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 5 6 7 8 9 10 11 |

`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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