In [ ]:

    

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

import pandas as pd
import numpy as np
import math,cobra

ome = base.Session()
#model = cobra.io.read_sbml_model('/Users/dbuser/Dropbox/om_data/annotation/iJO1366.xml')


    

In [ ]:

    

ome.query(GeneGroup).all()


    

In [2]:

    

from IPython.display import display
from IPython.html import widgets as W
from IPython.utils import traitlets as T

class HeatmapWidget(W.DOMWidget):
    _view_name = T.Unicode('HeatmapView', sync=True)
    heatmap_data = T.Unicode(sync=True)
    row_labels = T.Unicode(sync=True)
    col_labels = T.Unicode(sync=True)
    html_style = T.Unicode(sync=True)


    

In [3]:

    

ged = GeneExpressionData
x = ome.query(ged).filter(and_(ged.gene_name.in_(['sucA','sucB','sucC','sucD','frdA','frdB','frdC','frdD','gapA']),
                           ged.dataset_type == 'array_experiment')).all()


    

In [4]:

    

x


    

    
Out[4]:





[Gene: (b0726, sucA), Value:  8.87, std: 0.20, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b0726, sucA), Value: 13.67, std: 0.02, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b0726, sucA), Value: 13.28, std: 0.14, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b0726, sucA), Value:  9.97, std: 0.76, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b0726, sucA), Value:  8.49, std: 0.09, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b0726, sucA), Value:  8.69, std: 0.16, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b0726, sucA), Value:  8.74, std: 0.23, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b0727, sucB), Value:  9.84, std: 0.26, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b0727, sucB), Value: 13.90, std: 0.04, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b0727, sucB), Value: 13.64, std: 0.20, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b0727, sucB), Value: 11.08, std: 0.54, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b0727, sucB), Value:  9.69, std: 0.12, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b0727, sucB), Value:  9.72, std: 0.10, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b0727, sucB), Value:  9.78, std: 0.18, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b0728, sucC), Value: 10.77, std: 0.15, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b0728, sucC), Value: 14.50, std: 0.05, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b0728, sucC), Value: 14.50, std: 0.16, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b0728, sucC), Value: 12.07, std: 0.41, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b0728, sucC), Value: 10.72, std: 0.04, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b0728, sucC), Value: 10.68, std: 0.03, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b0728, sucC), Value: 10.78, std: 0.08, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b0729, sucD), Value:  5.88, std: 0.13, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b0729, sucD), Value: 11.41, std: 0.12, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b0729, sucD), Value: 11.16, std: 0.40, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b0729, sucD), Value:  7.56, std: 0.73, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b0729, sucD), Value:  5.79, std: 0.05, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b0729, sucD), Value:  5.73, std: 0.07, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b0729, sucD), Value:  5.79, std: 0.05, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b1779, gapA), Value: 15.26, std: 0.05, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b1779, gapA), Value: 15.20, std: 0.06, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b1779, gapA), Value: 15.07, std: 0.07, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b1779, gapA), Value: 15.07, std: 0.06, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b1779, gapA), Value: 15.31, std: 0.02, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b1779, gapA), Value: 15.27, std: 0.02, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b1779, gapA), Value: 15.31, std: 0.02, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b4151, frdD), Value:  7.53, std: 1.33, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b4151, frdD), Value:  5.54, std: 0.71, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b4151, frdD), Value:  4.73, std: 0.12, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b4151, frdD), Value:  4.02, std: 0.62, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b4151, frdD), Value:  9.76, std: 0.32, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b4151, frdD), Value:  9.07, std: 0.23, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b4151, frdD), Value:  8.50, std: 0.36, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b4152, frdC), Value:  4.63, std: 0.45, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b4152, frdC), Value:  3.66, std: 0.66, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b4152, frdC), Value:  2.58, std: 0.06, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b4152, frdC), Value:  2.36, std: 0.09, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b4152, frdC), Value:  5.23, std: 0.28, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b4152, frdC), Value:  4.75, std: 0.21, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b4152, frdC), Value:  5.11, std: 0.26, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b4153, frdB), Value:  9.59, std: 0.56, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b4153, frdB), Value:  8.70, std: 0.58, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b4153, frdB), Value:  7.41, std: 0.07, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b4153, frdB), Value:  5.66, std: 0.66, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b4153, frdB), Value:  9.84, std: 0.20, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b4153, frdB), Value:  9.92, std: 0.05, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b4153, frdB), Value: 10.19, std: 0.24, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b4154, frdA), Value: 11.04, std: 0.57, Condition: glucose, NH4Cl, anaerobic, Strain: wt, array_experiment,
 Gene: (b4154, frdA), Value: 10.09, std: 0.48, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcA, array_experiment,
 Gene: (b4154, frdA), Value:  9.40, std: 0.06, Condition: glucose, NH4Cl, anaerobic, Strain: delta-arcAfnr, array_experiment,
 Gene: (b4154, frdA), Value:  8.06, std: 0.84, Condition: glucose, NH4Cl, anaerobic, Strain: delta-fnr, array_experiment,
 Gene: (b4154, frdA), Value: 11.52, std: 0.33, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narL, array_experiment,
 Gene: (b4154, frdA), Value: 11.50, std: 0.10, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narLnarP, array_experiment,
 Gene: (b4154, frdA), Value: 11.77, std: 0.17, Condition: glucose, NH4Cl, anaerobic, Strain: delta-narP, array_experiment,
