tnsPlotSRE,TNS-method {RTNsurvival} | R Documentation

## Plot Subgroup Regulon Enrichment for TNS-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

    ## S4 method for signature 'TNS'
    tnsPlotSRE(
      tns,
      subgroup = NULL,
      by = "nGroups",
      nGroupsEnriched = 1,
      nTopEnriched = 10,
      breaks = seq(-1.5, 1.5, 0.1),
      markEnriched = FALSE,
      ...
    )

### Arguments

`tns` | A A TNS object.
`subgroup` | a character vector. It must be the name of a column in the survivalData featuring the grouping information as a categorical variable.
`by` | one of 'nGroups' or 'groupTop'. If by = 'nGroups', the nGroupsEnriched value will be used to select regulons. If by = 'groupTop', 'nTopEnriched' will be used to select regulons for plotting.
`nGroupsEnriched` | a single integer. It represents in how many subgroups a regulon has to be enriched for it to appear in the rows of the heatmap.
`nTopEnriched` | a single integer. If by = 'groupTop', this represents how regulons will be shown for each group (duplicates are removed. The top regulons are chosen by significance.
`breaks` | a numerical vector of breaks for the heatmap.
`markEnriched` | a single logical value. If TRUE, asterisks are added to cells of heatmap that were found to be significant by tnsSRE.
`...` | parameters passed to pheatmap::pheatmap for customization.

### Value

A heatmap of the subgroup regulon enrichment results.

### Examples

    # load survival data
    data(survival.data)
    # load TNI-object
    data(stni, package = "RTN")

    # create TNS object
    stns <- tni2tnsPreprocess(stni, survivalData = survival.data,
                              keycovar = c('Grade','Age'), time = 1, event = 2)
    stns <- tnsGSEA2(stns)

    # run subgroup regulon enrichment analysis
    stns <- tnsSRE(stns, "ER+")
    tnsPlotSRE(stns)

[Package RTNsurvival version 1.11.2 Index]