In [ ]:
In [6]:
# import data from url
from py2cytoscape.data.cyrest_client import CyRestClient
from IPython.display import Image
import json
# Create REST client for Cytoscape
cy = CyRestClient()
# Reset current session for fresh start
cy.session.delete()
# Load a sample network
network = cy.network.create_from('http://chianti.ucsd.edu/~kono/data/galFiltered.sif')
# Apply layout to the cytoscape network object
cy.layout.apply(network = network)
# Show it!!
Image(network.get_png(height=400))
Out[6]:
In [15]:
# As Cytoscape.js (dict)
network_json = network.to_json()
print(json.dumps(network_json, indent=4))
{
"data": {
"__Annotations": [],
"name": "galFiltered.sif",
"SUID": 12778,
"shared_name": "galFiltered.sif",
"selected": true
},
"format_version": "1.0",
"target_cytoscapejs_version": "~2.1",
"elements": {
"edges": [
{
"data": {
"name": "YDR277C (pp) YDL194W",
"SUID": 13479,
"shared_interaction": "pp",
"source": "13476",
"id": "13479",
"interaction": "pp",
"target": "13478",
"shared_name": "YDR277C (pp) YDL194W",
"selected": false
}
},
{
"data": {
"name": "YDR277C (pp) YJR022W",
"SUID": 13477,
"shared_interaction": "pp",
"source": "13476",
"id": "13477",
"interaction": "pp",
"target": "12836",
"shared_name": "YDR277C (pp) YJR022W",
"selected": false
}
},
{
"data": {
"name": "YPR145W (pp) YMR117C",
"SUID": 13471,
"shared_interaction": "pp",
"source": "13470",
"id": "13471",
"interaction": "pp",
"target": "13419",
"shared_name": "YPR145W (pp) YMR117C",
"selected": false
}
},
{
"data": {
"name": "YER054C (pp) YBR045C",
"SUID": 13469,
"shared_interaction": "pp",
"source": "13467",
"id": "13469",
"interaction": "pp",
"target": "13464",
"shared_name": "YER054C (pp) YBR045C",
"selected": false
}
},
{
"data": {
"name": "YER054C (pp) YER133W",
"SUID": 13468,
"shared_interaction": "pp",
"source": "13467",
"id": "13468",
"interaction": "pp",
"target": "13179",
"shared_name": "YER054C (pp) YER133W",
"selected": false
}
},
{
"data": {
"name": "YBR045C (pp) YOR178C",
"SUID": 13466,
"shared_interaction": "pp",
"source": "13464",
"id": "13466",
"interaction": "pp",
"target": "13181",
"shared_name": "YBR045C (pp) YOR178C",
"selected": false
}
},
{
"data": {
"name": "YBR045C (pp) YIL045W",
"SUID": 13465,
"shared_interaction": "pp",
"source": "13464",
"id": "13465",
"interaction": "pp",
"target": "13364",
"shared_name": "YBR045C (pp) YIL045W",
"selected": false
}
},
{
"data": {
"name": "YBL079W (pp) YDL088C",
"SUID": 13463,
"shared_interaction": "pp",
"source": "13462",
"id": "13463",
"interaction": "pp",
"target": "13429",
"shared_name": "YBL079W (pp) YDL088C",
"selected": false
}
},
{
"data": {
"name": "YLR345W (pp) YLR321C",
"SUID": 13461,
"shared_interaction": "pp",
"source": "13460",
"id": "13461",
"interaction": "pp",
"target": "13125",
"shared_name": "YLR345W (pp) YLR321C",
"selected": false
}
},
{
"data": {
"name": "YGR136W (pp) YGR058W",
"SUID": 13445,
"shared_interaction": "pp",
"source": "13444",
"id": "13445",
"interaction": "pp",
"target": "12983",
"shared_name": "YGR136W (pp) YGR058W",
"selected": false
}
},
{
"data": {
"name": "YDL023C (pp) YJL159W",
"SUID": 13443,
"shared_interaction": "pp",
"source": "13442",
"id": "13443",
"interaction": "pp",
"target": "13015",
"shared_name": "YDL023C (pp) YJL159W",
"selected": false
}
},
{
"data": {
"name": "YBR170C (pp) YGR048W",
"SUID": 13439,
"shared_interaction": "pp",
"source": "13438",
"id": "13439",
"interaction": "pp",
