kda2cytoscape.colorize: Trace module memberships of genes
In Mergeomics: Integrative network analysis of omics data

Description Usage Arguments Value Author(s) References See Also Examples

kda2cytoscape.colorize assigns color to each node of the given module. If a node belongs to more than one module, different colors will be assigned to that node, as each color representing one module (shared nodes are illustrated as pie charts in the graph).

1	kda2cytoscape.colorize(noddata, moddata, modpool, palette)

`noddata`	node information of the entire graph
`moddata`	module data including node (member gene) list
`modpool`	unique module list including significant key drivers
`palette`	assigned unique color map for all modules

res

data frame including the assigned color labels for the nodes of the given module. If a node is concurrently member of many modules, multiple colors will be assigned to that node (one color for each of these modules)

Zeyneb Kurt

Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen V-P, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC genomics. 2016;17(1):874.

kda2cytoscape

## Trace module memberships for each KD and its neighbors
## If a KD (and its neigbor nodes) is member of multiple modules, assign 
## multiple colors to these multi-member nodes.
## We need to know data of all possible modules and all possible module ids
## to assign multiple colors to a shared node (between modules) when needed
if(exists("valdata"))
cat("Marker pvalues will be used to determine node sizes 
in the network illustration")
# noddata <- kda2cytoscape.colorize(neighs, job.kda$moddata, modpool, palette)