 Gene: (b0726, sucA), Value: 11.86, std: 0.10, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b0726, sucA), Value: 13.67, std: 0.08, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0727, sucB), Value: 12.23, std: 0.06, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b0727, sucB), Value: 13.92, std: 0.04, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0728, sucC), Value: 11.91, std: 0.03, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b0728, sucC), Value: 14.21, std: 0.03, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0729, sucD), Value: 12.22, std: 0.03, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b0729, sucD), Value: 14.49, std: 0.03, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b1779, gapA), Value: 14.93, std: 0.01, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b1779, gapA), Value: 15.05, std: 0.04, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4151, frdD), Value:  4.60, std: 0.27, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b4151, frdD), Value:  7.23, std: 1.11, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4152, frdC), Value:  3.98, std: 0.17, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b4152, frdC), Value:  6.66, std: 1.32, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4153, frdB), Value:  7.90, std: 0.29, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b4153, frdB), Value: 11.45, std: 0.91, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4154, frdA), Value:  7.42, std: 0.19, Condition: fructose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b4154, frdA), Value: 12.05, std: 0.45, Condition: fructose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0726, sucA), Value: 12.88, std: 0.06, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b0726, sucA), Value: 13.23, std: 0.18, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0726, sucA), Value: 13.54, std: 0.12, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b0726, sucA), Value: 13.23, std: 0.03, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b0726, sucA), Value: 12.78, std: 0.09, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b0726, sucA), Value: 12.89, std: 0.05, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b0726, sucA), Value: 13.49, std: 0.06, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b0726, sucA), Value: 12.17, std: 0.26, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b0727, sucB), Value: 13.10, std: 0.02, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b0727, sucB), Value: 13.54, std: 0.10, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0727, sucB), Value: 13.71, std: 0.14, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b0727, sucB), Value: 13.56, std: 0.07, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b0727, sucB), Value: 13.30, std: 0.12, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b0727, sucB), Value: 13.35, std: 0.03, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b0727, sucB), Value: 13.64, std: 0.02, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b0727, sucB), Value: 13.08, std: 0.08, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b0728, sucC), Value: 12.99, std: 0.02, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b0728, sucC), Value: 14.01, std: 0.25, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0728, sucC), Value: 14.45, std: 0.08, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b0728, sucC), Value: 14.47, std: 0.08, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b0728, sucC), Value: 13.96, std: 0.16, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b0728, sucC), Value: 13.18, std: 0.05, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b0728, sucC), Value: 13.72, std: 0.03, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b0728, sucC), Value: 12.97, std: 0.02, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b0729, sucD), Value: 13.26, std: 0.06, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b0729, sucD), Value: 11.71, std: 1.73, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0729, sucD), Value: 11.57, std: 0.13, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b0729, sucD), Value: 11.21, std: 0.24, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b0729, sucD), Value: 10.60, std: 0.39, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b0729, sucD), Value: 13.35, std: 0.00, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b0729, sucD), Value: 13.88, std: 0.06, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b0729, sucD), Value: 13.35, std: 0.00, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b1779, gapA), Value: 14.66, std: 0.02, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b1779, gapA), Value: 14.74, std: 0.22, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b1779, gapA), Value: 14.75, std: 0.11, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b1779, gapA), Value: 14.95, std: 0.03, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b1779, gapA), Value: 14.78, std: 0.04, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b1779, gapA), Value: 15.12, std: 0.02, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b1779, gapA), Value: 15.04, std: 0.09, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b1779, gapA), Value: 15.12, std: 0.01, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b4151, frdD), Value:  4.41, std: 0.37, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b4151, frdD), Value:  4.11, std: 0.38, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4151, frdD), Value:  3.27, std: 0.00, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b4151, frdD), Value:  2.86, std: 0.34, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b4151, frdD), Value:  3.15, std: 0.00, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b4151, frdD), Value: 11.15, std: 0.13, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b4151, frdD), Value:  7.80, std: 1.34, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b4151, frdD), Value: 11.39, std: 0.72, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b4152, frdC), Value:  4.12, std: 0.08, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b4152, frdC), Value:  2.54, std: 0.36, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4152, frdC), Value:  2.26, std: 0.01, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b4152, frdC), Value:  2.25, std: 0.00, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b4152, frdC), Value:  2.25, std: 0.00, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b4152, frdC), Value: 11.38, std: 0.08, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b4152, frdC), Value:  8.11, std: 1.75, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b4152, frdC), Value: 11.52, std: 0.46, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b4153, frdB), Value:  9.12, std: 0.26, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b4153, frdB), Value:  4.88, std: 0.30, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4153, frdB), Value:  4.68, std: 0.05, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b4153, frdB), Value:  4.40, std: 0.00, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b4153, frdB), Value:  4.61, std: 0.00, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b4153, frdB), Value: 13.79, std: 0.11, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b4153, frdB), Value: 12.77, std: 0.72, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b4153, frdB), Value: 13.94, std: 0.25, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b4154, frdA), Value:  8.82, std: 0.19, Condition: glucose, NH4Cl, O2, Strain: delta-crp, array_experiment,
 Gene: (b4154, frdA), Value:  6.32, std: 0.97, Condition: glucose, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4154, frdA), Value:  7.24, std: 0.21, Condition: glucose, NH4Cl, O2, Strain: delta-arcA, array_experiment,
 Gene: (b4154, frdA), Value:  6.47, std: 0.70, Condition: glucose, NH4Cl, O2, Strain: delta-arcAfnr, array_experiment,
 Gene: (b4154, frdA), Value:  6.96, std: 0.29, Condition: glucose, NH4Cl, O2, Strain: delta-fnr, array_experiment,
 Gene: (b4154, frdA), Value: 13.60, std: 0.08, Condition: glucose, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b4154, frdA), Value: 13.08, std: 0.45, Condition: glucose, NH4Cl, O2, Strain: delta-lrp, array_experiment,
 Gene: (b4154, frdA), Value: 13.85, std: 0.04, Condition: glucose, NH4Cl, O2, Strain: delta-purR, array_experiment,