"target": "13169",
"shared_name": "YBR170C (pp) YGR048W",
"selected": false
}
},
{
"data": {
"name": "YGR074W (pp) YBR043C",
"SUID": 13475,
"shared_interaction": "pp",
"source": "13435",
"id": "13475",
"interaction": "pp",
"target": "13474",
"shared_name": "YGR074W (pp) YBR043C",
"selected": false
}
},
{
"data": {
"name": "YGL202W (pp) YGR074W",
"SUID": 13436,
"shared_interaction": "pp",
"source": "13434",
"id": "13436",
"interaction": "pp",
"target": "13435",
"shared_name": "YGL202W (pp) YGR074W",
"selected": false
}
},
{
"data": {
"name": "YLR197W (pp) YOR310C",
"SUID": 13433,
"shared_interaction": "pp",
"source": "13431",
"id": "13433",
"interaction": "pp",
"target": "12904",
"shared_name": "YLR197W (pp) YOR310C",
"selected": false
}
},
{
"data": {
"name": "YLR197W (pp) YDL014W",
"SUID": 13432,
"shared_interaction": "pp",
"source": "13431",
"id": "13432",
"interaction": "pp",
"target": "12903",
"shared_name": "YLR197W (pp) YDL014W",
"selected": false
}
},
{
"data": {
"name": "YDL088C (pp) YER110C",
"SUID": 13430,
"shared_interaction": "pp",
"source": "13429",
"id": "13430",
"interaction": "pp",
"target": "13256",
"shared_name": "YDL088C (pp) YER110C",
"selected": false
}
},
{
"data": {
"name": "YMR117C (pp) YPR010C",
"SUID": 13422,
"shared_interaction": "pp",
"source": "13419",
"id": "13422",
"interaction": "pp",
"target": "13421",
"shared_name": "YMR117C (pp) YPR010C",
"selected": false
}
},
{
"data": {
"name": "YMR117C (pp) YCL032W",
"SUID": 13420,
"shared_interaction": "pp",
"source": "13419",
"id": "13420",
"interaction": "pp",
"target": "12939",
"shared_name": "YMR117C (pp) YCL032W",
"selected": false
}
},
{
"data": {
"name": "YML114C (pp) YDR167W",
"SUID": 13418,
"shared_interaction": "pp",
"source": "13417",
"id": "13418",
"interaction": "pp",
"target": "13271",
"shared_name": "YML114C (pp) YDR167W",
"selected": false
}
},
{
"data": {
"name": "YNL036W (pp) YIR009W",
"SUID": 13416,
"shared_interaction": "pp",
"source": "13415",
"id": "13416",
"interaction": "pp",
"target": "12961",
"shared_name": "YNL036W (pp) YIR009W",
"selected": false
}
},
{
"data": {
"name": "YOR212W (pp) YLR362W",
"SUID": 13440,
"shared_interaction": "pp",
"source": "13413",
"id": "13440",
"interaction": "pp",
"target": "12942",
"shared_name": "YOR212W (pp) YLR362W",
"selected": false
}
},
{
"data": {
"name": "YDR070C (pp) YFL017C",
"SUID": 13411,
"shared_interaction": "pp",
"source": "13410",
"id": "13411",
"interaction": "pp",
"target": "12806",
"shared_name": "YDR070C (pp) YFL017C",
"selected": false
}
},
{
"data": {
"name": "YGR046W (pp) YNL236W",
"SUID": 13402,
"shared_interaction": "pp",
"source": "13401",
"id": "13402",
"interaction": "pp",
"target": "12970",
"shared_name": "YGR046W (pp) YNL236W",
"selected": false
}
},
{
"data": {
"name": "YIL070C (pp) YML054C",
"SUID": 13396,
"shared_interaction": "pp",
"source": "13395",
"id": "13396",
"interaction": "pp",
"target": "12989",
"shared_name": "YIL070C (pp) YML054C",
"selected": false
}
},
{
"data": {
"name": "YPR113W (pd) YMR043W",
"SUID": 13394,
"shared_interaction": "pd",
"source": "13393",
"id": "13394",
"interaction": "pd",
"target": "13012",
"shared_name": "YPR113W (pd) YMR043W",
"selected": false
}
},
{
"data": {
"name": "YER081W (pp) YIL074C",
"SUID": 13392,
"shared_interaction": "pp",
"source": "13391",
"id": "13392",
"interaction": "pp",
"target": "13349",
"shared_name": "YER081W (pp) YIL074C",
