plotConsensusProfiles {pwOmics}R Documentation

Plot consensus graph profiles of static consensus molecules.

Description

Consensus graph profiles of static consensus molecules plotted as heatmap to pdf file stored in current working directory.

Usage

plotConsensusProfiles(consensusGraphs, data_omics, subsel = TRUE, ...)

Arguments

consensusGraphs

result from static analysis: consensus graph generated by staticConsensusNet function.

data_omics

OmicsData object.

subsel

character vector of selected consensus molecules for plotting; if TRUE all consensus molecules are plotted

...

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)
plotConsensusProfiles(statConsNet, data_omics, subsel = TRUE)

## End(Not run)

[Package pwOmics version 1.24.0 Index]