To compare the force-directed layout with the ULG and the Yifan multilevel layout, we asked the participants to comment "why did you prefer to the ULG and the Yifan multilevel layout than the force-directed layout?" The comments are as follows: "Yifan multilevel layout is easier to read than other layouts.
The performance of the Multilevel Layout algorithm, with and without the clustering option (referred to as MLL and MLL-C), was compared against three built-in layout algorithms in Cytoscape.
Combining all of the nodes in the detected clusters could also further improve the multilevel layout solutions, especially in networks such as the AP/MS-Combined, which show exceptionally high and extensive clustering structure.
We implemented a modified layout plug-in, named Multilevel Layout, which applies the conventional layout algorithms within a multilevel optimization framework to better capture the hierarchical modularity of many biological networks.
A limitation of the current implementation of the multilevel layout algorithm is its relatively lengthy running times in the largest network graphs.
The Java implementation of the multilevel layout algorithm is distributed as an open-source Cytoscape plug-in, named Multilevel Layout, licensed with GNU GPLv2 license [ 34].
In the present work, we investigated whether the multilevel layout approach could provide also biologically meaningful network visualizations, in addition to being visually attractive.
To this end, we compared the multilevel layout solutions to those generated by popular layout algorithms in the Cytoscpape platform, in terms of their capacity at capturing the semantic similarity information about underlying biological processes.
PS, JT and HV implemented the Multilevel Layout plug-in.
In addition to the multilevel layout, we have also introduced here a novel way of evaluating layout solutions in terms of their biological relevance.
