In [1]:
import pandas as pd
In [2]:
leafdf=pd.read_csv('Col0_leaf-KEGG.csv')
rootdf=pd.read_csv('Col0_root-KEGG.csv')
this experiment has 8 timepoints and several replicates for each timepoint.
In [3]:
kegg = leafdf['KEGG']
In [4]:
leafdf.filter(regex="^[0-9]+")
Out[4]:
14_L03_full_1
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...
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In [5]:
timepoints=["14","16","18","20","22","24","26","28"]
In [6]:
kegg.name='KEGG'
leafmat=pd.concat([kegg])
rootmat=pd.concat([kegg])
for i in timepoints:
leafprofile = leafdf.filter(regex="^"+i)
rootprofile = rootdf.filter(regex="^"+i)
leafmean = leafprofile.mean(axis=1)
rootmean = rootprofile.mean(axis=1)
leafmat=pd.concat([leafmat,leafmean],axis=1)
rootmat=pd.concat([rootmat,rootmean],axis=1)
In [7]:
leafmat.columns = ["KEGG"] + timepoints
rootmat.columns = ["KEGG"] + timepoints
In [8]:
leafsum = leafmat.groupby('KEGG').sum()
rootsum = rootmat.groupby('KEGG').sum()
In [9]:
for i in leafsum.index:
foo = pd.concat([leafsum.ix[i], rootsum.ix[i]], axis=1)
foo.columns = ['leaf', 'root']
tmp = foo.plot(kind='bar', title=i)
fig = tmp.get_figure()
fig.savefig('./' + i + '.png')
fig.clear()
/Users/knishida/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py:424: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
max_open_warning, RuntimeWarning)
In [63]:
cpds = set(leafdf['KEGG'].unique()) & set(rootdf['KEGG'].unique())
In [64]:
cpds
Out[64]:
{'C00025',
'C00037',
'C00042',
'C00047',
'C00049',
'C00065',
'C00085',
'C00089',
'C00095',
'C00099',
'C00121',
'C00122',
'C00134',
'C00137',
'C00148',
'C00158',
'C00160',
'C00208',
'C00249',
'C00258',
'C00267',
'C00315',
'C00429',
'C00492',
'C00493',
'C01595',
'C01753',
'C01789'}
To search KEGG pathway mappable compounds, you can use keggutil package (http://github.com/kozo2/keggutil).
This function is not supported by KEGG mapper(http://www.genome.jp/kegg/mapper.html).
In [12]:
import keggutil
In [13]:
def addind(x):
return x.replace('C', 'cpd:C')
cpdsFor = keggutil.search_pathway_object(map(addind, cpds))
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path:map04122
path:map04140
path:map04141
path:map04142
path:map04144
path:map04145
path:map04150
path:map04151
path:map04152
path:map04260
path:map04261
path:map04270
path:map04310
path:map04340
path:map04360
path:map04370
path:map04380
path:map04510
path:map04530
path:map04540
path:map04610
path:map04611
path:map04614
path:map04621
path:map04623
path:map04626
path:map04650
path:map04660
path:map04662
path:map04664
path:map04666
path:map04670
path:map04672
path:map04710
path:map04713
path:map04720
path:map04721
path:map04722
path:map04723
path:map04724
path:map04725
path:map04726
path:map04727
path:map04728
path:map04730
path:map04740
path:map04742
path:map04744
path:map04745
path:map04750
path:map04810
path:map04910
path:map04911
path:map04912
path:map04913
path:map04914
path:map04915
path:map04916
path:map04917
path:map04918
path:map04919
path:map04920
path:map04921
path:map04922
path:map04930
path:map04932
path:map04940
path:map04960
path:map04961
path:map04962
