plotConsDynNet: Plot inferred net based on analysis analysis.

In MarenS2/pwOmics: Pathway-based data integration of omics data

Description

Dynamic analysis result is plotted to pdf file stored in current working directory.

Usage

plotConsDynNet(dynConsensusNet, sig.level, clarify = "TRUE",
  layout = layout.fruchterman.reingold, ...)

Arguments

dynConsensusNet	result of dynamic analysis: inferred net generated by consDynamicNet function.
sig.level	significance level for plotting edges in network (between 0 and 1).
clarify	indicating if unconnected nodes should be removed; default = "TRUE".
layout	igraph layout parameter; default is layout.fruchterman.reingold.
...	further plotting/legend parameters.

Value

pdf file in current working directory.

Examples

## Not run: 
data(OmicsExampleData)
data_omics = readOmics(tp_prots = c(0.25, 1, 4, 8, 13, 18, 24), 
tp_genes = c(1, 4, 8, 13, 18, 24), OmicsExampleData,
PWdatabase = c("biocarta", "kegg", "nci", "reactome"), 
TFtargetdatabase = c("userspec"))
data_omics = readPhosphodata(data_omics, 
phosphoreg = system.file("extdata", "phospho_reg_table.txt", 
package = "pwOmics.newupdown")) 
data_omics = readTFdata(data_omics, 
TF_target_path = system.file("extdata", "TF_targets.txt", 
package = "pwOmics.newupdown"))
data_omics_plus = readPWdata(data_omics,  
loadgenelists = system.file("extdata/Genelists", package = "pwOmics.newupdown")) 

## End(Not run)
## Not run: 
data_omics_plus = identifyPR(data_omics_plus)
setwd(system.file("extdata/Genelists", package = "pwOmics.newupdown"))
data_omics = identifyPWs(data_omics_plus)
data_omics = identifyTFs(data_omics)
data_omics = identifyRsofTFs(data_omics, 
noTFs_inPW = 1, order_neighbors = 10)
data_omics = identifyPWTFTGs(data_omics)
statConsNet = staticConsensusNet(data_omics)
dynConsNet = consDynamicNet(data_omics, statConsNet)
plotConsDynNet(dynConsNet, sig.level = 0.8)

## End(Not run)

MarenS2/pwOmics documentation built on May 17, 2019, 9:10 a.m.