tnsPlotSRE,TNS-method {RTNsurvival} | R Documentation |
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.
## 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, ... )
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. |
A heatmap of the subgroup regulon enrichment results.
# 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)