 Gene: (b0726, sucA), Value:  9.26, std: 0.22, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b0726, sucA), Value:  9.11, std: 0.08, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b0726, sucA), Value:  8.46, std: 0.35, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b0726, sucA), Value:  9.29, std: 0.14, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b0727, sucB), Value: 10.81, std: 0.14, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b0727, sucB), Value: 10.06, std: 0.12, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b0727, sucB), Value:  9.83, std: 0.20, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b0727, sucB), Value: 10.31, std: 0.13, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b0728, sucC), Value: 11.91, std: 0.16, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b0728, sucC), Value: 11.50, std: 0.11, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b0728, sucC), Value: 11.05, std: 0.13, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b0728, sucC), Value: 11.67, std: 0.05, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b0729, sucD), Value:  6.23, std: 0.25, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b0729, sucD), Value:  6.14, std: 0.15, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b0729, sucD), Value:  5.75, std: 0.04, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b0729, sucD), Value:  6.43, std: 0.00, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b1779, gapA), Value: 15.15, std: 0.04, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b1779, gapA), Value: 15.19, std: 0.01, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b1779, gapA), Value: 15.33, std: 0.04, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b1779, gapA), Value: 15.14, std: 0.04, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b4151, frdD), Value:  3.77, std: 0.43, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b4151, frdD), Value:  9.26, std: 0.26, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b4151, frdD), Value:  8.16, std: 0.76, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b4151, frdD), Value:  3.21, std: 0.06, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b4152, frdC), Value:  2.25, std: 0.00, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b4152, frdC), Value:  4.98, std: 0.23, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b4152, frdC), Value:  4.64, std: 0.30, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b4152, frdC), Value:  2.25, std: 0.00, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b4153, frdB), Value:  4.50, std: 0.04, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b4153, frdB), Value:  9.78, std: 0.07, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b4153, frdB), Value:  9.49, std: 0.23, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b4153, frdB), Value:  4.62, std: 0.01, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b4154, frdA), Value:  6.48, std: 0.46, Condition: glucose, NH4Cl, NO3, Strain: wt, array_experiment,
 Gene: (b4154, frdA), Value: 11.32, std: 0.33, Condition: glucose, NH4Cl, NO3, Strain: delta-narL, array_experiment,
 Gene: (b4154, frdA), Value: 11.31, std: 0.15, Condition: glucose, NH4Cl, NO3, Strain: delta-narLnarP, array_experiment,
 Gene: (b4154, frdA), Value:  7.09, std: 0.00, Condition: glucose, NH4Cl, NO3, Strain: delta-narP, array_experiment,
 Gene: (b0726, sucA), Value: 14.35, std: 0.05, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0726, sucA), Value: 14.53, std: 0.02, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b0727, sucB), Value: 14.50, std: 0.02, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0727, sucB), Value: 14.64, std: 0.01, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b0728, sucC), Value: 14.75, std: 0.01, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0728, sucC), Value: 14.84, std: 0.03, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b0729, sucD), Value: 15.04, std: 0.02, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b0729, sucD), Value: 15.01, std: 0.07, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b1779, gapA), Value: 14.38, std: 0.01, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b1779, gapA), Value: 15.18, std: 0.02, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b4151, frdD), Value:  9.18, std: 0.18, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4151, frdD), Value:  7.75, std: 0.18, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b4152, frdC), Value:  8.98, std: 0.28, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4152, frdC), Value:  6.74, std: 0.11, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b4153, frdB), Value: 12.79, std: 0.04, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4153, frdB), Value: 11.74, std: 0.16, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b4154, frdA), Value: 13.01, std: 0.14, Condition: acetate, NH4Cl, O2, Strain: wt, array_experiment,
 Gene: (b4154, frdA), Value: 11.87, std: 0.30, Condition: acetate, NH4Cl, O2, Strain: delta-cra, array_experiment,
 Gene: (b0726, sucA), Value: 13.54, std: 0.03, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b0726, sucA), Value: 13.23, std: 0.07, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b0727, sucB), Value: 13.65, std: 0.03, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b0727, sucB), Value: 13.39, std: 0.02, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b0728, sucC), Value: 13.51, std: 0.02, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b0728, sucC), Value: 13.46, std: 0.01, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b0729, sucD), Value: 13.68, std: 0.02, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b0729, sucD), Value: 13.64, std: 0.07, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b1779, gapA), Value: 14.65, std: 0.03, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b1779, gapA), Value: 15.02, std: 0.02, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b4151, frdD), Value:  6.33, std: 0.04, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b4151, frdD), Value:  6.90, std: 1.02, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b4152, frdC), Value:  5.72, std: 0.23, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b4152, frdC), Value:  6.87, std: 1.02, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b4153, frdB), Value: 10.71, std: 0.22, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b4153, frdB), Value: 12.55, std: 0.38, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b4154, frdA), Value: 10.63, std: 0.43, Condition: glucose, leucine, O2, Strain: wt, array_experiment,
 Gene: (b4154, frdA), Value: 12.57, std: 0.24, Condition: glucose, leucine, O2, Strain: delta-lrp, array_experiment,
 Gene: (b0726, sucA), Value: 11.36, std: 0.17, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b0726, sucA), Value: 11.45, std: 0.74, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment,
 Gene: (b0727, sucB), Value: 12.31, std: 0.06, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b0727, sucB), Value: 12.69, std: 0.33, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment,
 Gene: (b0728, sucC), Value: 11.71, std: 0.04, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b0728, sucC), Value: 12.13, std: 0.36, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment,
 Gene: (b0729, sucD), Value: 12.26, std: 0.26, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b0729, sucD), Value: 12.23, std: 0.38, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment,
 Gene: (b1779, gapA), Value: 14.40, std: 0.09, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b1779, gapA), Value: 14.43, std: 0.15, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment,
 Gene: (b4151, frdD), Value:  4.34, std: 0.62, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b4151, frdD), Value:  3.73, std: 0.51, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment,
 Gene: (b4152, frdC), Value:  2.95, std: 0.07, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b4152, frdC), Value:  2.98, std: 0.12, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment,
 Gene: (b4153, frdB), Value:  5.56, std: 0.20, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b4153, frdB), Value:  5.74, std: 0.50, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment,
 Gene: (b4154, frdA), Value:  5.98, std: 0.35, Condition: glucose, adenine, O2, Strain: wt, array_experiment,
 Gene: (b4154, frdA), Value:  7.71, std: 2.86, Condition: glucose, adenine, O2, Strain: delta-purR, array_experiment]

