Difference between revisions of "Cytoscape layout analysis"

From irefindex
(New page: Here we have given results of a analysis we did for selecting a layout algorithm for iRefsCape plug-in.)
 
 
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Here we have given results of a analysis we did for selecting a layout algorithm for iRefsCape plug-in.
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Here we have given results of a analysis we did for selecting a layout algorithm for iRefsCape plug-in. The analysis was conducted only for freely accessible layouts.
 +
 
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Network used for the analysis; 
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directed, 641 nodes , 1586 Edges, (search results for Raf1, type=geneSymbol, taxid=any from iRefsCape )
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{| {{table}}
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| align="center" style="background:#f0f0f0;"|'''Initial'''
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| align="center" style="background:#f0f0f0;"|'''Final algorithm'''
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| align="center" style="background:#f0f0f0;"|'''Time taken'''
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|-
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| Grid||jgraph-circle ||14 minutes :42 seconds
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|-
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| Grid||attribute-circle ||64 milliseconds
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|-
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| Grid||jgraph-radial-tree ||14 minutes :22 seconds
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|-
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| Grid||jgraph-gem ||14 minutes :47 seconds
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|-
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| Grid||kamada-kawai-noweight ||25 seconds
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|-
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| Grid||circular ||207 milliseconds
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|-
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| Grid||jgraph-sugiyama ||14 minutes :18 seconds
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|-
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| Grid||attributes- ||46 milliseconds
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|-
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| Grid||grid ||17 milliseconds
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|-
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| Grid||jgraph-tree ||14 minutes :25 seconds
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|-
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| Grid||force-directed ||3 seconds
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|-
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| Grid||degree-circle ||517 milliseconds
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|-
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| Grid||kamada-kawai ||13 seconds
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|-
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| Grid||fruchterman-rheingold ||53 seconds
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|-
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| Grid||jgraph-spring ||14 minutes :30 seconds
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|-
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| Grid||Jgraph-annealing||Not evaluated
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|-
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| Grid||Isom||Not evaluated
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|-
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| Grid||Jgraph-moen||Not evaluated
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|-
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|
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|}
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 +
{| {{table}}
 +
| align="center" style="background:#f0f0f0;"|'''Initial'''
 +
| align="center" style="background:#f0f0f0;"|'''Final algorithm'''
 +
| align="center" style="background:#f0f0f0;"|'''Time taken'''
 +
|-
 +
| jgraph-circle ||Grid||30 milliseconds
 +
|-
 +
| attribute-circle ||Grid||25 milliseconds
 +
|-
 +
| jgraph-radial-tree ||Grid||27 milliseconds
 +
|-
 +
| jgraph-gem ||Grid||31 milliseconds
 +
|-
 +
| kamada-kawai-noweight ||Grid||31 milliseconds
 +
|-
 +
| circular ||Grid||31 milliseconds
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|-
 +
| jgraph-sugiyama ||Grid||25 milliseconds
 +
|-
 +
| attributes- ||Grid||30 milliseconds
 +
|-
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| grid ||Grid||16 milliseconds
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|-
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| jgraph-tree ||Grid||30 milliseconds
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|-
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| ||||
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|-
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| force-directed ||Grid||29 milliseconds
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|-
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| degree-circle ||Grid||30 milliseconds
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|-
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| kamada-kawai ||Grid||31 milliseconds
 +
|-
 +
| fruchterman-rheingold ||Grid||29 milliseconds
 +
|-
 +
| jgraph-spring ||Grid||285 milliseconds
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|-
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|
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|}

Latest revision as of 12:08, 11 April 2010

Here we have given results of a analysis we did for selecting a layout algorithm for iRefsCape plug-in. The analysis was conducted only for freely accessible layouts.

Network used for the analysis; directed, 641 nodes , 1586 Edges, (search results for Raf1, type=geneSymbol, taxid=any from iRefsCape )

Initial Final algorithm Time taken
Grid jgraph-circle 14 minutes :42 seconds
Grid attribute-circle 64 milliseconds
Grid jgraph-radial-tree 14 minutes :22 seconds
Grid jgraph-gem 14 minutes :47 seconds
Grid kamada-kawai-noweight 25 seconds
Grid circular 207 milliseconds
Grid jgraph-sugiyama 14 minutes :18 seconds
Grid attributes- 46 milliseconds
Grid grid 17 milliseconds
Grid jgraph-tree 14 minutes :25 seconds
Grid force-directed 3 seconds
Grid degree-circle 517 milliseconds
Grid kamada-kawai 13 seconds
Grid fruchterman-rheingold 53 seconds
Grid jgraph-spring 14 minutes :30 seconds
Grid Jgraph-annealing Not evaluated
Grid Isom Not evaluated
Grid Jgraph-moen Not evaluated
Initial Final algorithm Time taken
jgraph-circle Grid 30 milliseconds
attribute-circle Grid 25 milliseconds
jgraph-radial-tree Grid 27 milliseconds
jgraph-gem Grid 31 milliseconds
kamada-kawai-noweight Grid 31 milliseconds
circular Grid 31 milliseconds
jgraph-sugiyama Grid 25 milliseconds
attributes- Grid 30 milliseconds
grid Grid 16 milliseconds
jgraph-tree Grid 30 milliseconds
force-directed Grid 29 milliseconds
degree-circle Grid 30 milliseconds
kamada-kawai Grid 31 milliseconds
fruchterman-rheingold Grid 29 milliseconds
jgraph-spring Grid 285 milliseconds
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