In [1]:

    

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())


    

    




/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandas/io/excel.py:626: UserWarning: Installed openpyxl is not supported at this time. Use >=1.6.1 and <2.0.0.
  .format(openpyxl_compat.start_ver, openpyxl_compat.stop_ver))






    
Out[1]:

In [2]:

    

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


    

In [3]:

    

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


    

In [4]:

    

session.query(GeneGroup).all()


    

    
Out[4]:





[Gene Group (#1, Glycolysis / Gluconeogenesis) 40 genes,
 Gene Group (#2, Citrate cycle (TCA cycle)) 28 genes,
 Gene Group (#3, Pentose phosphate pathway) 30 genes,
 Gene Group (#4, Pentose and glucuronate interconversions) 27 genes,
 Gene Group (#5, Fructose and mannose metabolism) 38 genes,
 Gene Group (#6, Galactose metabolism) 33 genes,
 Gene Group (#7, Ascorbate and aldarate metabolism) 14 genes,
 Gene Group (#8, Fatty acid biosynthesis) 12 genes,
 Gene Group (#9, Fatty acid metabolism) 16 genes,
 Gene Group (#10, Ubiquinone and other terpenoid-quinone biosynthesis) 17 genes,
 Gene Group (#11, Oxidative phosphorylation) 41 genes,
 Gene Group (#12, Purine metabolism) 87 genes,
 Gene Group (#13, Pyrimidine metabolism) 53 genes,
 Gene Group (#14, Alanine, aspartate and glutamate metabolism) 29 genes,
 Gene Group (#15, Glycine, serine and threonine metabolism) 32 genes,
 Gene Group (#16, Cysteine and methionine metabolism) 28 genes,
 Gene Group (#17, Valine, leucine and isoleucine degradation) 12 genes,
 Gene Group (#18, Geraniol degradation) 6 genes,
 Gene Group (#19, Valine, leucine and isoleucine biosynthesis) 21 genes,
 Gene Group (#20, Lysine biosynthesis) 16 genes,
 Gene Group (#21, Lysine degradation) 11 genes,
 Gene Group (#22, Arginine and proline metabolism) 43 genes,
 Gene Group (#23, Histidine metabolism) 9 genes,
 Gene Group (#24, Tyrosine metabolism) 9 genes,
 Gene Group (#25, Phenylalanine metabolism) 18 genes,
 Gene Group (#26, gamma-Hexachlorocyclohexane degradation) 5 genes,
 Gene Group (#27, Benzoate degradation via hydroxylation) 5 genes,
 Gene Group (#28, Fluorobenzoate degradation) 1 genes,
 Gene Group (#29, Tryptophan metabolism) 11 genes,
 Gene Group (#30, Phenylalanine, tyrosine and tryptophan biosynthesis) 21 genes,
 Gene Group (#31, Novobiocin biosynthesis) 4 genes,
 Gene Group (#32, beta-Alanine metabolism) 15 genes,
 Gene Group (#33, Taurine and hypotaurine metabolism) 6 genes,
 Gene Group (#34, Phosphonate and phosphinate metabolism) 2 genes,
 Gene Group (#35, Selenoamino acid metabolism) 14 genes,
 Gene Group (#36, Cyanoamino acid metabolism) 6 genes,
 Gene Group (#37, D-Glutamine and D-glutamate metabolism) 5 genes,
 Gene Group (#38, D-Alanine metabolism) 4 genes,
 Gene Group (#39, Glutathione metabolism) 17 genes,
 Gene Group (#40, Starch and sucrose metabolism) 32 genes,
 Gene Group (#41, Other glycan degradation) 4 genes,
 Gene Group (#42, Amino sugar and nucleotide sugar metabolism) 44 genes,
 Gene Group (#43, Streptomycin biosynthesis) 9 genes,
 Gene Group (#44, Polyketide sugar unit biosynthesis) 6 genes,
 Gene Group (#45, Lipopolysaccharide biosynthesis) 27 genes,
 Gene Group (#46, Peptidoglycan biosynthesis) 23 genes,
 Gene Group (#47, Glycerolipid metabolism) 13 genes,
 Gene Group (#48, Inositol phosphate metabolism) 3 genes,
 Gene Group (#49, Glycerophospholipid metabolism) 28 genes,
 Gene Group (#50, Arachidonic acid metabolism) 2 genes,
 Gene Group (#51, alpha-Linolenic acid metabolism) 3 genes,
