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:

• Nnode: the number of (internal) nodes
• tip.label: a vector giving the names of the tips (i.e., "left_id" to define the post-ordered binary tree structure)
• node.label: a vector giving the names of the internal nodes (i.e., "left_id" to define the post-ordered binary tree structure)
• genome_info: a matrix of all nodes (including tips and internal nodes) X 8, giving extant/ancestral genome information: "left_id" (unique and used as internal id), "right_id" (used in combination with "left_id" to define the post-ordered binary tree structure), "taxon_id" (NCBI taxonomy id, if matched), "genome" (2-letter genome identifiers used in SUPERFAMILY, if being extant), "name" (NCBI taxonomy name, if matched), "rank" (NCBI taxonomy rank, if matched), "branchlength" (branch length in relevance to the parent), and "common_name" (NCBI taxonomy common name, if matched and existed)
• edge: a two-column matrix of mode numeric where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers; the tips are numbered 1, 2, ..., and the internal nodes are numbered after the tips. For each row, the first column gives the ancestor
• edge.length: a numeric vector giving the lengths of the branches given by 'edge'
• root.length: a numeric value giving the length of the branch at the root
• connectivity: a matrix of internal nodes X all nodes (including tips and internal nodes), with 1 for the presence of a ancestor-descenant path, and 0 otherwise

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


Phylogenetic tree with 438 tips and 437 internal nodes.

Tip labels:
	37, 40, 42, 46, 49, 52, ...
Node labels:
	3, 4, 5, 6, 7, 8, ...

Rooted; includes branch lengths.

# list all components
names(eTOL)

[1] "edge"         "Nnode"        "tip.label"    "edge.length"  "node.label"  
[6] "root.edge"    "connectivity" "genome_info" 

# extract information about the first 5 genomes
eTOL$genome_info[1:5,]

  left_id right_id taxon_id genome      name         rank branchlength
3       3     1752     2759    Eukaryota superkingdom  0.032247873
4       4     1749       NA                    0.022275411
5       5     1546       NA                    0.004497603
6       6     1499       NA                    0.003496342
7       7     1360       NA                    0.005465982
  common_name
3  eucaryotes
4        
5        
6        
7        

# look at the dimension of connectivity
dim(eTOL$connectivity)

[1] 437 875

# 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)