kda2cytoscape.colorize {Mergeomics} | R Documentation

## 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)

### Author(s)

Zeyneb Kurt

### References

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.

### See Also

`kda2cytoscape`

### Examples

    ## 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)

[Package Mergeomics version 1.20.0 Index]