"selected": false
}
},
{
"data": {
"name": "YGR088W (pd) YLR256W",
"SUID": 13390,
"shared_interaction": "pd",
"source": "13389",
"id": "13390",
"interaction": "pd",
"target": "12988",
"shared_name": "YGR088W (pd) YLR256W",
"selected": false
}
},
{
"data": {
"name": "YDR395W (pp) YPR102C",
"SUID": 13459,
"shared_interaction": "pp",
"source": "13386",
"id": "13459",
"interaction": "pp",
"target": "13305",
"shared_name": "YDR395W (pp) YPR102C",
"selected": false
}
},
{
"data": {
"name": "YDR395W (pp) YOL127W",
"SUID": 13458,
"shared_interaction": "pp",
"source": "13386",
"id": "13458",
"interaction": "pp",
"target": "12880",
"shared_name": "YDR395W (pp) YOL127W",
"selected": false
}
},
{
"data": {
"name": "YDR395W (pp) YIL052C",
"SUID": 13457,
"shared_interaction": "pp",
"source": "13386",
"id": "13457",
"interaction": "pp",
"target": "13456",
"shared_name": "YDR395W (pp) YIL052C",
"selected": false
}
},
{
"data": {
"name": "YDR395W (pp) YER056CA",
"SUID": 13455,
"shared_interaction": "pp",
"source": "13386",
"id": "13455",
"interaction": "pp",
"target": "13454",
"shared_name": "YDR395W (pp) YER056CA",
"selected": false
}
},
{
"data": {
"name": "YDR395W (pp) YNL069C",
"SUID": 13453,
"shared_interaction": "pp",
"source": "13386",
"id": "13453",
"interaction": "pp",
"target": "13452",
"shared_name": "YDR395W (pp) YNL069C",
"selected": false
}
},
{
"data": {
"name": "YDR395W (pp) YIL133C",
"SUID": 13451,
"shared_interaction": "pp",
"source": "13386",
"id": "13451",
"interaction": "pp",
"target": "12861",
"shared_name": "YDR395W (pp) YIL133C",
"selected": false
}
},
{
"data": {
"name": "YDR395W (pp) YDL075W",
"SUID": 13450,
"shared_interaction": "pp",
"source": "13386",
"id": "13450",
"interaction": "pp",
"target": "13449",
"shared_name": "YDR395W (pp) YDL075W",
"selected": false
}
},
{
"data": {
"name": "YGR085C (pp) YDR395W",
"SUID": 13387,
"shared_interaction": "pp",
"source": "13384",
"id": "13387",
"interaction": "pp",
"target": "13386",
"shared_name": "YGR085C (pp) YDR395W",
"selected": false
}
},
{
"data": {
"name": "YGR085C (pp) YLR075W",
"SUID": 13385,
"shared_interaction": "pp",
"source": "13384",
"id": "13385",
"interaction": "pp",
"target": "13304",
"shared_name": "YGR085C (pp) YLR075W",
"selected": false
}
},
{
"data": {
"name": "YDL030W (pp) YMR005W",
"SUID": 13376,
"shared_interaction": "pp",
"source": "13373",
"id": "13376",
"interaction": "pp",
"target": "13375",
"shared_name": "YDL030W (pp) YMR005W",
"selected": false
}
},
{
"data": {
"name": "YDL030W (pp) YDL013W",
"SUID": 13374,
"shared_interaction": "pp",
"source": "13373",
"id": "13374",
"interaction": "pp",
"target": "12849",
"shared_name": "YDL030W (pp) YDL013W",
"selected": false
}
},
{
"data": {
"name": "YER079W (pp) YNL154C",
"SUID": 13372,
"shared_interaction": "pp",
"source": "13370",
"id": "13372",
"interaction": "pp",
"target": "13098",
"shared_name": "YER079W (pp) YNL154C",
"selected": false
}
},
{
"data": {
"name": "YER079W (pp) YHR135C",
"SUID": 13371,
"shared_interaction": "pp",
"source": "13370",
"id": "13371",
"interaction": "pp",
"target": "13093",
"shared_name": "YER079W (pp) YHR135C",
"selected": false
}
},
{
"data": {
"name": "YDL215C (pp) YLR432W",
"SUID": 13369,
"shared_interaction": "pp",
"source": "13367",
"id": "13369",
"interaction": "pp",
"target": "13272",
"shared_name": "YDL215C (pp) YLR432W",
"selected": false
}
},
{
"data": {
"name": "YDL215C (pd) YER040W",
"SUID": 13368,