path:map04964
path:map04966
path:map04970
path:map04971
path:map04972
path:map04973
path:map04974
path:map04975
path:map04976
path:map04977
path:map04978
path:map05010
path:map05012
path:map05014
path:map05016
path:map05020
path:map05030
path:map05031
path:map05032
path:map05033
path:map05034
path:map05110
path:map05111
path:map05120
path:map05130
path:map05131
path:map05132
path:map05133
path:map05134
path:map05140
path:map05142
path:map05143
path:map05144
path:map05145
path:map05146
path:map05150
path:map05152
path:map05160
path:map05162
path:map05164
path:map05166
path:map05169
path:map05200
path:map05204
path:map05205
path:map05211
path:map05212
path:map05213
path:map05214
path:map05215
path:map05217
path:map05218
path:map05220
path:map05221
path:map05222
path:map05223
path:map05230
path:map05231
path:map05310
path:map05320
path:map05322
path:map05323
path:map05330
path:map05332
path:map05410
path:map05412
path:map05414
path:map07011
path:map07012
path:map07013
path:map07014
path:map07015
path:map07016
path:map07023
path:map07024
path:map07026
path:map07030
path:map07032
path:map07033
path:map07034
path:map07035
path:map07037
path:map07039
path:map07040
path:map07042
path:map07053
path:map07055
path:map07110
path:map07112
path:map07114
path:map07117
path:map07211
path:map07212
path:map07214
path:map07216
path:map07217
path:map07218
path:map07220
path:map07221
path:map07222
path:map07224
path:map07225
path:map07226
path:map07227
path:map07229
path:map07230
path:map07232
path:map07235
In [14]:
cpdsFor
Out[14]:
{'notFound': set(),
'path:map00010': {'cpd:C00022', 'cpd:C00267'},
'path:map00020': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00122',
'cpd:C00158'},
'path:map00030': {'cpd:C00022', 'cpd:C00121', 'cpd:C00258'},
'path:map00040': {'cpd:C00022', 'cpd:C00026', 'cpd:C00181'},
'path:map00051': {'cpd:C00095', 'cpd:C00267'},
'path:map00052': {'cpd:C00089',
'cpd:C00095',
'cpd:C00137',
'cpd:C00267',
'cpd:C00492'},
'path:map00053': {'cpd:C00022', 'cpd:C00026', 'cpd:C00137', 'cpd:C05422'},
'path:map00061': {'cpd:C00249'},
'path:map00062': {'cpd:C00249'},
'path:map00071': {'cpd:C00249'},
'path:map00073': {'cpd:C00249'},
'path:map00100': {'cpd:C01753', 'cpd:C01789'},
'path:map00120': {'cpd:C00037'},
'path:map00190': {'cpd:C00042', 'cpd:C00122'},
'path:map00230': {'cpd:C00037'},
'path:map00240': {'cpd:C00099', 'cpd:C00429'},
'path:map00250': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00042',
'cpd:C00049',
'cpd:C00122',
'cpd:C00158',
'cpd:C00334'},
'path:map00260': {'cpd:C00022',
'cpd:C00037',
'cpd:C00049',
'cpd:C00065',
'cpd:C00078',
'cpd:C00258'},
'path:map00270': {'cpd:C00022', 'cpd:C00049', 'cpd:C00065', 'cpd:C00073'},
'path:map00280': {'cpd:C00123', 'cpd:C00183', 'cpd:C00407'},
'path:map00290': {'cpd:C00022', 'cpd:C00123', 'cpd:C00183', 'cpd:C00407'},
'path:map00300': {'cpd:C00026', 'cpd:C00047', 'cpd:C00049'},
'path:map00310': {'cpd:C00037', 'cpd:C00047'},
'path:map00311': {'cpd:C00183'},
'path:map00330': {'cpd:C00022',
'cpd:C00025',
'cpd:C00049',
'cpd:C00122',
'cpd:C00134',
'cpd:C00148',
'cpd:C00315',
'cpd:C00334'},
