Commit the man pages and make aggregate public again

man/dbtree.Rd

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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/taxoDBtree.R
+\name{dbtree}
+\alias{dbtree}
+\title{Construct a taxonomic tree from a list of taxa}
+\usage{
+dbtree(x)
+}
+\arguments{
+\item{x}{a table containing the taxonomic path of the references. Typically an output from get.classic.taxonomy}
+}
+\value{
+g a directed graph displaying the taxonomy hierarchy of the input data. Stored in a \code{\link{igraph}} object 
+        where the taxonomic ranks of the vertices are added to the vertices attributes
+}
+\description{
+Construct a graph from a table containing the taxonomic path of sequences
+}
+\examples{
+
+data(termes)
+
+taxo=default.taxonomy()
+
+termes.taxo.table = get.classic.taxonomy(termes, taxo, "taxid")
+head(termes.taxo.table)
+
+graph.tax.termes = dbtree(termes.taxo.table[,1:7])
+library(igraph)
+
+#plot the tree
+coord = layout.reingold.tilford(graph.tax.termes, root=1, circular=F)
+v.cex = as.factor(V(graph.tax.termes)$rank)
+levels(v.cex) = match(levels(v.cex), colnames(termes.taxo.table))
+plot(graph.tax.termes, vertex.size=1, vertex.label.cex=2*(as.numeric(as.vector(v.cex))^-1), edge.arrow.size=0, layout=coord)
+
+
+#Vizualization with sequence counts
+tax.count = log10(colSums(termes$reads)[match(as.vector(V(graph.tax.termes)$name), termes$motus$scientific_name)])
+tax.count[is.na(tax.count)|tax.count<0] = 0.01
+V(graph.tax.termes)$count = unname(tax.count)
+
+plot(graph.tax.termes, vertex.size=V(graph.tax.termes)$count, vertex.label.cex=2*(as.numeric(as.vector(v.cex))^-1), edge.arrow.size=0, layout=coord)
+
+  
+}
+\seealso{
+\code{\link{get.classic.taxonomy}}
+}
+\author{
+Lucie Zinger
+}