Download FCModeler User`s Manual

8.1.3
Cycle Search ......................................................................................................... 23
8.1.4
Cycle XML Files................................................................................................... 24
8.2
Alternate Paths between Nodes .................................................................................... 25
8.3
Clustering Cycles .......................................................................................................... 25
9
FCModeler and R.................................................................................................................. 28
10
References......................................................................................................................... 28
10.1 Publications relating to FCModeler .............................................................................. 28
10.2 Open Source Code Used in FCModeler........................................................................ 28
List of Figures
Figure 1. The open graph dialog box. ............................................................................................ 7
Figure 2. The save graph dialog box.............................................................................................. 7
Figure 3. Simple dot layout............................................................................................................ 8
Figure 4. Rank-cluster dot layout................................................................................................... 9
Figure 5: Example of a GEM layout............................................................................................. 11
Figure 6 shows the manipulation of node and edge objects in FCModeler.................................. 14
Figure 7 shows how to save graph coordinates using the save function under the File menu. .... 15
Figure 8. Property viewer showing property values of selected nodes and edges....................... 17
Figure 9. Mapping editor. ............................................................................................................ 18
Figure 10. Animation control....................................................................................................... 21
Figure 11. The subgraph creation dialog box. ............................................................................. 22
Figure 12 Example of selecting cycles and strongly connected components as subgraphs. ........ 23
Figure 13. The cycle search dialog box. ...................................................................................... 24
Figure 14. Map view showing results of the SOM algorithm. Each graph shows the model of
the corresponding map unit, which is the generalized median of the cycles assigned to that
map unit. ............................................................................................................................... 26
Figure 15. Full view of the bottom-left map unit, showing ten cycles clustered together........... 27
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