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Up: Component summary
Component
GraphMetricsComputes various graph metrics for a GraphML file. Undirected and directed graphs are supported. Basic metrics include graph diameter, average shortest path length and average degree. There are also several metrics that are computed for each vertex. These include clustering coefficient, degree centrality, closeness centrality, betweenness centrality and eigenvector centrality.
For an introduction to these metrics, see Mason, O. and Verwoerd, M., Graph Theory and Networks in Biology, 2006.
| Version | 1.0 |
|---|---|
| Bundle | tools |
| Categories | Graph |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | collections-generic-4.01.jar (jar) ; colt.jar (jar) ; csbl-javatools.jar (jar) ; jung-algorithms-2.0.jar (jar) ; jung-api-2.0.jar (jar) ; jung-graph-impl-2.0.jar (jar) ; jung-io-2.0.jar (jar) |
| Source files | component.xml GraphMetricsComponent.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| graph | GraphML | Mandatory | Graph of interest |
Outputs| Name | Type | Description |
|---|---|---|
| graphMetrics | CSV | Metrics that are computed once for the whole graph. There is one row for each metric. Column names are Metric and Value. The following metrics are present: NumVertices, NumEdges, Diameter, MeanDegree, MeanShortestPath. |
| vertexMetrics | CSV | Metrics that are computed individually for each vertex. There is one row for each vertex. The following columns are present: Vertex (vertex ID), InDegree (in-degree of the vertex), OutDegree, ClusteringCoeff (clustering coefficient), DegreeCentrality, ClosenessCentrality, BetweennessCentrality, EigenvectorCentrality. For undirected graphs, InDegree is equal to OutDegree and gives the (unique) vertex degree. Also, for each centrality measure a rank column is present (e.g. DegreeCentralityRank) that shows the rank of the vertex in range 0 to 1 so that 0 is the vertex with lowest measure. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| nameAttribute | string | "" | If given, the Vertex column in vertexMetrics contains values taken from this vertex attribute. If empty, the ID of vertices are used. |
| normalize | boolean | true | If true, normalize centrality measures (degree, closeness and betweenness) to range 0 to 1. If false, report raw centrality measures. Note that for DegreeCentrality, the raw value is the degree of the node. Eigenvector centrality is always in the range 0 to 1. |
Test cases| Test case | Parameters▼ | IN graph |
OUT graphMetrics |
OUT vertexMetrics |
||
|---|---|---|---|---|---|---|
| case1 | properties | graph | graphMetrics | vertexMetrics | ||
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normalize=false |
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| case2 | properties | graph | graphMetrics | vertexMetrics | ||
|
nameAttribute=name |
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| case3_directed | properties | graph | graphMetrics | vertexMetrics | ||
|
normalize=false |
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