"shared_interaction": "pd",
"source": "13367",
"id": "13368",
"interaction": "pd",
"target": "13056",
"shared_name": "YDL215C (pd) YER040W",
"selected": false
}
},
{
"data": {
"name": "YPR041W (pp) YMR309C",
"SUID": 13360,
"shared_interaction": "pp",
"source": "13358",
"id": "13360",
"interaction": "pp",
"target": "12913",
"shared_name": "YPR041W (pp) YMR309C",
"selected": false
}
},
{
"data": {
"name": "YPR041W (pp) YOR361C",
"SUID": 13359,
"shared_interaction": "pp",
"source": "13358",
"id": "13359",
"interaction": "pp",
"target": "12912",
"shared_name": "YPR041W (pp) YOR361C",
"selected": false
}
},
{
"data": {
"name": "YOR120W (pd) YPL248C",
"SUID": 13357,
"shared_interaction": "pd",
"source": "13356",
"id": "13357",
"interaction": "pd",
"target": "12957",
"shared_name": "YOR120W (pd) YPL248C",
"selected": false
}
},
{
"data": {
"name": "YIL074C (pp) YNL311C",
"SUID": 13350,
"shared_interaction": "pp",
"source": "13349",
"id": "13350",
"interaction": "pp",
"target": "13143",
"shared_name": "YIL074C (pp) YNL311C",
"selected": false
}
},
{
"data": {
"name": "YDR299W (pd) YJL194W",
"SUID": 13348,
"shared_interaction": "pd",
"source": "13347",
"id": "13348",
"interaction": "pd",
"target": "13330",
"shared_name": "YDR299W (pd) YJL194W",
"selected": false
}
},
{
"data": {
"name": "YHR005C (pp) YLR362W",
"SUID": 13409,
"shared_interaction": "pp",
"source": "13345",
"id": "13409",
"interaction": "pp",
"target": "12942",
"shared_name": "YHR005C (pp) YLR362W",
"selected": false
}
},
{
"data": {
"name": "YLR452C (pp) YHR005C",
"SUID": 13346,
"shared_interaction": "pp",
"source": "13344",
"id": "13346",
"interaction": "pp",
"target": "13345",
"shared_name": "YLR452C (pp) YHR005C",
"selected": false
}
},
{
"data": {
"name": "YMR255W (pp) YGL122C",
"SUID": 13363,
"shared_interaction": "pp",
"source": "13342",
"id": "13363",
"interaction": "pp",
"target": "12789",
"shared_name": "YMR255W (pp) YGL122C",
"selected": false
}
},
{
"data": {
"name": "YBR274W (pp) YMR255W",
"SUID": 13343,
"shared_interaction": "pp",
"source": "13341",
"id": "13343",
"interaction": "pp",
"target": "13342",
"shared_name": "YBR274W (pp) YMR255W",
"selected": false
}
},
{
"data": {
"name": "YHR084W (pd) YFL026W",
"SUID": 13383,
"shared_interaction": "pd",
"source": "13339",
"id": "13383",
"interaction": "pd",
"target": "13027",
"shared_name": "YHR084W (pd) YFL026W",
"selected": false
}
},
{
"data": {
"name": "YHR084W (pd) YDR461W",
"SUID": 13382,
"shared_interaction": "pd",
"source": "13339",
"id": "13382",
"interaction": "pd",
"target": "13021",
"shared_name": "YHR084W (pd) YDR461W",
"selected": false
}
},
{
"data": {
"name": "YHR084W (pp) YMR043W",
"SUID": 13381,
"shared_interaction": "pp",
"source": "13339",
"id": "13381",
"interaction": "pp",
"target": "13012",
"shared_name": "YHR084W (pp) YMR043W",
"selected": false
}
},
{
"data": {
"name": "YBL050W (pp) YOR036W",
"SUID": 13337,
"shared_interaction": "pp",
"source": "13336",
"id": "13337",
"interaction": "pp",
"target": "13052",
"shared_name": "YBL050W (pp) YOR036W",
"selected": false
}
},
{
"data": {
"name": "YBL026W (pp) YOR167C",
"SUID": 13480,
"shared_interaction": "pp",
"source": "13334",
"id": "13480",
"interaction": "pp",
"target": "12834",
"shared_name": "YBL026W (pp) YOR167C",
"selected": false
}
},
{
"data": {
"name": "YJL194W (pd) YMR043W",
"SUID": 13331,
"shared_interaction": "pd",
"source": "13330",
"id": "13331",
