kda2cytoscape.colorize: Trace module memberships of genes

Description

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).

Usage

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

Arguments

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

Value

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)

References

Shu L, Zhao Y, Kurt Z, Byars S, Tukiainen T, Kettunen J, Ripatti S, Zhang B, Inouye M, Makinen VP, Yang X. Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems. bioRxiv doi: http://dx.doi.org/10.1101/036012

Examples

Run this code

## 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)