TreeAndLeaf-package: TreeAndLeaf: An alternative to dendrogram visualization and...

In leonardokume/TreeAndLeaf: An alternative to dendrogram visualization and insertion of multiple layers of information

Description

TreeAndLeaf package comes as an alternative to solve problems regarding dendrogram plotting, such as the lack of space when the dendrogram is too large and the need for adding more layers of information. It treats a whole dendrogram as a tree, in which the observations are represented by the leaves.

Details

Package:	TreeAndLeaf
Type:	Package
Depends:	R (>= 4.0)
Imports:	RedeR, igraph, ape
Suggests:	knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, RColorBrewer
License:	Artistic-2.0
biocViews:	NetworkEnrichment, GraphAndNetwork

Index

formatTree:	a function for formatting an igraph to be shown in RedeR.
hclust2igraph:	a function for converting a hclust object to an igraph.
phylo2igraph:	a function for converting a phylo object to an igraph.
treeAndLeaf:	a function for layout creation and plotting of the TreeAndLeaf in RedeR.

Further information is available in the vignettes by typing vignette("TreeAndLeaf"). Documented topics are also available in HTML by typing help.start() and selecting the TreeAndLeaf package from the menu.

Author(s)

Leonardo W. Kume, Luis E. A. Rizzardi, Milena A. Cardoso, Mauro A. A. Castro

References

CASTRO, M. A. et al. RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations. Genome Biology, v. 13, n. 4, p. R29, 2012.

CASTRO, M. A. A. et al. Regulators of genetic risk of breast cancer identified by integrative network analysis. Nature Genetics, v. 48, n. 1, p. 12–21, jan. 2016.

RUSU, A.; SANTIAGO, C. Grid Drawings of Binary Trees: An Experimental Study. Journal of Graph Algorithms and Applications, v. 12, n. 2, p. 131–195, 2008.

leonardokume/TreeAndLeaf documentation built on July 10, 2020, 4:57 p.m.