In [5]:

    

genes = [ome.query(Gene).filter(Gene.name == x).one() for x in ['gapA','sucA','sucB','sucC']]
genes_data = {gene: gene.data for gene in genes}

col_labels = [x.data_set.name for x in genes_data.itervalues().next()]
row_labels = [x.name for x in genes_data.keys()]

heatmap_data = []
for i,gene in enumerate(genes_data):
    for j,data in enumerate(genes_data[gene]):
        if data.value < 0: value = 1.
        else: value = data.value
        heatmap_data.append({"row": i+1, "col": j+1, "value": int(np.log(value))})


    

In [6]:

    

%%javascript

require.config({paths: {d3: "https://mpld3.github.io/js/d3.v3.min"}});

require(["widgets/js/widget", "d3"], function(WidgetManager, d3){
    var HeatmapView = IPython.DOMWidgetView.extend({

        render: function(){
            
            this.$el.append(this.model.get("html_style"));
            this.svg = d3.select(this.el).append("svg")
                .attr({
                    width: 600,
                    height: 600
                });
            
            
            this.update();
        },
        update: function(){
            var margin = { top: 150, right: 10, bottom: 50, left: 100 },
  cellSize=12,
  width = cellSize*col_number, // - margin.left - margin.right,
  height = cellSize*row_number , // - margin.top - margin.bottom,
  //gridSize = Math.floor(width / 24),
  legendElementWidth = cellSize*2.5,
  colorBuckets = 21,
  colors = ['#005824','#1A693B','#347B53','#4F8D6B','#699F83','#83B09B','#9EC2B3','#B8D4CB','#D2E6E3','#EDF8FB','#FFFFFF','#F1EEF6','#E6D3E1','#DBB9CD','#D19EB9','#C684A4','#BB6990','#B14F7C','#A63467','#9B1A53','#91003F'],
  hcrow = [1,2,4,3], //,18,6,12,20,19,33,32,26,44,35,38,3,23,41,22,10,2,15,16,36,8,25,29,7,27,34,48,31,45,43,14,9,39,1,37,47,42,21,40,5,28,46,50,17,24,13], // change to gene name or probe id
  hccol = [2,1,5,3,6,4]; //,42,21,58,56,14,16,43,15,17,46,47,48,54,49,37,38,25,22,7,8,2,45,9,20,24,44,23,19,13,40,11,1,39,53,10,52,3,26,27,60,50,51,59,18,31,32,30,4,55,28,29,57,36,34,33,35], // change to gene name or probe id
  //rowLabel = ['1','2','1759080_s_at','1759302_s_at','1759502_s_at','1759540_s_at','1759781_s_at','1759828_s_at','1759829_s_at','1759906_s_at','1760088_s_at','1760164_s_at','1760453_s_at','1760516_s_at','1760594_s_at','1760894_s_at','1760951_s_at','1761030_s_at','1761128_at','1761145_s_at','1761160_s_at','1761189_s_at','1761222_s_at','1761245_s_at','1761277_s_at','1761434_s_at','1761553_s_at','1761620_s_at','1761873_s_at','1761884_s_at','1761944_s_at','1762105_s_at','1762118_s_at','1762151_s_at','1762388_s_at','1762401_s_at','1762633_s_at','1762701_s_at','1762787_s_at','1762819_s_at','1762880_s_at','1762945_s_at','1762983_s_at','1763132_s_at','1763138_s_at','1763146_s_at','1763198_s_at','1763383_at','1763410_s_at','1763426_s_at','1763490_s_at','1763491_s_at'], // change to gene name or probe id
  //colLabel = ['3','4','con1027','con1028','con1029','con103','con1030','con1031','con1032','con1033','con1034','con1035','con1036','con1037','con1038','con1039','con1040','con1041','con108','con109','con110','con111','con112','con125','con126','con127','con128','con129','con130','con131','con132','con133','con134','con135','con136','con137','con138','con139','con14','con15','con150','con151','con152','con153','con16','con17','con174','con184','con185','con186','con187','con188','con189','con191','con192','con193','con194','con199','con2','con200','con201','con21']; // change to contrast name
    
  var rowLabel = JSON.parse(this.model.get("row_labels"));
  var colLabel = JSON.parse(this.model.get("col_labels"));
  var data = JSON.parse(this.model.get("heatmap_data"));
 
            
  var col_number = colLabel.length,
      row_number = rowLabel.length;
            
  var colorScale = d3.scale.quantile()
      .domain([ -10 , 0, 10])
      .range(colors);
  
  var svg = this.svg;
            
  var rowSortOrder=false;
  var colSortOrder=false;
  var rowLabels = svg.append("g")
      .selectAll(".rowLabelg")
      .data(rowLabel)
      .enter()
      .append("text")
      .text(function (d) { return d; })
      .attr("x", 0)
      .attr("y", function (d, i) { return hcrow.indexOf(i+1) * cellSize; })
      .style("text-anchor", "end")
      .attr("transform", "translate(-6," + cellSize / 1.5 + ")")
      .attr("class", function (d,i) { return "rowLabel mono r"+i;} ) 
      .on("mouseover", function(d) {d3.select(this).classed("text-hover",true);})
      .on("mouseout" , function(d) {d3.select(this).classed("text-hover",false);})
      .on("click", function(d,i) {rowSortOrder=!rowSortOrder; sortbylabel("r",i,rowSortOrder);d3.select("#order").property("selectedIndex", 4).node().focus();;})
      ;

  var colLabels = svg.append("g")
      .selectAll(".colLabelg")
      .data(colLabel)
      .enter()
      .append("text")
      .text(function (d) { return d; })
      .attr("x", 0)
      .attr("y", function (d, i) { return hccol.indexOf(i+1) * cellSize; })
      .style("text-anchor", "left")
      .attr("transform", "translate("+cellSize/2 + ",-6) rotate (-90)")
      .attr("class",  function (d,i) { return "colLabel mono c"+i;} )
      .on("mouseover", function(d) {d3.select(this).classed("text-hover",true);})
      .on("mouseout" , function(d) {d3.select(this).classed("text-hover",false);})
      .on("click", function(d,i) {colSortOrder=!colSortOrder;  sortbylabel("c",i,colSortOrder);d3.select("#order").property("selectedIndex", 4).node().focus();;})
      ;

  var heatMap = svg.append("g").attr("class","g3")
        .selectAll(".cellg")
        .data(data,function(d){return d.row+":"+d.col;})
        .enter()
        .append("rect")
        .attr("x", function(d) { return hccol.indexOf(d.col) * cellSize; })
        .attr("y", function(d) { return hcrow.indexOf(d.row) * cellSize; })
        .attr("class", function(d){return "cell cell-border cr"+(d.row-1)+" cc"+(d.col-1);})
        .attr("width", cellSize)
        .attr("height", cellSize)
        .style("fill", function(d) { return colorScale(d.value); })
        /* .on("click", function(d) {
               var rowtext=d3.select(".r"+(d.row-1));
               if(rowtext.classed("text-selected")==false){
                   rowtext.classed("text-selected",true);
               }else{
                   rowtext.classed("text-selected",false);
               }
        })*/
        .on("mouseover", function(d){
               //highlight text
               d3.select(this).classed("cell-hover",true);
               d3.selectAll(".rowLabel").classed("text-highlight",function(r,ri){ return ri==(d.row-1);});
               d3.selectAll(".colLabel").classed("text-highlight",function(c,ci){ return ci==(d.col-1);});
        
               //Update the tooltip position and value
               d3.select("#tooltip")
                 .style("left", (d3.event.pageX+10) + "px")
                 .style("top", (d3.event.pageY-10) + "px")
                 .select("#value")
                 .text("lables:"+rowLabel[d.row-1]+","+colLabel[d.col-1]+"\ndata:"+d.value+"\nrow-col-idx:"+d.col+","+d.row+"\ncell-xy "+this.x.baseVal.value+", "+this.y.baseVal.value);  
               //Show the tooltip
               d3.select("#tooltip").classed("hidden", false);
        })
        .on("mouseout", function(){
               d3.select(this).classed("cell-hover",false);
               d3.selectAll(".rowLabel").classed("text-highlight",false);
               d3.selectAll(".colLabel").classed("text-highlight",false);
               d3.select("#tooltip").classed("hidden", true);
        })
        ;

  var legend = svg.selectAll(".legend")
      .data([-10,-9,-8,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,8,9,10])
      .enter().append("g")
      .attr("class", "legend");
 
  legend.append("rect")
    .attr("x", function(d, i) { return legendElementWidth * i; })
    .attr("y", height+(cellSize*2))
    .attr("width", legendElementWidth)
    .attr("height", cellSize)
    .style("fill", function(d, i) { return colors[i]; });
 
  legend.append("text")
    .attr("class", "mono")
    .text(function(d) { return d; })
    .attr("width", legendElementWidth)
    .attr("x", function(d, i) { return legendElementWidth * i; })
    .attr("y", height + (cellSize*4));

