In [1]:

    

import flotilla


    

    




:0: FutureWarning: IPython widgets are experimental and may change in the future.

In [2]:

    

study = flotilla.embark("pag_demo")


    

    




2015-01-11 13:42:40	Reading datapackage from /home/jovyan/flotilla_projects/pag_demo/datapackage.json
2015-01-11 13:42:40	Parsing datapackage to create a Study object
https://s3-us-west-2.amazonaws.com/flotilla-projects/ercc/ERCC_Controls.txt has not been downloaded before.
	Downloading now to /home/jovyan/flotilla_projects/hg19/ERCC_Controls.txt
2015-01-11 13:43:41	Initializing Study
2015-01-11 13:43:41	Initializing Predictor configuration manager for Study
2015-01-11 13:43:41	Predictor ExtraTreesClassifier is of type <class 'sklearn.ensemble.forest.ExtraTreesClassifier'>
2015-01-11 13:43:41	Added ExtraTreesClassifier to default predictors
2015-01-11 13:43:41	Predictor ExtraTreesRegressor is of type <class 'sklearn.ensemble.forest.ExtraTreesRegressor'>
2015-01-11 13:43:41	Added ExtraTreesRegressor to default predictors
2015-01-11 13:43:41	Predictor GradientBoostingClassifier is of type <class 'sklearn.ensemble.gradient_boosting.GradientBoostingClassifier'>
2015-01-11 13:43:41	Added GradientBoostingClassifier to default predictors
2015-01-11 13:43:41	Predictor GradientBoostingRegressor is of type <class 'sklearn.ensemble.gradient_boosting.GradientBoostingRegressor'>
2015-01-11 13:43:41	Added GradientBoostingRegressor to default predictors
2015-01-11 13:43:41	Loading metadata
2015-01-11 13:43:41	Loading expression data
2015-01-11 13:43:41	Initializing expression
2015-01-11 13:43:41	Done initializing expression






    




Error loading species hg19 data Samples had too few mapped reads (<5.0e+05 reads):
	M_M2nd_23, M_M2nd_30, M_M2nd_31, M_M2nd_32, M_M3_10, P_P4_2, P_P8_12, P_P8_3, P_P8_4, P_P8_7, P_P8_8, P_P8_9, S_MSA_25
Removing technical outliers from consideration in expression:
	M_M2nd_23, M_M2nd_30, M_M2nd_31, M_M2nd_32, M_M3_10, P_P4_2, P_P8_12, P_P8_3, P_P8_4, P_P8_7, P_P8_8, P_P8_9, S_MSA_25
Removing technical outliers from consideration in splicing:
	M_M2nd_23, M_M2nd_30, M_M2nd_31, M_M2nd_32, M_M3_10, P_P4_2, P_P8_12, P_P8_3, P_P8_4, P_P8_7, P_P8_8, P_P8_9, S_MSA_25






    




2015-01-11 13:43:42	Loading splicing data
2015-01-11 13:43:42	Initializing splicing
2015-01-11 13:43:43	Done initializing splicing
2015-01-11 13:43:43	Successfully initialized a Study object!

In [ ]:

    

study.interactive_pca()


    

    




/usr/local/lib/python2.7/dist-packages/flotilla/data_model/metadata.py:186: UserWarning: MetaData.phenotype_series will be deprecated in 0.3.0
  warnings.warn('MetaData.phenotype_series will be deprecated in 0.3.0')
/usr/lib/pymodules/python2.7/matplotlib/font_manager.py:1236: UserWarning: findfont: Font family ['Helvetica', 'Arial'] not found. Falling back to Bitstream Vera Sans
  (prop.get_family(), self.defaultFamily[fontext]))






    




featurewise : False
y_pc : 2
data_type : expression
std_multiplier : 2.0
most_variant_features : False
show_point_labels : False
plot_violins : False
sample_subset : all_samples
feature_subset : variant
bokeh : False
color_samples_by : phenotype
x_pc : 1
list_link : 






    




WARNING: "TextWidget" is deprecated, please use "Text" instead.
WARNING: "ButtonWidget" is deprecated, please use "Button" instead.






    
Out[ ]:





<function flotilla.visualize.ipython_interact.do_interact>






    

In [ ]:

    

study = flotilla.embark("pag_demo", load_species_data=False)