pwOmics (version 1.4.0)

plotConsDynNet: Plot inferred net based on analysis analysis.

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

#please run with whole database files (prepared according to vignette)
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("chea", "pazar"))
## Not run: 
# data_omics = readTFdata(data_omics)
# data_omics_plus = readPWdata(data_omics,
# loadgenelists = FALSE)
# data_omics = identifyPWs(data_omics_plus)
# data_omics = identifyTFs(data_omics)
# data_omics = enrichPWs(data_omics)
# data_omics = identifyRsofTFs(data_omics, only_enriched = FALSE,
# noTFs_inPW = 1, order_neighbors = 10)
# data_omics = identifyPWTFTGs(data_omics, only_enriched = FALSE)
# statConsNet = staticConsensusNet(data_omics)
# dynConsNet = consDynamicNet(data_omics, statConsNet)
# plotConsDynNet(dynConsNet, sig.level = 0.8)
# ## End(Not run)