 Gene Group (#52, Sphingolipid metabolism) 3 genes,
 Gene Group (#53, Pyruvate metabolism) 43 genes,
 Gene Group (#54, Biphenyl degradation) 2 genes,
 Gene Group (#55, Toluene and xylene degradation) 2 genes,
 Gene Group (#56, 1- and 2-Methylnaphthalene degradation) 4 genes,
 Gene Group (#57, Naphthalene and anthracene degradation) 1 genes,
 Gene Group (#58, 1,4-Dichlorobenzene degradation) 3 genes,
 Gene Group (#59, Fluorene degradation) 3 genes,
 Gene Group (#60, Carbazole degradation) 2 genes,
 Gene Group (#61, Glyoxylate and dicarboxylate metabolism) 36 genes,
 Gene Group (#62, Benzoate degradation via CoA ligation) 16 genes,
 Gene Group (#63, Trinitrotoluene degradation) 7 genes,
 Gene Group (#64, Propanoate metabolism) 30 genes,
 Gene Group (#65, 3-Chloroacrylic acid degradation) 4 genes,
 Gene Group (#66, Ethylbenzene degradation) 4 genes,
 Gene Group (#67, Styrene degradation) 3 genes,
 Gene Group (#68, Butanoate metabolism) 35 genes,
 Gene Group (#69, C5-Branched dibasic acid metabolism) 9 genes,
 Gene Group (#70, One carbon pool by folate) 13 genes,
 Gene Group (#71, Methane metabolism) 15 genes,
 Gene Group (#72, Thiamine metabolism) 14 genes,
 Gene Group (#73, Riboflavin metabolism) 11 genes,
 Gene Group (#74, Vitamin B6 metabolism) 9 genes,
 Gene Group (#75, Nicotinate and nicotinamide metabolism) 17 genes,
 Gene Group (#76, Pantothenate and CoA biosynthesis) 21 genes,
 Gene Group (#77, Biotin metabolism) 7 genes,
 Gene Group (#78, Lipoic acid metabolism) 3 genes,
 Gene Group (#79, Folate biosynthesis) 12 genes,
 Gene Group (#80, Porphyrin and chlorophyll metabolism) 25 genes,
 Gene Group (#81, Terpenoid backbone biosynthesis) 13 genes,
 Gene Group (#82, Limonene and pinene degradation) 5 genes,
 Gene Group (#83, Nitrogen metabolism) 35 genes,
 Gene Group (#84, Sulfur metabolism) 13 genes,
 Gene Group (#85, Caprolactam degradation) 4 genes,
 Gene Group (#86, Aminoacyl-tRNA biosynthesis) 26 genes,
 Gene Group (#87, Biosynthesis of unsaturated fatty acids) 6 genes,
 Gene Group (#88, Biosynthesis of siderophore group nonribosomal peptides) 6 genes,
 Gene Group (#89, ABC transporters) 182 genes,
 Gene Group (#90, Two-component system) 130 genes,
 Gene Group (#91, Bacterial chemotaxis) 21 genes,
 Gene Group (#92, Flagellar assembly) 38 genes,
 Gene Group (#93, Phosphotransferase system (PTS)) 45 genes,
 Gene Group (#94, Ribosome) 79 genes,
 Gene Group (#95, RNA degradation) 15 genes,
 Gene Group (#96, RNA polymerase) 4 genes,
 Gene Group (#97, DNA replication) 17 genes,
 Gene Group (#98, Protein export) 19 genes,
 Gene Group (#99, Bacterial secretion system) 32 genes,
 Gene Group (#100, Base excision repair) 14 genes,
 Gene Group (#101, Nucleotide excision repair) 8 genes,
 Gene Group (#102, Mismatch repair) 22 genes,
 Gene Group (#103, Homologous recombination) 27 genes]

In [5]:

    

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


    

In [6]:

    

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


    

In [16]:

    

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)


    

In [17]:

    

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


    

In [9]:

    

genes = session.query(GeneGroup).filter(GeneGroup.name.ilike('%ABC%')).first().genes
heatmap_args = gene_heatmap(genes, analysis_type=ChIPPeakGeneExpression,
                                   dataset_type='%',
                                   strain1=session.query(Strain).all())


    

In [10]:

    

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


    

In [10]:

    




    

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