"interaction": "pd",
"target": "13012",
"shared_name": "YJL194W (pd) YMR043W",
"selected": false
}
},
{
"data": {
"name": "YLR258W (pp) YBR274W",
"SUID": 13366,
"shared_interaction": "pp",
"source": "13328",
"id": "13366",
"interaction": "pp",
"target": "13341",
"shared_name": "YLR258W (pp) YBR274W",
"selected": false
}
},
{
"data": {
"name": "YLR258W (pp) YIL045W",
"SUID": 13365,
"shared_interaction": "pp",
"source": "13328",
"id": "13365",
"interaction": "pp",
"target": "13364",
"shared_name": "YLR258W (pp) YIL045W",
"selected": false
}
},
{
"data": {
"name": "YGL134W (pp) YLR258W",
"SUID": 13329,
"shared_interaction": "pp",
"source": "13326",
"id": "13329",
"interaction": "pp",
"target": "13328",
"shared_name": "YGL134W (pp) YLR258W",
"selected": false
}
},
{
"data": {
"name": "YGL134W (pp) YPL031C",
"SUID": 13327,
"shared_interaction": "pp",
"source": "13326",
"id": "13327",
"interaction": "pp",
"target": "13205",
"shared_name": "YGL134W (pp) YPL031C",
"selected": false
}
},
{
"data": {
"name": "YPR124W (pd) YMR021C",
"SUID": 13321,
"shared_interaction": "pd",
"source": "13320",
"id": "13321",
"interaction": "pd",
"target": "13076",
"shared_name": "YPR124W (pd) YMR021C",
"selected": false
}
},
{
"data": {
"name": "YNL135C (pp) YDR174W",
"SUID": 13361,
"shared_interaction": "pp",
"source": "13318",
"id": "13361",
"interaction": "pp",
"target": "13080",
"shared_name": "YNL135C (pp) YDR174W",
"selected": false
}
},
{
"data": {
"name": "YER052C (pp) YNL135C",
"SUID": 13319,
"shared_interaction": "pp",
"source": "13317",
"id": "13319",
"interaction": "pp",
"target": "13318",
"shared_name": "YER052C (pp) YNL135C",
"selected": false
}
},
{
"data": {
"name": "YPL240C (pp) YOR036W",
"SUID": 13310,
"shared_interaction": "pp",
"source": "13308",
"id": "13310",
"interaction": "pp",
"target": "13052",
"shared_name": "YPL240C (pp) YOR036W",
"selected": false
}
},
{
"data": {
"name": "YPL240C (pp) YBR155W",
"SUID": 13309,
"shared_interaction": "pp",
"source": "13308",
"id": "13309",
"interaction": "pp",
"target": "12920",
"shared_name": "YPL240C (pp) YBR155W",
"selected": false
}
},
{
"data": {
"name": "YLR075W (pp) YPR102C",
"SUID": 13306,
"shared_interaction": "pp",
"source": "13304",
"id": "13306",
"interaction": "pp",
"target": "13305",
"shared_name": "YLR075W (pp) YPR102C",
"selected": false
}
},
{
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"data": {
"id": "12949",
"name": "YOL051W",
"SUID": 12949,
"shared_name": "YOL051W",
"selected": false
}
},
{
"data": {
"id": "12948",
"name": "YBR019C",
"SUID": 12948,
"shared_name": "YBR019C",
"selected": false
}
},
{
"data": {
"id": "12946",
"name": "YJR060W",
"SUID": 12946,
"shared_name": "YJR060W",
"selected": false
}
},
{
"data": {
"id": "12944",
"name": "YDR103W",
"SUID": 12944,
"shared_name": "YDR103W",
"selected": false
}
},
{
"data": {
"id": "12942",
"name": "YLR362W",
"SUID": 12942,
"shared_name": "YLR362W",
"selected": false
}
},
{
"data": {
"id": "12940",
"name": "YDR032C",
"SUID": 12940,
"shared_name": "YDR032C",
"selected": false
}
},
{
"data": {
"id": "12939",
"name": "YCL032W",
"SUID": 12939,
"shared_name": "YCL032W",
"selected": false
}
},
{
"data": {
"id": "12937",
"name": "YLR109W",
"SUID": 12937,
"shared_name": "YLR109W",
"selected": false
}
},
{
"data": {
"id": "12935",
"name": "YHR141C",
"SUID": 12935,
"shared_name": "YHR141C",
"selected": false
}
},
{
"data": {
"id": "12934",
"name": "YMR138W",