'path:map00332': {'cpd:C00025', 'cpd:C00148'},
'path:map00340': {'cpd:C00025', 'cpd:C00026', 'cpd:C00049'},
'path:map00350': {'cpd:C00022', 'cpd:C00042', 'cpd:C00122'},
'path:map00360': {'cpd:C00022', 'cpd:C00042', 'cpd:C00122'},
'path:map00361': {'cpd:C00042', 'cpd:C00160'},
'path:map00362': {'cpd:C00022'},
'path:map00365': {'cpd:C00026'},
'path:map00380': {'cpd:C00078', 'cpd:C02938'},
'path:map00400': {'cpd:C00078', 'cpd:C00493'},
'path:map00401': {'cpd:C00148'},
'path:map00410': {'cpd:C00049',
'cpd:C00099',
'cpd:C00315',
'cpd:C00334',
'cpd:C00429'},
'path:map00430': {'cpd:C00022', 'cpd:C00025', 'cpd:C00026'},
'path:map00440': {'cpd:C00022'},
'path:map00460': {'cpd:C00037',
'cpd:C00049',
'cpd:C00065',
'cpd:C00183',
'cpd:C00407'},
'path:map00471': {'cpd:C00025', 'cpd:C00026'},
'path:map00473': {'cpd:C00022'},
'path:map00480': {'cpd:C00025',
'cpd:C00037',
'cpd:C00134',
'cpd:C00315',
'cpd:C05422'},
'path:map00500': {'cpd:C00089',
'cpd:C00095',
'cpd:C00181',
'cpd:C00208',
'cpd:C00267',
'cpd:C01083'},
'path:map00520': {'cpd:C00181', 'cpd:C00267'},
'path:map00521': {'cpd:C00137'},
'path:map00524': {'cpd:C00025'},
'path:map00561': {'cpd:C00258'},
'path:map00562': {'cpd:C00137'},
'path:map00591': {'cpd:C01595'},
'path:map00600': {'cpd:C00065'},
'path:map00620': {'cpd:C00022', 'cpd:C00042', 'cpd:C00122'},
'path:map00621': {'cpd:C00022'},
'path:map00622': {'cpd:C00022'},
'path:map00625': {'cpd:C00160'},
'path:map00630': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00037',
'cpd:C00042',
'cpd:C00065',
'cpd:C00158',
'cpd:C00160',
'cpd:C00258'},
'path:map00640': {'cpd:C00042', 'cpd:C00099'},
'path:map00643': {'cpd:C00122'},
'path:map00650': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00042',
'cpd:C00122',
'cpd:C00334'},
'path:map00660': {'cpd:C00022', 'cpd:C00025', 'cpd:C00026'},
'path:map00680': {'cpd:C00022',
'cpd:C00037',
'cpd:C00065',
'cpd:C00085',
'cpd:C00258'},
'path:map00710': {'cpd:C00022', 'cpd:C00049', 'cpd:C00085'},
'path:map00720': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00122',
'cpd:C00158'},
'path:map00730': {'cpd:C00022', 'cpd:C00037'},
'path:map00760': {'cpd:C00022',
'cpd:C00049',
'cpd:C00122',
'cpd:C00253',
'cpd:C00334'},
'path:map00770': {'cpd:C00022',
'cpd:C00049',
'cpd:C00099',
'cpd:C00183',
'cpd:C00429'},
'path:map00780': {'cpd:C00047'},
'path:map00860': {'cpd:C00025', 'cpd:C00037'},
'path:map00900': {'cpd:C00022'},
'path:map00901': {'cpd:C00078'},
'path:map00905': {'cpd:C01789'},
'path:map00910': {'cpd:C00025'},
'path:map00920': {'cpd:C00042', 'cpd:C00065'},
'path:map00940': {'cpd:C00315'},
'path:map00960': {'cpd:C00047', 'cpd:C00134', 'cpd:C00253', 'cpd:C00407'},
'path:map00966': {'cpd:C00073',
'cpd:C00078',
'cpd:C00123',
'cpd:C00183',
'cpd:C00407'},
'path:map00970': {'cpd:C00025',
'cpd:C00037',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00123',
'cpd:C00148',
'cpd:C00183',
'cpd:C00407'},
'path:map01040': {'cpd:C00249', 'cpd:C01595'},
'path:map01060': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00037',
'cpd:C00042',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00122',
'cpd:C00123',
'cpd:C00134',
'cpd:C00158',
