Description Usage Arguments Value Examples
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.
1 2 3 4 |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 | # 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)
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