eTOL {dcGOR}R Documentation

eukaryotic Tree Of Life (eTOL)

Description

A 'phylo' object that contains information about eukaryotic part of species tree of life (eTOL). It is a rooted binary tree. Tips represent extant genomes. Since its reconstruction is guided under the NCBI taxonomy, each internal node is either mapped onto a unique taxonomic identifier or left empty (assumedly a hypothetical unknown ancestral genome).

Usage

data(eTOL)

Value

an object of class "phylo" with the following components:

References

Fang et al. (2013) A daily-updated tree of (sequenced) life as a reference for genome research. Scientific reports, 3:2015.

Examples

data(eTOL)
eTOL
# list all components
names(eTOL)
# extract information about the first 5 genomes
eTOL$genome_info[1:5,]
# look at the dimension of connectivity
dim(eTOL$connectivity)
## Not run: 
# visualise the connectivity matrix
Ntip <- length(eTOL$tip.label) # number of tips
Nnode <- eTOL$Nnode # number of internal nodes
data <- eTOL$connectivity
visHeatmapAdv(data, Rowv=FALSE,Colv=FALSE, zlim=c(0,1),
colormap="gray-black",
add.expr=abline(v=c(1,Ntip+1,(Ntip+Nnode+1))-0.5, col="white"),
key=FALSE, labRow=NA, labCol=NA)

## End(Not run)

[Package dcGOR version 1.0.6 Index]