'cpd:C00183',
'cpd:C00249',
'cpd:C00253',
'cpd:C00267',
'cpd:C00407',
'cpd:C00493',
'cpd:C01595',
'cpd:C01753',
'cpd:C01789'},
'path:map01061': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00078',
'cpd:C00122',
'cpd:C00158',
'cpd:C00267',
'cpd:C00493'},
'path:map01062': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00122',
'cpd:C00158',
'cpd:C00267',
'cpd:C01753',
'cpd:C01789'},
'path:map01063': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00078',
'cpd:C00122',
'cpd:C00158',
'cpd:C00183',
'cpd:C00267',
'cpd:C00493'},
'path:map01064': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00042',
'cpd:C00047',
'cpd:C00049',
'cpd:C00122',
'cpd:C00134',
'cpd:C00158',
'cpd:C00253',
'cpd:C00267',
'cpd:C00407'},
'path:map01065': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00122',
'cpd:C00123',
'cpd:C00158',
'cpd:C00267'},
'path:map01066': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00122',
'cpd:C00158',
'cpd:C00267'},
'path:map01070': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00049',
'cpd:C00073',
'cpd:C00078',
'cpd:C00122',
'cpd:C00158',
'cpd:C00267',
'cpd:C00493',
'cpd:C01789'},
'path:map01100': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00037',
'cpd:C00042',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00085',
'cpd:C00089',
'cpd:C00095',
'cpd:C00099',
'cpd:C00122',
'cpd:C00123',
'cpd:C00134',
'cpd:C00137',
'cpd:C00148',
'cpd:C00158',
'cpd:C00160',
'cpd:C00181',
'cpd:C00183',
'cpd:C00208',
'cpd:C00249',
'cpd:C00253',
'cpd:C00258',
'cpd:C00267',
'cpd:C00315',
'cpd:C00334',
'cpd:C00407',
'cpd:C00429',
'cpd:C00493',
'cpd:C01083',
'cpd:C01595',
'cpd:C01789',
'cpd:C05422'},
'path:map01110': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00037',
'cpd:C00042',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00099',
'cpd:C00122',
'cpd:C00123',
'cpd:C00134',
'cpd:C00137',
'cpd:C00148',
'cpd:C00158',
'cpd:C00160',
'cpd:C00183',
'cpd:C00253',
'cpd:C00258',
'cpd:C00267',
'cpd:C00407',
'cpd:C00493',
'cpd:C01083',
'cpd:C01753',
'cpd:C01789'},
'path:map01120': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00037',
'cpd:C00042',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00085',
'cpd:C00095',
'cpd:C00122',
'cpd:C00137',
'cpd:C00158',
'cpd:C00160',
'cpd:C00253',
'cpd:C00258',
'cpd:C00267'},
'path:map01200': {'cpd:C00022',
'cpd:C00026',
'cpd:C00037',
'cpd:C00042',
'cpd:C00049',
'cpd:C00065',
'cpd:C00085',
'cpd:C00122',
'cpd:C00158',
'cpd:C00258',
'cpd:C00267'},
'path:map01210': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00047',
'cpd:C00049',
'cpd:C00073',
'cpd:C00078',
'cpd:C00123',
'cpd:C00158',
'cpd:C00183',
'cpd:C00407'},
'path:map01212': {'cpd:C00249'},
'path:map01220': {'cpd:C00022', 'cpd:C00042', 'cpd:C00122'},
'path:map01230': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00037',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00123',
'cpd:C00148',
'cpd:C00158',
'cpd:C00183',
'cpd:C00407',
'cpd:C00493'},
'path:map01502': {'cpd:C00022', 'cpd:C00037', 'cpd:C00065'},
'path:map02010': {'cpd:C00025',
'cpd:C00037',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00089',
