In the introduction we have analysed a IC50 input file. We performed a full analysis that is we analyse all associations between all drugs and all features. This may take a while and sometimes one is just interested in a single drug or a sub set of drugs. In this notebook, we show how to restrict the analysis.
%pylab inline
matplotlib.rcParams['figure.figsize'] = (10,6)
Populating the interactive namespace from numpy and matplotlib
As before, we create an ANOVA instance. Pur input IC50 will be the test file
from gdsctools import ANOVA, ic50_test
an = ANOVA(ic50_test)
WARNING: column named 'MEDIA_FACTOR' not found TISSUE FACTOR : included MEDIA FACTOR : NOT included MSI FACTOR : included FEATURE FACTOR : included
Drugs are stored in the drugIds in case you forgot the drug you are interested in.. eg. the first drug identifer is
drug_name = an.drugIds[0]
results = an.anova_one_drug(drug_name)
[-----------------100%-----------------] 47 of 47 complete in 0.3 sec
Now, you can create an HTML report or simply call one of the volcano plot
# These 4 lines are for the notebook only if mpld3 is enabled,
# the matploltib figure does not show up
try:
mpld3.disable_notebook()
except:
pass
results.volcano()
import mpld3
mpld3.enable_notebook()
mpld3.display(results.handle_volcano.current_fig)
# 1. hover the mouse on circles to get more information.
# 2. in the bottom right corner you can find small icons to click on to focus in the images. Click again
# to be able to hover the mouse agains