Change the package path

R/taxoDBtree.R

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+#'@include 02_class_metabarcoding.data.R
+#'@import ROBITaxonomy 
+
+NULL
+
+#' Construct a taxonomic tree from a list of taxa
+#' 
+#' Construct a graph from a table containing the taxonomic path of sequences
+#' 
+#' 
+#' @param x a table containing the taxonomic path of the references. Typically an output from get.classic.taxonomy
+#' 
+#' @return 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
+#'
+#' @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)$count, vertex.label.cex=2*(as.numeric(as.vector(v.cex))^-1), edge.arrow.size=0, layout=coord)
+#' 
+#'   
+#' @seealso \code{\link{get.classic.taxonomy}}
+#' @author Lucie Zinger
+#' @export
+
+dbtree = function(x) {
+  
+  #dealing with noranks
+  x2 = x
+  for (i in 1:ncol(x2)) {
+    x2[,i] = as.character(x[,i])
+    if(length(which(is.na(x[,i])==T))!=0) {
+      if(i==1) {
+        x2[which(is.na(x[,i])==T),i] = "NR"
+      } else {
+        x2[which(is.na(x[,i])==T),i] = as.character(x2[,i-1])[which(is.na(x2[,i])==T)]
+      }
+    }
+  }
+      
+  #prepare an edgelist
+  edgelist = list()
+  
+  for (i in 1:(ncol(x2)-1)){
+    out = x2[,c(i,i+1)]
+    out2 = out[-which(duplicated(out)==T),]
+    colnames(out2) = c("parent", "kid")
+    edgelist[[i]] = out2[which(out2[,1]!=out2[,2]),]
+  } 
+  
+  edgelist = do.call("rbind", edgelist)
+  
+  
+  #construct the graph
+  
+  g = igraph::graph.edgelist(as.matrix(edgelist), directed=T)
+  
+  #get taxorank for each taxa
+  ranks = do.call("rbind", lapply(1:ncol(x), function(y) {
+    out = cbind(unique(as.character(x[,y])), colnames(x)[y])
+    out
+  }))
+  
+  #Assign nodes to taxorank
+  igraph::V(g)$rank = ranks[match(igraph::V(g)$name, ranks[,1]),2]
+    
+  return(g)
+}