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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,135 @@ | ||
| # Given a collection of taxon lists, construct a rooted taxonomic tree. | ||
| # Each taxon list is defined by an parent name and the names of its children (i.e., immediate descendants). | ||
| # Rules: | ||
| # Each taxon must appear at most once as an parent and at most once as a child. | ||
| # Any taxa found as parents but not as children, will be assumed to descend directly from the root. If only one such taxon was found, it will become the root itself. | ||
| # Any taxa found as a child but not as an parent, will become tips. | ||
| # Any parents without children will be considered tips. | ||
| # Since the returned tree is a taxonomy, it will contain no edge lengths. | ||
| tree_from_taxa = function(taxa){ | ||
| # basic input checking | ||
| NTL = length(taxa) | ||
| if(!(class(taxa) %in% c("list"))) stop("taxa must be a list of vectors") | ||
| parent_names = names(taxa) | ||
| if(any(parent_names=="")) stop("One of the parent names is empty, which is not allowed") | ||
| duplicate_parents = unique(parent_names[duplicated(parent_names)]) | ||
| if(length(duplicate_parents)>0) stop(sprintf("%d %s multiple times as parent: %s",length(duplicate_parents),ifelse(length(duplicate_parents)==1,"taxon appears","taxa appear"),paste(duplicate_parents,collapse=", "))) | ||
| child_names = unlist(taxa) | ||
| duplicate_children = unique(child_names[duplicated(child_names)]) | ||
| if(length(duplicate_children)>0) stop(sprintf("%d %s multiple times as a child: %s",length(duplicate_children),ifelse(length(duplicate_children)==1,"taxon appears","taxa appear"),paste(duplicate_children,collapse=", "))) | ||
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| # determine tips & nodes | ||
| taxon_sizes = sapply(taxa, FUN=function(taxon_list) length(taxon_list)) | ||
| node_names = parent_names[taxon_sizes>=1] | ||
| tip_names = c(setdiff(child_names, node_names), parent_names[taxon_sizes==0]) | ||
| root_names = setdiff(parent_names, child_names) | ||
| if(length(root_names)==0) stop("Missing root: All parents also appear as children") | ||
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| # determine tree dimensions | ||
| Ntips = length(tip_names) | ||
| Nnodes = ifelse(length(root_names)==1, length(node_names), length(node_names)+1) | ||
| Nclades = Ntips + Nnodes | ||
| Nedges = sum(taxon_sizes) + ifelse(length(root_names)==1, 0, length(root_names)) | ||
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| # define edges | ||
| edges = matrix(0L, nrow=Nedges, ncol=2) | ||
| if(length(root_names)==1){ | ||
| # found a unique root. By convention, this should be the first node in the tree. | ||
| node_names = c(root_names, setdiff(node_names,root_names)) | ||
| clade_name2index = setNames(c(1:Nclades), nm=c(tip_names,node_names)) | ||
| next_edge = 1 | ||
| }else{ | ||
| # found multiple roots, so combine them as children of a single true root with empty name ("") | ||
| # By convention, the root will be the first node in the tree | ||
| node_names = c("", node_names) | ||
| clade_name2index = setNames(c(1:Nclades), nm=c(tip_names,node_names)) | ||
| edges[1:length(root_names),1] = Ntips+1 | ||
| edges[1:length(root_names),2] = clade_name2index[root_names] | ||
| next_edge = 1 + length(root_names) | ||
| } | ||
| for(tl in seq_len(NTL)){ | ||
| # define edges connecting the parent of this taxon list to all of its children | ||
| parent_clade = clade_name2index[parent_names[tl]] | ||
| child_clades = clade_name2index[taxa[[tl]]] | ||
| edges[next_edge:(next_edge+taxon_sizes[tl]-1),1] = parent_clade | ||
| edges[next_edge:(next_edge+taxon_sizes[tl]-1),2] = child_clades | ||
| next_edge = next_edge + taxon_sizes[tl] | ||
| } | ||
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| # construct the tree object | ||
| tree = list(Nnode = Nnodes, | ||
| tip.label = tip_names, | ||
| node.label = node_names, | ||
| edge = edges, | ||
| root = Ntips+1) | ||
| class(tree) = "phylo" | ||
| attr(tree,"order") = NULL | ||
| return(tree) | ||
| } | ||
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| # construct a rooted tree from taxon lists loaded from a text file | ||
| # Each taxon list in the text file begins with the parent name, followed by the children names in separate lines. | ||
| # Taxon lists are separated by at least one empty line. | ||
| # Comments are allowed, and must be preceded by the character #. | ||
| # For example: | ||
| # Enterobacteriaceae # family | ||
| # Enterobacter # genus | ||
| # Escherichia # genus | ||
| # Klebsielle # genus | ||
| # | ||
| # Erwiniaceae # family | ||
