R: Plot Subgroup Regulon Enrichment for TNI-class objects.

tni.plot.sre {RTN}

R Documentation

Plot Subgroup Regulon Enrichment for TNI-class objects.

Description

This method plots the results of the subgroup regulon enrichment analysis in a heatmap. The rows of the heatmap represent enriched regulons, while the columns show the subgroups. The plotted values correspond to average regulon activity for a regulon in a subgroup. Enriched values can be marked.

Usage

tni.plot.sre(object, nGroupsEnriched = NULL, nTopEnriched = NULL, 
             colors = c("blue","white","red"), breaks = seq(-1.5, 1.5, 0.1), 
             markEnriched = TRUE, ...)

Arguments

`object`	A TNI-class object.
`nGroupsEnriched`	a filter to keep 'nGroupsEnriched' regulons; a single integer specifying how many subgroups a regulon has to be enriched for it to appear in the rows of the heatmap (it must be use either 'nGroupsEnriched' or 'nTopEnriched').
`nTopEnriched`	a filter to keep 'nTopEnriched' regulons; a single integer specifying how many regulons will be shown for each group. The top regulons are chosen by significance (it must be use either 'nTopEnriched' or 'nGroupsEnriched').
`colors`	a vector of color for the 'pheatmap'.
`breaks`	a numerical vector of breaks for the 'pheatmap'.
`markEnriched`	a single logical value. If TRUE, asterisks are added to cells of heatmap that were found to be significant.
`...`	parameters passed to 'pheatmap' for customization.

Value

A heatmap of the subgroup regulon enrichment results.

Examples

# load tniData
data(tniData)

## Not run: 

# preprocessing
rtni <- tni.constructor(expData=tniData$expData, 
        regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), 
        rowAnnotation=tniData$rowAnnotation)
        
# permutation analysis (infers the reference/relevance network)
rtni <- tni.permutation(rtni)

# dpi filter (infers the transcriptional network)
rtni <- tni.dpi.filter(rtni)

#run GSEA2 analysis pipeline
rtni <- tni.gsea2(rtni)

# set sample groups
colAnnotation <- tni.get(rtni, "colAnnotation")
sampleGroups <- list(G1=colAnnotation$ID[1:60], 
                G2=colAnnotation$ID[61:90], 
                G3=colAnnotation$ID[91:120])

# run subgroup regulon enrichment analysis
rtni <- tni.sre(rtni, sampleGroups)

# plot results
tni.plot.sre(rtni)

## End(Not run)