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from om import base, settings
from om.components import *
from om.data import *
from om.util import *

from IPython.display import Javascript

session = base.Session()

ged = GeneExpressionData
dged = DifferentialGeneExpressionData
cpge = ChIPPeakGeneExpression


Javascript(open('lib/heatmap.js','r').read())


    

    




cobra/io/__init__.py:17 UserWarning: cobra.io.sbml requires libsbml






    
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genes = session.query(GeneGroup).filter(GeneGroup.name.ilike('crp_cat%')).first().genes

heatmap_args = gene_heatmap(genes, analysis_type=GeneExpressionData,
                                   dataset_type='rnaseq_experiment',
                                   strain1=session.query(Strain).filter(Strain.name.in_(['wt','delta-fur'])).all())


    

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heatmap_diagram = HeatmapWidget(**heatmap_args)
display(heatmap_diagram)


    

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heatmap_args = gene_heatmap(genes, analysis_type=GeneExpressionData,
                                   dataset_type='array_experiment',
                                   strain1=session.query(Strain).all())


    

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heatmap_diagram = HeatmapWidget(**heatmap_args)
display(heatmap_diagram)


    

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genes = ome.query(GeneGroup).filter(GeneGroup.name.ilike('Arg%')).first().genes

environments1 = session.query(InVivoEnvironment).filter(InVivoEnvironment.nitrogen_source.in_(['cytidine','glutamine','cytosine'])).all()
environments2 = session.query(InVivoEnvironment).filter_by(nitrogen_source='NH4Cl').all()

heatmap_args = gene_heatmap(genes, analysis_type=DifferentialGeneExpressionData,
                                   strain1=session.query(Strain).all(),
                                   environments1 = environments1,
                                   environments2 = environments2)


    

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heatmap_diagram = HeatmapWidget(**heatmap_args)
display(heatmap_diagram)


    

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genes = session.query(GeneGroup).filter(GeneGroup.name.ilike('crp_cat%')).first().genes
heatmap_args = gene_heatmap(genes, analysis_type=ChIPPeakGeneExpression,
                                   strain1=session.query(Strain).all())
#heatmap_args['maxval'] = 3.
#heatmap_args['minval'] = -3.


    

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heatmap_diagram = HeatmapWidget(**heatmap_args)
display(heatmap_diagram)


    

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