| Title: | Displaying binary trees with focus on dendrogram leaves |
|---|---|
| Description: | The TreeAndLeaf package combines unrooted and force-directed graph algorithms in order to layout binary trees, aiming to represent multiple layers of information onto dendrogram leaves. |
| Authors: | Leonardo W. Kume, Luis E. A. Rizzardi, Milena A. Cardoso, Mauro A. A. Castro |
| Maintainer: | Milena A. Cardoso <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.17.0 |
| Built: | 2024-07-17 11:16:10 UTC |
| Source: | https://github.com/bioc/TreeAndLeaf |
The TreeAndLeaf package combines unrooted and force-directed graph algorithms in order to layout binary trees, aiming to represent multiple layers of information onto dendrogram leaves.
| 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 |
| formatTree: | A theme function for tree-and-leaf igraph objects. |
| treeAndLeaf: | Layout a TreeAndLeaf diagram. |
Further information is available from the vignettes
vignette("TreeAndLeaf").
Leonardo W. Kume, Luis E. A. Rizzardi, Milena A. Cardoso, Mauro A. A. Castro
CASTRO, M. A. et al. RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations. Genome Biology, 13(4):R29, 2012.
CASTRO, M. A. A. et al. Regulators of genetic risk of breast cancer identified by integrative network analysis. Nature Genetics, 48(1):12–21, 2016.
RUSU, A.; SANTIAGO, C. Grid Drawings of Binary Trees: An Experimental Study. Journal of Graph Algorithms and Applications, 12(2):131–195, 2008.
This function sets attributes of a tree-and-leaf igraph object for plotting in the RedeR app interface.
formatTree(tal, theme = 1)formatTree(tal, theme = 1)
tal |
An igraph object generated by the |
theme |
An integer ranging from 1 to 5 with desired theme. |
An igraph object with attributes for RedeR application.
library(RedeR) hc <- hclust(dist(USArrests), "ave") tal <- treeAndLeaf(hc) tal <- formatTree(tal, theme = 5)library(RedeR) hc <- hclust(dist(USArrests), "ave") tal <- treeAndLeaf(hc) tal <- formatTree(tal, theme = 5)
Species metadata used in a phylo object.
data(phylo_species)data(phylo_species)
An object of class "data.frame"
Szklarczyk D. et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47:D607-613, 2019.
A phylo object for the species tree available from the STRING-db v11.
data(phylo_tree)data(phylo_tree)
An object of class "phylo"
Szklarczyk D. et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47:D607-613, 2019.
Data from the NCBI Genome Database for eukaryotes with complete genome sequence. The list of organisms were obtained from the KEGG Organisms Database, and taxonomy IDs were obtained from the NCBI Taxonomy Database.
data(spdata)data(spdata)
An object of class "data.frame"
NCBI Genome Database https://www.ncbi.nlm.nih.gov/genome Accessed: August 15, 2019.
NCBI Taxonomy Database https://www.ncbi.nlm.nih.gov/taxonomy Accessed: August 15, 2019.
KEGG Organisms Database https://www.genome.jp/kegg/catalog/org_list.html Accessed: August 15, 2019.
data(spdata)data(spdata)
This function tranforms hclust and phylo objects into tree-and-leaf igraph objects.
treeAndLeaf(obj)treeAndLeaf(obj)
obj |
An object of class 'hclust' or 'phylo'. |
A tree-and-leaf igraph object.
library(RedeR) rdp <- RedPort() hc <- hclust(dist(USArrests), "ave") tal <- treeAndLeaf(hc) ## Not run: calld(rdp) addGraph(obj=rdp, tal) ## End(Not run)library(RedeR) rdp <- RedPort() hc <- hclust(dist(USArrests), "ave") tal <- treeAndLeaf(hc) ## Not run: calld(rdp) addGraph(obj=rdp, tal) ## End(Not run)