"SUID": 12934,
"shared_name": "YMR138W",
"selected": false
}
},
{
"data": {
"id": "12932",
"name": "YMR300C",
"SUID": 12932,
"shared_name": "YMR300C",
"selected": false
}
},
{
"data": {
"id": "12930",
"name": "YOL058W",
"SUID": 12930,
"shared_name": "YOL058W",
"selected": false
}
},
{
"data": {
"id": "12928",
"name": "YBR248C",
"SUID": 12928,
"shared_name": "YBR248C",
"selected": false
}
},
{
"data": {
"id": "12925",
"name": "YOR202W",
"SUID": 12925,
"shared_name": "YOR202W",
"selected": false
}
},
{
"data": {
"id": "12923",
"name": "YMR108W",
"SUID": 12923,
"shared_name": "YMR108W",
"selected": false
}
},
{
"data": {
"id": "12922",
"name": "YEL009C",
"SUID": 12922,
"shared_name": "YEL009C",
"selected": false
}
},
{
"data": {
"id": "12920",
"name": "YBR155W",
"SUID": 12920,
"shared_name": "YBR155W",
"selected": false
}
},
{
"data": {
"id": "12919",
"name": "YMR186W",
"SUID": 12919,
"shared_name": "YMR186W",
"selected": false
}
},
{
"data": {
"id": "12917",
"name": "YGL106W",
"SUID": 12917,
"shared_name": "YGL106W",
"selected": false
}
},
{
"data": {
"id": "12916",
"name": "YOR326W",
"SUID": 12916,
"shared_name": "YOR326W",
"selected": false
}
},
{
"data": {
"id": "12913",
"name": "YMR309C",
"SUID": 12913,
"shared_name": "YMR309C",
"selected": false
}
},
{
"data": {
"id": "12912",
"name": "YOR361C",
"SUID": 12912,
"shared_name": "YOR361C",
"selected": false
}
},
{
"data": {
"id": "12910",
"name": "YIL105C",
"SUID": 12910,
"shared_name": "YIL105C",
"selected": false
}
},
{
"data": {
"id": "12908",
"name": "YLR134W",
"SUID": 12908,
"shared_name": "YLR134W",
"selected": false
}
},
{
"data": {
"id": "12906",
"name": "YER179W",
"SUID": 12906,
"shared_name": "YER179W",
"selected": false
}
},
{
"data": {
"id": "12904",
"name": "YOR310C",
"SUID": 12904,
"shared_name": "YOR310C",
"selected": false
}
},
{
"data": {
"id": "12903",
"name": "YDL014W",
"SUID": 12903,
"shared_name": "YDL014W",
"selected": false
}
},
{
"data": {
"id": "12901",
"name": "YPR119W",
"SUID": 12901,
"shared_name": "YPR119W",
"selected": false
}
},
{
"data": {
"id": "12899",
"name": "YLR117C",
"SUID": 12899,
"shared_name": "YLR117C",
"selected": false
}
},
{
"data": {
"id": "12897",
"name": "YGL013C",
"SUID": 12897,
"shared_name": "YGL013C",
"selected": false
}
},
{
"data": {
"id": "12895",
"name": "YCR086W",
"SUID": 12895,
"shared_name": "YCR086W",
"selected": false
}
},
{
"data": {
"id": "12894",
"name": "YDR412W",
"SUID": 12894,
"shared_name": "YDR412W",
"selected": false
}
},
{
"data": {
"id": "12892",
"name": "YPL201C",
"SUID": 12892,
"shared_name": "YPL201C",
"selected": false
}
},
{
"data": {
"id": "12891",
"name": "YER062C",
"SUID": 12891,
"shared_name": "YER062C",
"selected": false
}
},
{
"data": {
"id": "12889",
"name": "YOR327C",
"SUID": 12889,
"shared_name": "YOR327C",
"selected": false
}
},
{
"data": {
"id": "12887",
"name": "YER143W",
"SUID": 12887,
"shared_name": "YER143W",
"selected": false
}
},
{
"data": {
"id": "12886",
"name": "YAL030W",
"SUID": 12886,
"shared_name": "YAL030W",
"selected": false
}
},
{
"data": {
"id": "12884",
"name": "YOL086C",
"SUID": 12884,
"shared_name": "YOL086C",
"selected": false
}
},
{
"data": {
"id": "12882",
"name": "YDR050C",
"SUID": 12882,
"shared_name": "YDR050C",
"selected": false
}
},
{
"data": {
"id": "12880",
"name": "YOL127W",
"SUID": 12880,
"shared_name": "YOL127W",
"selected": false
}
},
{
"data": {
"id": "12877",
"name": "YIL069C",
"SUID": 12877,
