Outputs
The cellmaps_generate_hierarchycmd.py script produces a collection of output files in the specified output directory. Each of these files serves a specific purpose in the hierarchy generation and interaction mapping processes.
CX2 Interactome and Hierarchy Outputs
These files represent the final interactome and hierarchy in CX2 format:
hierarchy.cx2:The main output file containing the generated hierarchy in HCX format.
[
{
"CXVersion": "2.0",
"hasFragments": false
},
{
"metaData": [
{
"elementCount": 1,
"name": "attributeDeclarations"
},
{
"elementCount": 1,
"name": "networkAttributes"
},
{
"elementCount": 3,
"name": "nodes"
},
{
"elementCount": 2,
"name": "edges"
}
]
},
{
"attributeDeclarations": [removed for readability of the example]
},
{
"networkAttributes": [
{
"name": "Sample Network",
"description": "This is a sample network for demonstration."
"ndexSchema": "hierarchy_v0.1",
"HCX::modelFileCount": 2,
"HCX::interactionNetworkName": "hierarchy_parent.cx2"
}
]
},
{
"nodes": [
{
"id": 0,
"v": {
"name": "Node1",
"represents": "Data1"
"HCX::isRoot": true,
"HCX::members": [
0,
1,
2]
}
},
{
"id": 1,
"v": {
"name": "Node2",
"represents": "Data2"
"HCX::isRoot": false,
"HCX::members": [
1]
}
},
{
"id": 2,
"v": {
"name": "Node3",
"represents": "Data3"
"HCX::isRoot": true,
"HCX::members": [
2]
}
}
]
},
{
"edges": [
{
"id": 0,
"s": 0,
"t": 1
},
{
"id": 1,
"s": 0,
"t": 2
}
]
},
{
"status": [
{
"error": "",
"success": true
}
]
}
]
hierarchy_parent.cx2:The parent or primary network used as a reference for generating the hierarchy in CX2 format.
[
{
"CXVersion": "2.0",
"hasFragments": false
},
{
"metaData": [
{"elementCount": 1, "name": "attributeDeclarations"},
{"elementCount": 1, "name": "networkAttributes"},
{"elementCount": 3, "name": "nodes"},
{"elementCount": 2, "name": "edges"}
]
},
{
"attributeDeclarations": [
{
"networkAttributes": {"name": {"d": "string"}, "description": {"d": "string"}},
"nodes": {"name": {"a": "n", "d": "string"}, "represents": {"a": "r", "d": "string"}},
"edges": {"interaction": {"a": "i", "d": "string"}, "Weight": {"d": "double"}}
}
]
},
{
"networkAttributes": [
{"name": "Example PPI Network", "description": "Simplified Protein-Protein Interaction network example"}
]
},
{
"nodes": [
{"id": 0, "v": {"n": "ProteinA", "r": "ProteinA"}},
{"id": 1, "v": {"n": "ProteinB", "r": "ProteinB"}},
{"id": 2, "v": {"n": "ProteinC", "r": "ProteinC"}}
]
},
{
"edges": [
{"id": 0, "s": 0, "t": 1, "v": {"Weight": 0.5, "i": "interacts-with"}},
{"id": 1, "s": 0, "t": 2, "v": {"Weight": 0.6, "i": "interacts-with"}},
]
}
]
Interaction Network Outputs
Intermediate processing step files that represent protein-protein interaction networks at different cutoff thresholds:
ppi_cutoff_*.cx:Protein-Protein Interaction networks in CX format. Can be omitted.
ppi_cutoff_*.id.edgelist.tsv:Edgelist representation of the Protein-Protein Interaction networks.
