plotConsDynNet {pwOmics} | R Documentation |
Dynamic analysis result is plotted to pdf file stored in current working directory.
plotConsDynNet(dynConsensusNet, sig.level, clarify = "TRUE", layout = layout.fruchterman.reingold, ...)
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. |
pdf file in current working directory.
## 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)