tnsPlotSRE-methods: Plot Subgroup Regulon Enrichment for TNS-class objects

In csgroen/RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

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)

csgroen/RTNsurvival documentation built on May 20, 2019, 1:49 p.m.