// Change ordering of cells

  function sortbylabel(rORc,i,sortOrder){
       var t = svg.transition().duration(3000);
       var log2r=[];
       var sorted; // sorted is zero-based index
       d3.selectAll(".c"+rORc+i) 
         .filter(function(ce){
            log2r.push(ce.value);
          })
       ;
       if(rORc=="r"){ // sort log2ratio of a gene
         sorted=d3.range(col_number).sort(function(a,b){ if(sortOrder){ return log2r[b]-log2r[a];}else{ return log2r[a]-log2r[b];}});
         t.selectAll(".cell")
           .attr("x", function(d) { return sorted.indexOf(d.col-1) * cellSize; })
           ;
         t.selectAll(".colLabel")
          .attr("y", function (d, i) { return sorted.indexOf(i) * cellSize; })
         ;
       }else{ // sort log2ratio of a contrast
         sorted=d3.range(row_number).sort(function(a,b){if(sortOrder){ return log2r[b]-log2r[a];}else{ return log2r[a]-log2r[b];}});
         t.selectAll(".cell")
           .attr("y", function(d) { return sorted.indexOf(d.row-1) * cellSize; })
           ;
         t.selectAll(".rowLabel")
          .attr("y", function (d, i) { return sorted.indexOf(i) * cellSize; })
         ;
       }
  }

  d3.select("#order").on("change",function(){
    order(this.value);
  });
  
  function order(value){
   if(value=="hclust"){
    var t = svg.transition().duration(3000);
    t.selectAll(".cell")
      .attr("x", function(d) { return hccol.indexOf(d.col) * cellSize; })
      .attr("y", function(d) { return hcrow.indexOf(d.row) * cellSize; })
      ;

    t.selectAll(".rowLabel")
      .attr("y", function (d, i) { return hcrow.indexOf(i+1) * cellSize; })
      ;

    t.selectAll(".colLabel")
      .attr("y", function (d, i) { return hccol.indexOf(i+1) * cellSize; })
      ;

   }else if (value=="probecontrast"){
    var t = svg.transition().duration(3000);
    t.selectAll(".cell")
      .attr("x", function(d) { return (d.col - 1) * cellSize; })
      .attr("y", function(d) { return (d.row - 1) * cellSize; })
      ;

    t.selectAll(".rowLabel")
      .attr("y", function (d, i) { return i * cellSize; })
      ;

    t.selectAll(".colLabel")
      .attr("y", function (d, i) { return i * cellSize; })
      ;

   }else if (value=="probe"){
    var t = svg.transition().duration(3000);
    t.selectAll(".cell")
      .attr("y", function(d) { return (d.row - 1) * cellSize; })
      ;

    t.selectAll(".rowLabel")
      .attr("y", function (d, i) { return i * cellSize; })
      ;
   }else if (value=="contrast"){
    var t = svg.transition().duration(3000);
    t.selectAll(".cell")
      .attr("x", function(d) { return (d.col - 1) * cellSize; })
      ;
    t.selectAll(".colLabel")
      .attr("y", function (d, i) { return i * cellSize; })
      ;
   }
  }
  // 
  var sa=d3.select(".g3")
      .on("mousedown", function() {
          if( !d3.event.altKey) {
             d3.selectAll(".cell-selected").classed("cell-selected",false);
             d3.selectAll(".rowLabel").classed("text-selected",false);
             d3.selectAll(".colLabel").classed("text-selected",false);
          }
         var p = d3.mouse(this);
         sa.append("rect")
         .attr({
             rx      : 0,
             ry      : 0,
             class   : "selection",
             x       : p[0],
             y       : p[1],
             width   : 1,
             height  : 1
         })
      })
      .on("mousemove", function() {
         var s = sa.select("rect.selection");
      
         if(!s.empty()) {
             var p = d3.mouse(this),
                 d = {
                     x       : parseInt(s.attr("x"), 10),
                     y       : parseInt(s.attr("y"), 10),
                     width   : parseInt(s.attr("width"), 10),
                     height  : parseInt(s.attr("height"), 10)
                 },
                 move = {
                     x : p[0] - d.x,
                     y : p[1] - d.y
                 }
             ;
      
             if(move.x < 1 || (move.x*2<d.width)) {
                 d.x = p[0];
                 d.width -= move.x;
             } else {
                 d.width = move.x;       
             }
      
             if(move.y < 1 || (move.y*2<d.height)) {
                 d.y = p[1];
                 d.height -= move.y;
             } else {
                 d.height = move.y;       
             }
             s.attr(d);
      
                 // deselect all temporary selected state objects
             d3.selectAll('.cell-selection.cell-selected').classed("cell-selected", false);
             d3.selectAll(".text-selection.text-selected").classed("text-selected",false);

             d3.selectAll('.cell').filter(function(cell_d, i) {
                 if(
                     !d3.select(this).classed("cell-selected") && 
                         // inner circle inside selection frame
                     (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && 
                     (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height
                 ) {
      
                     d3.select(this)
                     .classed("cell-selection", true)
                     .classed("cell-selected", true);

                     d3.select(".r"+(cell_d.row-1))
                     .classed("text-selection",true)
                     .classed("text-selected",true);

                     d3.select(".c"+(cell_d.col-1))
                     .classed("text-selection",true)
                     .classed("text-selected",true);
                 }
             });
         }
      })
      .on("mouseup", function() {
            // remove selection frame
         sa.selectAll("rect.selection").remove();
      
             // remove temporary selection marker class
         d3.selectAll('.cell-selection').classed("cell-selection", false);
         d3.selectAll(".text-selection").classed("text-selection",false);
      })
      .on("mouseout", function() {
         if(d3.event.relatedTarget.tagName=='html') {
                 // remove selection frame
             sa.selectAll("rect.selection").remove();
                 // remove temporary selection marker class
             d3.selectAll('.cell-selection').classed("cell-selection", false);
             d3.selectAll(".rowLabel").classed("text-selected",false);
             d3.selectAll(".colLabel").classed("text-selected",false);
         }
      });

            
        }
    });
    WidgetManager.register_widget_view("HeatmapView", HeatmapView);
});


    

In [9]:

    

#circles = CirclesWidget(radii=[1,2,3], sets=json.dumps(sets), overlaps=json.dumps(overlaps))
heatmap_diagram = HeatmapWidget(row_labels=json.dumps(row_labels), 
                                col_labels=json.dumps(col_labels), 
                                heatmap_data=json.dumps(heatmap_data), html_style=html_style)
display(heatmap_diagram)


    

In [8]:

