kda2cytoscape: Generate input files for Cytoscape

In Mergeomics: Integrative network analysis of omics data

Description

kda2cytoscape generates input files for Cytoscape to visualize the graph and hubnets after the wKDA process finished. The network visualization is a streamlined depiction of the module enrichment in hub neighborhoods.

Usage

kda2cytoscape(job, node.list = NULL, modules = NULL, ndrivers = 5, 
depth = 1)

Arguments

job	wKDA result data list as returned by kda.finish
node.list	array of node/gene names to be visualized with their neighbor node. if this is not specified top ndrivers of each module and their neighborhoods will be illustrated.
modules	array of module names to be visualized
ndrivers	maximum number of drivers per module
depth	depth for neighborhood search in the graph

Details

kda2cytoscape first, selects top scoring key drivers for each module; then, assigns a colormap to modules, processes each module separately, finds key nodes' neighborhoods within a particular search depth, and saves the edge and node lists of the modules to the specified output folder. Besides, it returns this configuration data to the user. Created file list for Cytoscape are given below:

kda2cytoscape.top.kds.txt: top key drivers of the modules are
listed in this file. Number of the key drivers can be set by
user with ndrivers parameter. 
kda2cytoscape.edges.txt: edge lists of the integrated graph 
that includes the subnetworks of all modules.
kda2cytoscape.nodes.txt: node lists of the integrated graph 
that includes the subnetworks of all modules.
module.color.mapping.txt: color mapping for the  modules, 
i.e. one color is assigned to each module.

Value

job	updated data list including the node and edge information of the modules converted to Cytoscape format

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

kda.analyze, kda.finish

Examples

## get the prepared and KDA applied dataset:(see kda.analyze for details)
data(job_kda_analyze)
## set the relevant parameters:
job.kda$label<-"HDLC"
## parent folder for results
job.kda$folder<-"Results"
## Input a network
## columns: TAIL HEAD WEIGHT
job.kda$netfile<-system.file("extdata","network.mouseliver.mouse.txt", 
package="Mergeomics")
## Gene sets derived from ModuleMerge, containing two columns, MODULE, 
## NODE, delimited by tab 
job.kda$modfile<- system.file("extdata","mergedModules.txt", 
package="Mergeomics")
## "0" means we do not consider edge weights while 1 is opposite.
job.kda$edgefactor<-0.0
## The searching depth for the KDA
job.kda$depth<-1
## 0 means we do not consider the directions of the regulatory interactions
## while 1 is opposite.
job.kda$direction <- 1

## finish the KDA process
job.kda <- kda.finish(job.kda)

## prepare the cytoscape-ready files:
job.kda <- kda2cytoscape(job.kda)

## remove the results folder
unlink("Results", recursive = TRUE)

Example output

Finishing results...

Writing to file... 
Saved 374 rows in 'Results/kda/HDLC.hubs.txt'.

Writing to file... 
Saved 446 rows in 'Results/kda/HDLC.results.txt'.

Writing to file... 
Saved 446 rows in 'Results/kda/HDLC.pvalues.txt'.

Writing to file... 
Saved 12 rows in 'Results/kda/HDLC.tophits.txt'.

Forwarding KDA results to Cytoscape...

Writing to file... 
Saved 55 rows in 'Results/cytoscape/kda2cytoscape.top.kds.txt'.

Writing to file... 
Saved 499 rows in 'Results/cytoscape/kda2cytoscape.edges.txt'.

Writing to file... 
Saved 267 rows in 'Results/cytoscape/kda2cytoscape.nodes.txt'.

Information is stored into relevant files.

Mergeomics documentation built on Nov. 8, 2020, 6:58 p.m.