yulab-smu / ggtreedendro Goto Github PK

This package offers autoplot methods to allow automatically visualizing tree objects (hclust, dendrogram, etc.) using ggtree.

Coverage:

• agnes object defined in cluster package
• bclust object defined in flexclust (S4) or e1071 (S3) package
• ClusterExperiment object defined in ClusterExperiment package
• dendro object defined in ggdendro package
• dendrogram object defined in stats package
  • FCPS::HierarchicalDBSCAN()[['Dendrogram']]
  • FCPS::HierarchicalClustering()[['Dendrogram']]
  • BHC::bhc()
• diana object defined in cluster package
• genoMatriXeR object defined in the regioneReloaded package
• hclust object defined in stats package
  • amap::hcluster()
  • fastcluster::hclust()
  • genieclust::gclust()
  • FactoClass::ward.cluster()
  • goSTAG::performHierarchicalClustering()
  • HGC::HGC.dendrogram()
• hdbscan object defined in dbscan package
• hkmeans object defined in factoextra package
• linkage object defined in the mdendro package
• multiLocalZScore object defined in the regioneReloaded package
• protoclust object defined in protoclust package
• pvclust object defined in pvclust package
• twins object defined in cluster package

It also provides plot_xx functions to visualize analysis output that is stored using R's built-in data type (e.g., list).

• plot_wgcna() for WGCNA::blockwiseModules() output