    

html_style = """
     <style>
      /* disable text selection */
      svg *::selection {
         background : transparent;
      }
     
      svg *::-moz-selection {
         background:transparent;
      } 
     
      svg *::-webkit-selection {
         background:transparent;
      }
      rect.selection {
        stroke          : #333;
        stroke-dasharray: 4px;
        stroke-opacity  : 0.5;
        fill            : transparent;
      }

      rect.cell-border {
        stroke: #eee;
        stroke-width:0.3px;   
      }

      rect.cell-selected {
        stroke: rgb(51,102,153);
        stroke-width:0.5px;   
      }

      rect.cell-hover {
        stroke: #F00;
        stroke-width:0.3px;   
      }

      text.mono {
        font-size: 9pt;
        font-family: Consolas, courier;
        fill: #aaa;
      }

      text.text-selected {
        fill: #000;
      }

      text.text-highlight {
        fill: #c00;
      }
      text.text-hover {
        fill: #00C;
      }
      #tooltip {
        position: fixed;
        width: 200px;
        height: auto;
        padding: 10px;
        background-color: white;
        -webkit-border-radius: 10px;
        -moz-border-radius: 10px;
        border-radius: 10px;
        -webkit-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
        -moz-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
        box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
        pointer-events: none;
      }

      #tooltip.hidden {
        display: none;
      }

      #tooltip p {
        margin: 0;
        font-family: sans-serif;
        font-size: 12px;
        line-height: 20px;
      }
    </style>


<div id="tooltip" class="hidden">
        <p><span id="value"></p>
</div>

 
  <select id="order">
  <option value="hclust">by cluster</option>
  <option value="probecontrast">by probe name and contrast name</option>
  <option value="probe">by probe name</option>
  <option value="contrast">by contrast name</option>
  <option value="custom">by log2 ratio</option>
  </select>
  </select>
<div id="chart" style='overflow:auto; width:960px; height:auto;'></div>
"""


    

In [69]:

    

%%html

     <style>
      /* disable text selection */
      svg *::selection {
         background : transparent;
      }
     
      svg *::-moz-selection {
         background:transparent;
      } 
     
      svg *::-webkit-selection {
         background:transparent;
      }
      rect.selection {
        stroke          : #333;
        stroke-dasharray: 4px;
        stroke-opacity  : 0.5;
        fill            : transparent;
      }

      rect.cell-border {
        stroke: #eee;
        stroke-width:0.3px;   
      }

      rect.cell-selected {
        stroke: rgb(51,102,153);
        stroke-width:0.5px;   
      }

      rect.cell-hover {
        stroke: #F00;
        stroke-width:0.3px;   
      }

      text.mono {
        font-size: 9pt;
        font-family: Consolas, courier;
        fill: #aaa;
      }

      text.text-selected {
        fill: #000;
      }

      text.text-highlight {
        fill: #c00;
      }
      text.text-hover {
        fill: #00C;
      }
      #tooltip {
        position: fixed;
        width: 200px;
        height: auto;
        padding: 10px;
        background-color: white;
        -webkit-border-radius: 10px;
        -moz-border-radius: 10px;
        border-radius: 10px;
        -webkit-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
        -moz-box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
        box-shadow: 4px 4px 10px rgba(0, 0, 0, 0.4);
        pointer-events: none;
      }

      #tooltip.hidden {
        display: none;
      }

      #tooltip p {
        margin: 0;
        font-family: sans-serif;
        font-size: 12px;
        line-height: 20px;
      }
    </style>


<div id="tooltip" class="hidden">
        <p><span id="value"></p>
</div>

 
  <select id="order">
  <option value="hclust">by cluster</option>
  <option value="probecontrast">by probe name and contrast name</option>
  <option value="probe">by probe name</option>
  <option value="contrast">by contrast name</option>
  <option value="custom">by log2 ratio</option>
  </select>
  </select>
<div id="chart" style='overflow:auto; width:960px; height:auto;'></div>


    

    






     



        



 
  
  by cluster
  by probe name and contrast name
  by probe name
  by contrast name
  by log2 ratio
  
  

In [70]:

    

%%javascript

require.config({paths: {d3: "https://mpld3.github.io/js/d3.v3.min"}});

require(["d3"], function(d3){

var margin = { top: 150, right: 10, bottom: 50, left: 100 },
  cellSize=12,
  col_number=6,
  row_number=4,
  width = cellSize*col_number, // - margin.left - margin.right,
  height = cellSize*row_number , // - margin.top - margin.bottom,
  //gridSize = Math.floor(width / 24),
  legendElementWidth = cellSize*2.5,
  colorBuckets = 21,
  colors = ['#005824','#1A693B','#347B53','#4F8D6B','#699F83','#83B09B','#9EC2B3','#B8D4CB','#D2E6E3','#EDF8FB','#FFFFFF','#F1EEF6','#E6D3E1','#DBB9CD','#D19EB9','#C684A4','#BB6990','#B14F7C','#A63467','#9B1A53','#91003F'],
  hcrow = [1, 2, 3, 4],
  hccol = [6, 2, 1, 3, 5, 4],
  rowLabel = ['1759302_s_at','1759080_s_at','1759502_s_at','1759540_s_at'],
  colLabel = ['con1027','con1028','con1029','con103','con1030','con1031'];

//d3.tsv("data/heatmap_data.tsv",
//function(d) {
  //return {
    //row:   +d.row_idx,
    //col:   +d.col_idx,
    //value: +d.log2ratio
  //};
//},

  var data = [{"col": 1, "value": 6, "row": 1}, {"col": 2, "value": 6, "row": 1}, {"col": 3, "value": 7, "row": 1}, {"col": 4, "value": 6, "row": 1}, {"col": 5, "value": 6, "row": 1}, {"col": 6, "value": 6, "row": 1}, {"col": 1, "value": 6, "row": 2}, {"col": 2, "value": 6, "row": 2}, {"col": 3, "value": 6, "row": 2}, {"col": 4, "value": 6, "row": 2}, {"col": 5, "value": 6, "row": 2}, {"col": 6, "value": 6, "row": 2}, {"col": 1, "value": 9, "row": 3}, {"col": 2, "value": 9, "row": 3}, {"col": 3, "value": 9, "row": 3}, {"col": 4, "value": 9, "row": 3}, {"col": 5, "value": 9, "row": 3}, {"col": 6, "value": 9, "row": 3}, {"col": 1, "value": 6, "row": 4}, {"col": 2, "value": 6, "row": 4}, {"col": 3, "value": 6, "row": 4}, {"col": 4, "value": 6, "row": 4}, {"col": 5, "value": 6, "row": 4}, {"col": 6, "value": 5, "row": 4}];
  console.log(data.slice(1,10));
  var colorScale = d3.scale.quantile()
      .domain([ -10 , 0, 10])
      .range(colors);
  
