 5 complete in 12.2 sec
df = report.drug_summary()
df = report.feature_summary()
df = report.get_significant_hits()
/home/cokelaer/Work/virtualenv/lib/python2.7/site-packages/pandas/computation/expressions.py:190: UserWarning: evaluating in Python space because the '+' operator is not supported by numexpr for the bool dtype, use '|' instead unsupported[op_str]))
# you can create an individual HTML page e.g. the MANOVA page
report.create_html_manova()
openning html_gdsc_anova/manova.html