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.

### See Also

`tni.sre`

### 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)

[Package RTN version 2.18.0 Index]