"shared_name": "YIL069C",
"selected": false
}
},
{
"data": {
"id": "12875",
"name": "YER074W",
"SUID": 12875,
"shared_name": "YER074W",
"selected": false
}
},
{
"data": {
"id": "12873",
"name": "YBR093C",
"SUID": 12873,
"shared_name": "YBR093C",
"selected": false
}
},
{
"data": {
"id": "12871",
"name": "YDR171W",
"SUID": 12871,
"shared_name": "YDR171W",
"selected": false
}
},
{
"data": {
"id": "12869",
"name": "YCL030C",
"SUID": 12869,
"shared_name": "YCL030C",
"selected": false
}
},
{
"data": {
"id": "12867",
"name": "YNL301C",
"SUID": 12867,
"shared_name": "YNL301C",
"selected": false
}
},
{
"data": {
"id": "12865",
"name": "YOL120C",
"SUID": 12865,
"shared_name": "YOL120C",
"selected": false
}
},
{
"data": {
"id": "12863",
"name": "YLR044C",
"SUID": 12863,
"shared_name": "YLR044C",
"selected": false
}
},
{
"data": {
"id": "12861",
"name": "YIL133C",
"SUID": 12861,
"shared_name": "YIL133C",
"selected": false
}
},
{
"data": {
"id": "12859",
"name": "YHR174W",
"SUID": 12859,
"shared_name": "YHR174W",
"selected": false
}
},
{
"data": {
"id": "12857",
"name": "YGR254W",
"SUID": 12857,
"shared_name": "YGR254W",
"selected": false
}
},
{
"data": {
"id": "12855",
"name": "YCR012W",
"SUID": 12855,
"shared_name": "YCR012W",
"selected": false
}
},
{
"data": {
"id": "12854",
"name": "YNL216W",
"SUID": 12854,
"shared_name": "YNL216W",
"selected": false
}
},
{
"data": {
"id": "12852",
"name": "YAL038W",
"SUID": 12852,
"shared_name": "YAL038W",
"selected": false
}
},
{
"data": {
"id": "12851",
"name": "YNL307C",
"SUID": 12851,
"shared_name": "YNL307C",
"selected": false
}
},
{
"data": {
"id": "12849",
"name": "YDL013W",
"SUID": 12849,
"shared_name": "YDL013W",
"selected": false
}
},
{
"data": {
"id": "12848",
"name": "YER116C",
"SUID": 12848,
"shared_name": "YER116C",
"selected": false
}
},
{
"data": {
"id": "12846",
"name": "YNR053C",
"SUID": 12846,
"shared_name": "YNR053C",
"selected": false
}
},
{
"data": {
"id": "12844",
"name": "YLR264W",
"SUID": 12844,
"shared_name": "YLR264W",
"selected": false
}
},
{
"data": {
"id": "12841",
"name": "YEL015W",
"SUID": 12841,
"shared_name": "YEL015W",
"selected": false
}
},
{
"data": {
"id": "12839",
"name": "YNL050C",
"SUID": 12839,
"shared_name": "YNL050C",
"selected": false
}
},
{
"data": {
"id": "12837",
"name": "YNR050C",
"SUID": 12837,
"shared_name": "YNR050C",
"selected": false
}
},
{
"data": {
"id": "12836",
"name": "YJR022W",
"SUID": 12836,
"shared_name": "YJR022W",
"selected": false
}
},
{
"data": {
"id": "12834",
"name": "YOR167C",
"SUID": 12834,
"shared_name": "YOR167C",
"selected": false
}
},
{
"data": {
"id": "12833",
"name": "YER112W",
"SUID": 12833,
"shared_name": "YER112W",
"selected": false
}
},
{
"data": {
"id": "12831",
"name": "YCL067C",
"SUID": 12831,
"shared_name": "YCL067C",
"selected": false
}
},
{
"data": {
"id": "12829",
"name": "YBR112C",
"SUID": 12829,
"shared_name": "YBR112C",
"selected": false
}
},
{
"data": {
"id": "12828",
"name": "YCR084C",
"SUID": 12828,
"shared_name": "YCR084C",
"selected": false
}
},
{
"data": {
"id": "12826",
"name": "YIL061C",
"SUID": 12826,
"shared_name": "YIL061C",
"selected": false
}
},
{
"data": {
"id": "12825",
"name": "YGR203W",
"SUID": 12825,
"shared_name": "YGR203W",
"selected": false
}
},
{
"data": {
"id": "12820",
"name": "YJL013C",
"SUID": 12820,
"shared_name": "YJL013C",
"selected": false
}
},
{
"data": {
"id": "12818",
"name": "YGL229C",
"SUID": 12818,