  var svg = d3.select("#chart").append("svg")
      .attr("width", width + margin.left + margin.right)
      .attr("height", height + margin.top + margin.bottom)
      .append("g")
      .attr("transform", "translate(" + margin.left + "," + margin.top + ")")
      ;
  var rowSortOrder=false;
  var colSortOrder=false;
  var rowLabels = svg.append("g")
      .selectAll(".rowLabelg")
      .data(rowLabel)
      .enter()
      .append("text")
      .text(function (d) { return d; })
      .attr("x", 0)
      .attr("y", function (d, i) { return hcrow.indexOf(i+1) * cellSize; })
      .style("text-anchor", "end")
      .attr("transform", "translate(-6," + cellSize / 1.5 + ")")
      .attr("class", function (d,i) { return "rowLabel mono r"+i;} ) 
      .on("mouseover", function(d) {d3.select(this).classed("text-hover",true);})
      .on("mouseout" , function(d) {d3.select(this).classed("text-hover",false);})
      .on("click", function(d,i) {rowSortOrder=!rowSortOrder; sortbylabel("r",i,rowSortOrder);d3.select("#order").property("selectedIndex", 4).node().focus();;})
      ;

  var colLabels = svg.append("g")
      .selectAll(".colLabelg")
      .data(colLabel)
      .enter()
      .append("text")
      .text(function (d) { return d; })
      .attr("x", 0)
      .attr("y", function (d, i) { return hccol.indexOf(i+1) * cellSize; })
      .style("text-anchor", "left")
      .attr("transform", "translate("+cellSize/2 + ",-6) rotate (-90)")
      .attr("class",  function (d,i) { return "colLabel mono c"+i;} )
      .on("mouseover", function(d) {d3.select(this).classed("text-hover",true);})
      .on("mouseout" , function(d) {d3.select(this).classed("text-hover",false);})
      .on("click", function(d,i) {colSortOrder=!colSortOrder;  sortbylabel("c",i,colSortOrder);d3.select("#order").property("selectedIndex", 4).node().focus();;})
      ;

  var heatMap = svg.append("g").attr("class","g3")
        .selectAll(".cellg")
        .data(data,function(d){return d.row+":"+d.col;})
        .enter()
        .append("rect")
        .attr("x", function(d) { return hccol.indexOf(d.col) * cellSize; })
        .attr("y", function(d) { return hcrow.indexOf(d.row) * cellSize; })
        .attr("class", function(d){return "cell cell-border cr"+(d.row-1)+" cc"+(d.col-1);})
        .attr("width", cellSize)
        .attr("height", cellSize)
        .style("fill", function(d) { return colorScale(d.value); })
        /* .on("click", function(d) {
               var rowtext=d3.select(".r"+(d.row-1));
               if(rowtext.classed("text-selected")==false){
                   rowtext.classed("text-selected",true);
               }else{
                   rowtext.classed("text-selected",false);
               }
        })*/
        .on("mouseover", function(d){
               //highlight text
               d3.select(this).classed("cell-hover",true);
               d3.selectAll(".rowLabel").classed("text-highlight",function(r,ri){ return ri==(d.row-1);});
               d3.selectAll(".colLabel").classed("text-highlight",function(c,ci){ return ci==(d.col-1);});
        
               //Update the tooltip position and value
               d3.select("#tooltip")
                 .style("left", (d3.event.pageX+10) + "px")
                 .style("top", (d3.event.pageY-10) + "px")
                 .select("#value")
                 .text("lables:"+rowLabel[d.row-1]+","+colLabel[d.col-1]+"\ndata:"+d.value+"\nrow-col-idx:"+d.col+","+d.row+"\ncell-xy "+this.x.baseVal.value+", "+this.y.baseVal.value);  
               //Show the tooltip
               d3.select("#tooltip").classed("hidden", false);
        })
        .on("mouseout", function(){
               d3.select(this).classed("cell-hover",false);
               d3.selectAll(".rowLabel").classed("text-highlight",false);
               d3.selectAll(".colLabel").classed("text-highlight",false);
               d3.select("#tooltip").classed("hidden", true);
        })
        ;

  var legend = svg.selectAll(".legend")
      .data([-10,-9,-8,-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,8,9,10])
      .enter().append("g")
      .attr("class", "legend");
 
  legend.append("rect")
    .attr("x", function(d, i) { return legendElementWidth * i; })
    .attr("y", height+(cellSize*2))
    .attr("width", legendElementWidth)
    .attr("height", cellSize)
    .style("fill", function(d, i) { return colors[i]; });
 
  legend.append("text")
    .attr("class", "mono")
    .text(function(d) { return d; })
    .attr("width", legendElementWidth)
    .attr("x", function(d, i) { return legendElementWidth * i; })
    .attr("y", height + (cellSize*4));

// Change ordering of cells

  function sortbylabel(rORc,i,sortOrder){
       var t = svg.transition().duration(3000);
       var log2r=[];
       var sorted; // sorted is zero-based index
       d3.selectAll(".c"+rORc+i) 
         .filter(function(ce){
            log2r.push(ce.value);
          })
       ;
       if(rORc=="r"){ // sort log2ratio of a gene
         sorted=d3.range(col_number).sort(function(a,b){ if(sortOrder){ return log2r[b]-log2r[a];}else{ return log2r[a]-log2r[b];}});
         t.selectAll(".cell")
           .attr("x", function(d) { return sorted.indexOf(d.col-1) * cellSize; })
           ;
         t.selectAll(".colLabel")
          .attr("y", function (d, i) { return sorted.indexOf(i) * cellSize; })
         ;
       }else{ // sort log2ratio of a contrast
         sorted=d3.range(row_number).sort(function(a,b){if(sortOrder){ return log2r[b]-log2r[a];}else{ return log2r[a]-log2r[b];}});
         t.selectAll(".cell")
           .attr("y", function(d) { return sorted.indexOf(d.row-1) * cellSize; })
           ;
         t.selectAll(".rowLabel")
          .attr("y", function (d, i) { return sorted.indexOf(i) * cellSize; })
         ;
       }
  }

  d3.select("#order").on("change",function(){
    order(this.value);
  });
  
  function order(value){
   if(value=="hclust"){
    var t = svg.transition().duration(3000);
    t.selectAll(".cell")
      .attr("x", function(d) { return hccol.indexOf(d.col) * cellSize; })
      .attr("y", function(d) { return hcrow.indexOf(d.row) * cellSize; })
      ;

    t.selectAll(".rowLabel")
      .attr("y", function (d, i) { return hcrow.indexOf(i+1) * cellSize; })
      ;

    t.selectAll(".colLabel")
      .attr("y", function (d, i) { return hccol.indexOf(i+1) * cellSize; })
      ;

   }else if (value=="probecontrast"){
    var t = svg.transition().duration(3000);
    t.selectAll(".cell")
      .attr("x", function(d) { return (d.col - 1) * cellSize; })
      .attr("y", function(d) { return (d.row - 1) * cellSize; })
      ;

    t.selectAll(".rowLabel")
      .attr("y", function (d, i) { return i * cellSize; })
      ;

    t.selectAll(".colLabel")
      .attr("y", function (d, i) { return i * cellSize; })
      ;