0 1
2 3
4 5
6 1
7 8
Other Outputs
{
"communityDetectionResult": "23,4,c-m;23,1,c-m;23,6,c-m;23,10,c-m;23,22,c-m;23,19,c-m;23,17,c-m;23,20,c-m;23,13,c-m;23,14,c-m;23,11,c-m;23,7,c-m;23,5,c-m;23,18,c-m;23,21,c-m;23,8,c-m;23,12,c-m;23,15,c-m;23,3,c-m;23,0,c-m;23,9,c-m;23,16,c-m;23,2,c-m;24,4,c-m;24,1,c-m;24,6,c-m;24,10,c-m;24,0,c-m;24,20,c-m;24,5,c-m;25,1,c-m;25,6,c-m;25,10,c-m;25,0,c-m;25,20,c-m;26,18,c-m;26,19,c-m;26,17,c-m;26,12,c-m;26,13,c-m;27,8,c-m;27,14,c-m;27,7,c-m;27,11,c-m;28,21,c-m;28,9,c-m;28,2,c-m;28,3,c-m;23,24,c-c;23,26,c-c;23,28,c-c;23,27,c-c;24,25,c-c;",
"nodeAttributesAsCX2": {
"attributeDeclarations": [
{
"nodes": {
"HiDeF_persistence": {
"d": "integer",
"a": "p1",
"v": 0
}
}
}
],
"nodes": [
{
"id": 23,
"v": {
"p1": 0
}
},
{
"id": 24,
"v": {
"p1": 119
}
},
{
"id": 25,
"v": {
"p1": 41
}
},
{
"id": 26,
"v": {
"p1": 171
}
},
{
"id": 27,
"v": {
"p1": 172
}
},
{
"id": 28,
"v": {
"p1": 177
}
}
]
}
}
hidef_output.edges:Contains the edges or interactions in the HiDeF generated hierarchy.
Cluster0-0 Cluster1-0 default
Cluster0-0 Cluster1-1 default
Cluster0-0 Cluster1-2 default
Cluster0-0 Cluster1-3 default
Cluster1-0 Cluster2-0 default
hidef_output.nodes:Contains the nodes or entities in the HiDeF generated hierarchy.
Cluster0-0 23 0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 0
Cluster1-0 7 0 1 10 20 4 5 6 119
Cluster1-1 5 12 13 17 18 19 171
Cluster2-0 5 0 1 10 20 6 41
Cluster1-2 4 2 21 3 9 177
Cluster1-3 4 11 14 7 8 172
hidef_output.pruned.edges:Contains pruned edges after certain filtering (maturing) processes on the original hierarchy.
Cluster0-0 Cluster1-0 default
Cluster0-0 Cluster1-1 default
Cluster0-0 Cluster1-2 default
Cluster0-0 Cluster1-3 default
Cluster1-0 Cluster2-0 default
hidef_output.pruned.nodes:Contains pruned nodes after certain filtering (maturing) processes on the original hierarchy.
Cluster0-0 23 3 17 21 4 20 1 10 12 9 14 8 2 15 19 5 11 7 16 18 0 13 22 6 0
Cluster1-0 7 20 1 5 4 10 0 6 119
Cluster2-0 5 20 1 10 0 6 41
Cluster1-1 5 18 19 17 12 13 171
Cluster1-3 4 14 11 8 7 172
Cluster1-2 4 21 3 2 9 177
hidef_output.weaver:Information related to the weaving process used in generating the hierarchy.
Logs and Metadata
error.log:Contains error messages and exceptions that might have occurred during execution.
output.log:Provides detailed logs about the steps performed and their outcomes.
ro-crate-metadata.json:Metadata in RO-Crate format, a community effort to establish a lightweight approach to packaging research data with their metadata.
It contains general information about the data i.a. ID, Type, Name, Description, contextual definitions, Software detail, as well as datasets details of each individual part of the data.
For example, the metadata for the content of hierarchy.cx provides unique id, context, type, url, name, keywords, etc. The url can be used to view the hierarchy in Cytoscape Web.
{ "@id": "00000000-0000-0000-0000-000000000000:dataset::4.hierarchy", "@context": { "@vocab": "https://schema.org/", "evi": "https://w3id.org/EVI#" }, "metadataType": "https://w3id.org/EVI#Dataset", "url": "https://idekerlab.ndexbio.org/cytoscape/network/aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa", "name": "Output Dataset", "keywords": [ "CM4AI", "Example", "interactome", "ppi", "network", "CX2", "file", "hierarchy", "network", "HCX" ], "description": "CM4AI Example Example input dataset AP-MS edgelist download|IF microscopy merged embedding AP-MS edgelist download|IF microscopy Example input dataset hierarchy model Hierarchy network file", "author": "cellmaps_generate_hierarchy", "datePublished": "2023-09-21", "version": "0.1.0a11", "associatedPublication": null, "additionalDocumentation": null, "format": "HCX", "schema": {}, "generatedBy": [], "derivedFrom": [], "usedBy": [], "contentUrl": "path/hierarchy.hcx" }
Additionally, it contains Computation Details, name, description, Run By etc.