"shared_name": "YGL229C",
"selected": false
}
},
{
"data": {
"id": "12817",
"name": "YJL030W",
"SUID": 12817,
"shared_name": "YJL030W",
"selected": false
}
},
{
"data": {
"id": "12815",
"name": "YGR014W",
"SUID": 12815,
"shared_name": "YGR014W",
"selected": false
}
},
{
"data": {
"id": "12814",
"name": "YPL211W",
"SUID": 12814,
"shared_name": "YPL211W",
"selected": false
}
},
{
"data": {
"id": "12812",
"name": "YGL044C",
"SUID": 12812,
"shared_name": "YGL044C",
"selected": false
}
},
{
"data": {
"id": "12811",
"name": "YOL123W",
"SUID": 12811,
"shared_name": "YOL123W",
"selected": false
}
},
{
"data": {
"id": "12808",
"name": "YAL003W",
"SUID": 12808,
"shared_name": "YAL003W",
"selected": false
}
},
{
"data": {
"id": "12806",
"name": "YFL017C",
"SUID": 12806,
"shared_name": "YFL017C",
"selected": false
}
},
{
"data": {
"id": "12804",
"name": "YDR429C",
"SUID": 12804,
"shared_name": "YDR429C",
"selected": false
}
},
{
"data": {
"id": "12803",
"name": "YMR146C",
"SUID": 12803,
"shared_name": "YMR146C",
"selected": false
}
},
{
"data": {
"id": "12801",
"name": "YLR293C",
"SUID": 12801,
"shared_name": "YLR293C",
"selected": false
}
},
{
"data": {
"id": "12799",
"name": "YBR118W",
"SUID": 12799,
"shared_name": "YBR118W",
"selected": false
}
},
{
"data": {
"id": "12797",
"name": "YPR080W",
"SUID": 12797,
"shared_name": "YPR080W",
"selected": false
}
},
{
"data": {
"id": "12796",
"name": "YLR249W",
"SUID": 12796,
"shared_name": "YLR249W",
"selected": false
}
},
{
"data": {
"id": "12794",
"name": "YOR204W",
"SUID": 12794,
"shared_name": "YOR204W",
"selected": false
}
},
{
"data": {
"id": "12792",
"name": "YGL097W",
"SUID": 12792,
"shared_name": "YGL097W",
"selected": false
}
},
{
"data": {
"id": "12791",
"name": "YGR218W",
"SUID": 12791,
"shared_name": "YGR218W",
"selected": false
}
},
{
"data": {
"id": "12789",
"name": "YGL122C",
"SUID": 12789,
"shared_name": "YGL122C",
"selected": false
}
},
{
"data": {
"id": "12788",
"name": "YKR026C",
"SUID": 12788,
"shared_name": "YKR026C",
"selected": false
}
}
]
},
"generated_by": "cytoscape-3.4.0"
}
In [16]:
# As NetworkX graph object
network_networkx = network.to_networkx()
num_nodes = network_networkx.number_of_nodes()
num_edges = network_networkx.number_of_edges()
print('Number of Nodes: ' + str(num_nodes))
print('Number of Edges: ' + str(num_edges))
Number of Nodes: 331
Number of Edges: 362
In [17]:
# As a simple, SIF-like DataFrame
network_df = network.to_dataframe()
network_df.head()
Out[17]:
source
interaction
target
0
13476
pp
13478
1
13476
pp
12836
2
13470
pp
13419
3
13467
pp
13464
4
13467
pp
13179
In [3]:
import py2cytoscape.util.util_igraph as util_ig
# convert cytoscape object to igraph object
network_igraph = util_ig.to_igraph(network.to_json())
In [5]:
import pandas as pd
df = pd.DataFrame({
"name" : ["YKR026C"],
"selected" : [True]
}
)
network.update_node_table(df = df, network_key_col = 'name', data_key_col = 'name')
Out[5]:
['Marquee',
'Sample1',
'Ripple',
'Big Labels',
'Sample2',
'Curved',
'default',
'Universe',
'Solid',
'Gradient1',
'Sample3',
'default black',
'Minimal',
'Directed',
'Nested Network Style']
In [7]:
import pandas as pd
df = pd.DataFrame({
"name" : ["YKR026C"],
"selected" : [True]
}
)
network.update_node_table(df = df, network_key_col = 'name', data_key_col = 'name')
In [ ]:
In [ ]:
In [ ]:
In [ ]:
In [ ]:
Content source: idekerlab/cyrest-examples
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