| # Erwinia # genus | ||
| # Buchnera # genus | ||
| # Pantoea # genus | ||
| # | ||
| # Escherichia # genus | ||
| # E. albertii # species | ||
| # E. coli # species | ||
| # E. hermannii # species | ||
| tree_from_taxa_file = function( file_path, # path to an input text file, containing taxon lists. This file may be gzipped. | ||
| prefix_sep = NULL){ # optional separator character, any part prior to which in taxon names will be omitted. For example, if ":", then "genus:Escherichia" will become "Escherichia", while "Staphylococcus" will remain "Staphylococcus". | ||
| fin = open_file(file_path, "rt") | ||
| lines = suppressWarnings(readLines(fin, file.info(file_path)$size)) | ||
| close(fin) | ||
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| new_taxon = TRUE | ||
| children = character(0) | ||
| parent = NULL | ||
| taxa = list() | ||
| for(line in lines){ | ||
| line = gsub("#.*","",line,fixed=FALSE) # remove any comments | ||
| line = trimws(line) # remove any flanking whitespace | ||
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| # remove prefix is applicable | ||
| if(!is.null(prefix_sep)){ | ||
| parts = strsplit(line, prefix_sep, fixed=TRUE)[[1]] | ||
| if(length(parts)>1){ | ||
| line = paste(parts[2:length(parts)], collapse=prefix_sep) | ||
| } | ||
| } | ||
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| if(line==""){ | ||
| if(!is.null(parent)){ | ||
| taxa[[parent]] = children | ||
| children = character(0) | ||
| parent = NULL | ||
| } | ||
| }else if(is.null(parent)){ | ||
| parent = line | ||
| }else{ | ||
| children = c(children, line) | ||
| } | ||
| } | ||
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| # add remaining taxon | ||
| if(!is.null(parent)){ | ||
| taxa[[parent]] = children | ||
| children = character(0) | ||
| parent = NULL | ||
| } | ||
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| return(list(taxa=taxa, tree=tree_from_taxa(taxa))) | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| \name{tree_from_taxa} | ||
| \alias{tree_from_taxa} | ||
| \title{ | ||
| Construct a rooted tree from lists of taxa. | ||
| } | ||
| \description{ | ||
| Given a collection of taxon lists, construct a rooted taxonomic tree. Each taxon list is defined by a parent name and the names of its children (i.e., immediate descendants). | ||
| } | ||
| \usage{ | ||
| tree_from_taxa(taxa) | ||
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| } | ||
| %- maybe also 'usage' for other objects documented here. | ||
| \arguments{ | ||
| \item{taxa}{ | ||
| Named list, whose elements are character vectors, each representing a parent and its children. The element names of \code{taxa} are parents. Each element \code{taxa[n]} is a character vector listing an arbitrary number of taxon names (the children), which immediately descend from taxon \code{names(taxa)[n]}. | ||
| } | ||
| } | ||
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| \details{ | ||
| The following rules apply: | ||
| \itemize{ | ||
| \item Each taxon must appear at most once as a parent and at most once as a child. | ||
| \item Any taxa found as parents but not as children, will be assumed to descend directly from the root. If only one such taxon was found, it will become the root itself. | ||
| \item Any taxa found as a child but not as a parent, will become tips. | ||
| \item Any parents without children will be considered tips. | ||
| \item Empty parent names (i.e., "") are not allowed. | ||
| \item Taxa can be specified in any arbitrary order, including breadth-first, depth-first etc. | ||
| } | ||
| Since the returned tree is a taxonomy, it will contain no edge lengths. | ||
| } | ||
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| \value{ | ||
| A rooted tree of class "phylo". | ||
| } | ||
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| \author{Stilianos Louca} | ||
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| %\references{ | ||
| %} | ||
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| \seealso{ | ||
| \code{\link{consensus_taxonomies}}, | ||
| \code{\link{place_tips_taxonomically}} | ||
| } | ||
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| \examples{ | ||
| # define a list of taxa, with taxon "A" being the root | ||
| # Taxa G, H, I, J, K, L, M, N and O will be tips | ||
| taxa = list(A = c("B","C","D"), | ||
| B = c("E","I"), | ||
| C = c("J","F"), | ||
| D = c("M", "N", "O"), | ||
| E = c("G", "H"), | ||
| F = c("K", "L")) | ||
| tree = castor::tree_from_taxa(taxa) | ||
| } | ||
| % Add one or more standard keywords, see file 'KEYWORDS' in the | ||
| % R documentation directory. | ||
| % Only 1 keyword per line | ||
| \keyword{taxonomy} |