   }else if (value=="probe"){
    var t = svg.transition().duration(3000);
    t.selectAll(".cell")
      .attr("y", function(d) { return (d.row - 1) * cellSize; })
      ;

    t.selectAll(".rowLabel")
      .attr("y", function (d, i) { return i * cellSize; })
      ;
   }else if (value=="contrast"){
    var t = svg.transition().duration(3000);
    t.selectAll(".cell")
      .attr("x", function(d) { return (d.col - 1) * cellSize; })
      ;
    t.selectAll(".colLabel")
      .attr("y", function (d, i) { return i * cellSize; })
      ;
   }
  }
  // 
  var sa=d3.select(".g3")
      .on("mousedown", function() {
          if( !d3.event.altKey) {
             d3.selectAll(".cell-selected").classed("cell-selected",false);
             d3.selectAll(".rowLabel").classed("text-selected",false);
             d3.selectAll(".colLabel").classed("text-selected",false);
          }
         var p = d3.mouse(this);
         sa.append("rect")
         .attr({
             rx      : 0,
             ry      : 0,
             class   : "selection",
             x       : p[0],
             y       : p[1],
             width   : 1,
             height  : 1
         })
      })
      .on("mousemove", function() {
         var s = sa.select("rect.selection");
      
         if(!s.empty()) {
             var p = d3.mouse(this),
                 d = {
                     x       : parseInt(s.attr("x"), 10),
                     y       : parseInt(s.attr("y"), 10),
                     width   : parseInt(s.attr("width"), 10),
                     height  : parseInt(s.attr("height"), 10)
                 },
                 move = {
                     x : p[0] - d.x,
                     y : p[1] - d.y
                 }
             ;
      
             if(move.x < 1 || (move.x*2<d.width)) {
                 d.x = p[0];
                 d.width -= move.x;
             } else {
                 d.width = move.x;       
             }
      
             if(move.y < 1 || (move.y*2<d.height)) {
                 d.y = p[1];
                 d.height -= move.y;
             } else {
                 d.height = move.y;       
             }
             s.attr(d);
      
                 // deselect all temporary selected state objects
             d3.selectAll('.cell-selection.cell-selected').classed("cell-selected", false);
             d3.selectAll(".text-selection.text-selected").classed("text-selected",false);

             d3.selectAll('.cell').filter(function(cell_d, i) {
                 if(
                     !d3.select(this).classed("cell-selected") && 
                         // inner circle inside selection frame
                     (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width && 
                     (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height
                 ) {
      
                     d3.select(this)
                     .classed("cell-selection", true)
                     .classed("cell-selected", true);

                     d3.select(".r"+(cell_d.row-1))
                     .classed("text-selection",true)
                     .classed("text-selected",true);

                     d3.select(".c"+(cell_d.col-1))
                     .classed("text-selection",true)
                     .classed("text-selected",true);
                 }
             });
         }
      })
      .on("mouseup", function() {
            // remove selection frame
         sa.selectAll("rect.selection").remove();
      
             // remove temporary selection marker class
         d3.selectAll('.cell-selection').classed("cell-selection", false);
         d3.selectAll(".text-selection").classed("text-selection",false);
      })
      .on("mouseout", function() {
         if(d3.event.relatedTarget.tagName=='html') {
                 // remove selection frame
             sa.selectAll("rect.selection").remove();
                 // remove temporary selection marker class
             d3.selectAll('.cell-selection').classed("cell-selection", false);
             d3.selectAll(".rowLabel").classed("text-selected",false);
             d3.selectAll(".colLabel").classed("text-selected",false);
         }
      })
      ;
//});

});


    

In [5]:

    




    

In [5]:

    




    

In [17]:

    

import simplejson as json
json.dumps([{'row': 1, 'col': 1, 'value':1},{'row': 1, 'col': 2, 'value':2},{'row': 2, 'col': 1, 'value':3},{'row': 2, 'col': 2, 'value':4}])


    

    
Out[17]:





'[{"col": 1, "value": 1, "row": 1}, {"col": 2, "value": 2, "row": 1}, {"col": 1, "value": 3, "row": 2}, {"col": 2, "value": 4, "row": 2}]'

In [17]:

    

genes = [ome.query(Gene).filter(Gene.name == x).one() for x in ['gapA','sucA','sucB','sucC','sucD']]
genes_data = {gene: gene.data for gene in genes}
json.dumps({
            "rowlabels" : [x.data_set.name for x in genes_data.itervalues().next()],
            "collabels" : [x.name for x in genes_data.keys()],
            "data" : [[{"row": i, "col": j, "value": data.value} for j,data in enumerate(genes_data[gene])] for i,gene in enumerate(genes_data)]})


    

    
Out[17]:





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{"col": 96, "value": 12.4256683086673, "row": 4}, {"col": 97, "value": 10.7072497467802, "row": 4}, {"col": 98, "value": 14.3867584713303, "row": 4}, {"col": 99, "value": 13.6911825990341, "row": 4}, {"col": 100, "value": 13.5735477975709, "row": 4}, {"col": 101, "value": 13.2781045596659, "row": 4}, {"col": 102, "value": 11.5294705929067, "row": 4}, {"col": 103, "value": 13.5111490179521, "row": 4}, {"col": 104, "value": 14.5002424441276, "row": 4}, {"col": 105, "value": 14.5503768151331, "row": 4}, {"col": 106, "value": 12.884706400654, "row": 4}, {"col": 107, "value": 11.9980110415735, "row": 4}, {"col": 108, "value": 11.8184821498611, "row": 4}, {"col": 109, "value": 12.8798488505069, "row": 4}, {"col": 110, "value": 13.5744928372611, "row": 4}, {"col": 111, "value": 13.4383093247762, "row": 4}, {"col": 112, "value": 13.3068118041082, "row": 4}, {"col": 113, "value": 11.914078238606, "row": 4}, {"col": 114, "value": 12.1890944983656, "row": 4}, {"col": 115, "value": 14.3817668055912, "row": 4}, {"col": 116, "value": 14.2845271638751, "row": 4}, {"col": 117, "value": 13.7573783517173, "row": 4}, {"col": 118, "value": 13.3754775135612, "row": 4}, {"col": 119, "value": 11.1989578790269, "row": 4}, {"col": 120, "value": 13.5289043326408, "row": 4}, {"col": 121, "value": 13.5754295756759, "row": 4}]]}'

In [14]:

    

[k for i,k in enumerate(genes_data)]


    

    
Out[14]:





[Gene: (b0727, sucB) 761521-762739 (+),
 Gene: (b0728, sucC) 763013-764180 (+),
 Gene: (b1779, gapA) 1862770-1863766 (+),
 Gene: (b0729, sucD) 764179-765049 (+),
 Gene: (b0726, sucA) 758705-761507 (+)]

In [16]:

    

[[{"row": i, "col": j, "value": data.value} for j,data in enumerate(genes_data[gene])] for i,gene in enumerate(genes_data)]


    

    
Out[16]:





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In [ ]: