Cytoscape3 Desktop: Dual Labels (from two columns) per Node?
I have a cytoscape graph for which I would like to present two labels simultaneously per node in the desktop application. Is there a way to do this ? Here is an example (image and export to cyjs). I would like to in addition to the current label (name), have the classID or the synonyms (note that this label is a list).
Here is the cyjs (Cytoscape JSON) for this network:
{
"format_version" : "1.0",
"generated_by" : "cytoscape-3.9.1",
"target_cytoscapejs_version" : "~2.1",
"data" : {
"shared_name" : "Alzheimer's Disease Ontology",
"name" : "Alzheimer's Disease Ontology",
"SUID" : 124,
"shared_name" : "Alzheimer's Disease Ontology",
"selected" : true
},
"elements" : {
"nodes" : [ {
"data" : {
"id" : "191",
"shared_name" : "NEURODEGENERATIVE DISEASE",
"classID" : "DOID_1289",
"synonyms" : [ "NEURODEGENERATIVE DISEASE", "DEGENERATIVE DISEASE" ],
"name" : "NEURODEGENERATIVE DISEASE",
"SUID" : 191,
"id_original" : "155",
"_foretell_labels" : [ "Disease" ],
"selected" : false
},
"position" : {
"x" : 18.285714285714292,
"y" : 67.0
},
"selected" : false
}, {
"data" : {
"id" : "188",
"shared_name" : "CENTRAL NERVOUS SYSTEM DISEASE",
"classID" : "DOID_331",
"name" : "CENTRAL NERVOUS SYSTEM DISEASE",
"SUID" : 188,
"id_original" : "182",
"_foretell_labels" : [ "Disease" ],
"selected" : false
},
"position" : {
"x" : 18.285714285714292,
"y" : 0.0
},
"selected" : false
}, {
"data" : {
"id" : "185",
"shared_name" : "NERVOUS SYSTEM DISEASE",
"classID" : "DOID_863",
"name" : "NERVOUS SYSTEM DISEASE",
"SUID" : 185,
"id_original" : "185",
"_foretell_labels" : [ "Disease" ],
"selected" : false
},
"position" : {
"x" : 18.079472132200525,
"y" : -73.37937578464862
},
"selected" : false
}, {
"data" : {
"id" : "182",
"shared_name" : "DISEASE",
"classID" : "DOID_4",
"name" : "DISEASE",
"SUID" : 182,
"id_original" : "188",
"_foretell_labels" : [ "Disease" ],
"selected" : false
},
"position" : {
"x" : 18.285714285714292,
"y" : -201.0
},
"selected" : false
}, {
"data" : {
"id" : "179",
"shared_name" : "DISEASE OF ANATOMICAL ENTITY",
"classID" : "DOID_7",
"name" : "DISEASE OF ANATOMICAL ENTITY",
"SUID" : 179,
"id_original" : "191",
"_foretell_labels" : [ "Disease" ],
"selected" : false
},
"position" : {
"x" : -103.76660535458818,
"y" : -137.18968789232434
},
"selected" : false
}, {
"data" : {
"id" : "176",
"shared_name" : "TAUOPATHY",
"classID" : "DOID_680",
"name" : "TAUOPATHY",
"SUID" : 176,
"id_original" : "194",
"_foretell_labels" : [ "Disease" ],
"selected" : false
},
"position" : {
"x" : 18.285714285714292,
"y" : 134.0
},
"selected" : false
}, {
"data" : {
"id" : "155",
"shared_name" : "ALZHEIMER'S DISEASE",
"classID" : "DOID_10652",
"synonyms" : [ "ALZHEIMERS DEMENTIA", "ALZHEIMER DISEASE" ],
"name" : "ALZHEIMER'S DISEASE",
"SUID" : 155,
"id_original" : "197",
"_foretell_labels" : [ "Disease" ],
"selected" : false
},
"position" : {
"x" : 18.285714285714292,
"y" : 201.0
},
"selected" : false
} ],
"edges" : [ {
"data" : {
"id" : "242",
"source" : "191",
"target" : "188",
"id_original" : "235",
"shared_interaction" : "IS_CHILD",
"source_original" : "155",
"shared_name" : "IS_CHILD",
"source_original" : "223",
"target_original" : "182",
"shared_name" : "IS_CHILD",
"shared_interaction" : "IS_CHILD",
"name" : "IS_CHILD",
"interaction" : "IS_CHILD",
"SUID" : 242,
"id_original" : "200",
"refid" : 903.0,
"selected" : false,
"target_original" : "220"
},
"selected" : false
}, {
"data" : {
"id" : "239",
"source" : "188",
"target" : "182",
"id_original" : "244",
"shared_interaction" : "IS_CHILD",
"source_original" : "182",
"shared_name" : "IS_CHILD",
"source_original" : "220",
"target_original" : "188",
"shared_name" : "IS_CHILD",
"shared_interaction" : "IS_CHILD",
"name" : "IS_CHILD",
"interaction" : "IS_CHILD",
"SUID" : 239,
"id_original" : "221",
"refid" : 6410.0,