'cpd:C00095',
'cpd:C00121',
'cpd:C00123',
'cpd:C00134',
'cpd:C00137',
'cpd:C00148',
'cpd:C00181',
'cpd:C00183',
'cpd:C00208',
'cpd:C00315',
'cpd:C00407',
'cpd:C00492',
'cpd:C01083'},
'path:map02020': {'cpd:C00025',
'cpd:C00042',
'cpd:C00049',
'cpd:C00122',
'cpd:C00158'},
'path:map02030': {'cpd:C00049', 'cpd:C00121', 'cpd:C00208'},
'path:map02060': {'cpd:C00022',
'cpd:C00089',
'cpd:C00095',
'cpd:C00208',
'cpd:C01083'},
'path:map04024': {'cpd:C00042', 'cpd:C00334'},
'path:map04066': {'cpd:C00022', 'cpd:C00026'},
'path:map04068': {'cpd:C00025'},
'path:map04070': {'cpd:C00137'},
'path:map04071': {'cpd:C00065'},
'path:map04080': {'cpd:C00025',
'cpd:C00037',
'cpd:C00049',
'cpd:C00099',
'cpd:C00334'},
'path:map04152': {'cpd:C00022', 'cpd:C00085'},
'path:map04540': {'cpd:C00025'},
'path:map04713': {'cpd:C00025'},
'path:map04720': {'cpd:C00025'},
'path:map04721': {'cpd:C00025', 'cpd:C00037', 'cpd:C00334'},
'path:map04723': {'cpd:C00025', 'cpd:C00334'},
'path:map04724': {'cpd:C00025'},
'path:map04726': {'cpd:C00078'},
'path:map04727': {'cpd:C00025', 'cpd:C00026', 'cpd:C00042', 'cpd:C00334'},
'path:map04730': {'cpd:C00025'},
'path:map04742': {'cpd:C00025', 'cpd:C00089'},
'path:map04911': {'cpd:C00022'},
'path:map04915': {'cpd:C00334'},
'path:map04922': {'cpd:C00022',
'cpd:C00026',
'cpd:C00042',
'cpd:C00085',
'cpd:C00122',
'cpd:C00158'},
'path:map04930': {'cpd:C00022'},
'path:map04964': {'cpd:C00025', 'cpd:C00026', 'cpd:C00267'},
'path:map04973': {'cpd:C00089', 'cpd:C00095', 'cpd:C00208'},
'path:map04974': {'cpd:C00025',
'cpd:C00037',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00099',
'cpd:C00123',
'cpd:C00134',
'cpd:C00148',
'cpd:C00183',
'cpd:C00407'},
'path:map04976': {'cpd:C00026', 'cpd:C00315'},
'path:map04978': {'cpd:C00037',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00123',
'cpd:C00148',
'cpd:C00183',
'cpd:C00407'},
'path:map05014': {'cpd:C00025'},
'path:map05016': {'cpd:C00025'},
'path:map05030': {'cpd:C00025'},
'path:map05031': {'cpd:C00025'},
'path:map05032': {'cpd:C00334'},
'path:map05033': {'cpd:C00025', 'cpd:C00334'},
'path:map05034': {'cpd:C00025'},
'path:map05133': {'cpd:C00253'},
'path:map05143': {'cpd:C00078'},
'path:map05200': {'cpd:C00122'},
'path:map05211': {'cpd:C00122'},
'path:map05230': {'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00037',
'cpd:C00042',
'cpd:C00049',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00085',
'cpd:C00122',
'cpd:C00123',
'cpd:C00148',
'cpd:C00158',
'cpd:C00183',
'cpd:C00407'}}
In [65]:
cpdsFor['path:map01230']
Out[65]:
{'cpd:C00022',
'cpd:C00025',
'cpd:C00026',
'cpd:C00037',
'cpd:C00047',
'cpd:C00049',
'cpd:C00065',
'cpd:C00073',
'cpd:C00078',
'cpd:C00123',
'cpd:C00148',
'cpd:C00158',
'cpd:C00183',
'cpd:C00407',
'cpd:C00493'}
In [55]:
import os
def apath(x):
foo = os.path.abspath('.') + "/" + x.replace("cpd:", "") + ".png"
return foo
pngpath = map(apath, cpdsFor['path:map01230'])
def rmcpdhead(x):
return x.replace("cpd:", "")
cpdid = map(rmcpdhead, cpdsFor['path:map01230'])
In [56]:
pngpath
Out[56]:
['/Users/knishida/projects/togotrial2014/C00049.png',
'/Users/knishida/projects/togotrial2014/C00493.png',
