Plot dendrogram of cluster averages

A plot showing the hierarchical clustering of the cluster averages (dendrogram). A tool made for showing how clusters (not individual gene-sets) relate to each other. The distance between two clusters is the average SNN distance (1 - SNN similarity) between their gene sets, and clusters are joined by complete linkage.

Usage

plotDendrogram(
  geneSetsList,
  resolution = NULL,
  removeClusterId = FALSE,
  highlightClusterNo = NULL
)

Arguments

geneSetsList

'gsList' object with clusters and labels.

resolution

The cluster resolution to plot. Default NULL uses the active resolution: the optimal resolution found by clusterGeneSets(), or the one last set with updateResolution() or updateClusterLabels().

removeClusterId

Logical, if TRUE the cluster number will be removed from each cluster label. Default: FALSE.

highlightClusterNo

A vector with the cluster numbers of the clusters (at the resolution) to highlight (in bold) in the plot.

Value

A ggplot object. The underlying hclust object is stored in its hclust attribute.

Examples

plotDendrogram(exampleGsList)

hc <- attr(plotDendrogram(exampleGsList), "hclust")