"selected" : false,
"target_original" : "214"
},
"selected" : false
}, {
"data" : {
"id" : "236",
"source" : "188",
"target" : "185",
"id_original" : "238",
"shared_interaction" : "IS_CHILD",
"source_original" : "182",
"shared_name" : "IS_CHILD",
"source_original" : "220",
"target_original" : "185",
"shared_name" : "IS_CHILD",
"shared_interaction" : "IS_CHILD",
"name" : "IS_CHILD",
"interaction" : "IS_CHILD",
"SUID" : 236,
"id_original" : "224",
"refid" : 6409.0,
"selected" : false,
"target_original" : "217"
},
"selected" : false
}, {
"data" : {
"id" : "233",
"source" : "185",
"target" : "182",
"id_original" : "232",
"shared_interaction" : "IS_CHILD",
"source_original" : "185",
"shared_name" : "IS_CHILD",
"source_original" : "217",
"target_original" : "188",
"shared_name" : "IS_CHILD",
"shared_interaction" : "IS_CHILD",
"name" : "IS_CHILD",
"interaction" : "IS_CHILD",
"SUID" : 233,
"id_original" : "227",
"refid" : 6951.0,
"selected" : false,
"target_original" : "214"
},
"selected" : false
}, {
"data" : {
"id" : "230",
"source" : "185",
"target" : "179",
"id_original" : "229",
"shared_interaction" : "IS_CHILD",
"source_original" : "185",
"shared_name" : "IS_CHILD",
"source_original" : "217",
"target_original" : "191",
"shared_name" : "IS_CHILD",
"shared_interaction" : "IS_CHILD",
"name" : "IS_CHILD",
"interaction" : "IS_CHILD",
"SUID" : 230,
"id_original" : "230",
"refid" : 6950.0,
"selected" : false,
"target_original" : "211"
},
"selected" : false
}, {
"data" : {
"id" : "227",
"source" : "179",
"target" : "182",
"id_original" : "226",
"shared_interaction" : "IS_CHILD",
"source_original" : "191",
"shared_name" : "IS_CHILD",
"source_original" : "211",
"target_original" : "188",
"shared_name" : "IS_CHILD",
"shared_interaction" : "IS_CHILD",
"name" : "IS_CHILD",
"interaction" : "IS_CHILD",
"SUID" : 227,
"id_original" : "233",
"refid" : 854.0,
"selected" : false,
"target_original" : "214"
},
"selected" : false
}, {
"data" : {
"id" : "224",
"source" : "176",
"target" : "191",
"id_original" : "241",
"shared_interaction" : "IS_CHILD",
"source_original" : "194",
"shared_name" : "IS_CHILD",
"source_original" : "208",
"target_original" : "155",
"shared_name" : "IS_CHILD",
"shared_interaction" : "IS_CHILD",
"name" : "IS_CHILD",
"interaction" : "IS_CHILD",
"SUID" : 224,
"id_original" : "236",
"refid" : 7129.0,
"selected" : false,
"target_original" : "223"
},
"selected" : false
}, {
"data" : {
"id" : "194",
"source" : "155",
"target" : "176",
"id_original" : "247",
"shared_interaction" : "IS_CHILD",
"source_original" : "197",
"shared_name" : "IS_CHILD",
"source_original" : "184",
"target_original" : "194",
"shared_name" : "IS_CHILD",
"shared_interaction" : "IS_CHILD",
"name" : "IS_CHILD",
"interaction" : "IS_CHILD",
"SUID" : 194,
"id_original" : "239",
"refid" : 14236.0,
"selected" : false,
"target_original" : "208"
},
"selected" : false
} ]
}
}
Solution
A solution to having two labels simultaneously for a graph in Cytoscape 3 Desktop is to concatenate two columns (containing the desired labels) either by using the CONCATENATE function or the & operator. In the example, the following was done to achieve this:
- In the node Table panel, Add a new single column of the type String (see image below)
- Using the function builder (see image below), add the function to concatenate the two columns, note that in this case the line break character was used
"\n". EitherCONCATENATE($name,"\n",$classID)or$name & "\n" & $classIDand insert formula for the entire column. - On the Style pannel, under Label select the newly created column, in this case
nameANDclassID.
Formula builder (concatenate the two columns):
Cytoscape Node Table with column (formula has been already inserted in entire column):
Alzheimer's Disease Ontology showing Ontological names and classID:
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