'/Users/knishida/projects/togotrial2014/C00407.png',
'/Users/knishida/projects/togotrial2014/C00026.png',
'/Users/knishida/projects/togotrial2014/C00078.png',
'/Users/knishida/projects/togotrial2014/C00037.png',
'/Users/knishida/projects/togotrial2014/C00025.png',
'/Users/knishida/projects/togotrial2014/C00022.png',
'/Users/knishida/projects/togotrial2014/C00148.png',
'/Users/knishida/projects/togotrial2014/C00158.png',
'/Users/knishida/projects/togotrial2014/C00123.png',
'/Users/knishida/projects/togotrial2014/C00073.png',
'/Users/knishida/projects/togotrial2014/C00047.png',
'/Users/knishida/projects/togotrial2014/C00183.png',
'/Users/knishida/projects/togotrial2014/C00065.png']
In [57]:
d = {'cgraph' : pd.Series(pngpath), 'plotcpd' : pd.Series(cpdid)}
In [58]:
df = pd.DataFrame(d)
In [59]:
df
Out[59]:
cgraph
plotcpd
0
/Users/knishida/projects/togotrial2014/C00049.png
C00049
1
/Users/knishida/projects/togotrial2014/C00493.png
C00493
2
/Users/knishida/projects/togotrial2014/C00407.png
C00407
3
/Users/knishida/projects/togotrial2014/C00026.png
C00026
4
/Users/knishida/projects/togotrial2014/C00078.png
C00078
5
/Users/knishida/projects/togotrial2014/C00037.png
C00037
6
/Users/knishida/projects/togotrial2014/C00025.png
C00025
7
/Users/knishida/projects/togotrial2014/C00022.png
C00022
8
/Users/knishida/projects/togotrial2014/C00148.png
C00148
9
/Users/knishida/projects/togotrial2014/C00158.png
C00158
10
/Users/knishida/projects/togotrial2014/C00123.png
C00123
11
/Users/knishida/projects/togotrial2014/C00073.png
C00073
12
/Users/knishida/projects/togotrial2014/C00047.png
C00047
13
/Users/knishida/projects/togotrial2014/C00183.png
C00183
14
/Users/knishida/projects/togotrial2014/C00065.png
C00065
In [31]:
import requests
PORT_NUMBER = 1234
BASE_URL = "http://localhost:" + str(PORT_NUMBER) + "/v1/"
HEADERS = {'Content-Type': 'application/json'}
# Make sure Cytoscape RESTful API App is running!
cytoscape_state = requests.get(BASE_URL)
print(json.dumps(json.loads(cytoscape_state.content), indent=4))
{
"memoryStatus": {
"usedMemory": 512,
"freeMemory": 2535,
"maxMemory": 13653,
"totalMemory": 3048
},
"numberOfCores": 8,
"apiVersion": "v1"
}
In [23]:
pathway_location = "http://rest.kegg.jp/get/rn01230/kgml"
res1 = requests.post(BASE_URL + "networks?source=url", data=json.dumps([pathway_location]), headers=HEADERS)
result = json.loads(res1.content)
pathway_suid = result[0]["networkSUID"][0]
print("Pathway SUID = " + str(pathway_suid))
Pathway SUID = 52
Finally you can visualize matplotlib images using Cytoscape custom node graphics.
When you paste cgraph urls to Cytoscape custom node graphics Passthrough mapping column and adjust the size, you should see following result.
Blue bars mean leaf profile, Green bars mean root profile.
You can recognize the difference at a glance.
For example, in branchin Valine, Leucine
In [67]:
from IPython.display import SVG
SVG(url='https://raw.githubusercontent.com/kozo2/togotrial2014/master/leaf-root.svg')
Out[67]:
In [ ]:
Content source: kozo2/togotrial2014
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