count_to_tree.RdWhile we start analysis from count matrix not sequences alignment, we could use clustering methods to get main tree in phylo object class of output as Newick format file. If the samples or elements have group information, we could use weighted clustering method to get a clear grouped structure.
count_to_tree(count, group = NULL, weight = 0)a data frame containing numberic values of abundance or other count.
a vector of character containing the group information. The length of the vector should be same with the count columns number. If using unweighted clustring, should ignore this parameter.
a number specifying the weight size of the group information. In most case, 1 is enough. If the value is between 0 and 1, it will make the weight of group information weak. If the value is more than 1, it will make the weight of group information strong.
a phylo class object containing
a vector of integers specifying edge id. The length of vector is double of node number
a vector of numbers specifying edge length
a vector of character specifying the tip label
a number specifying the number of nodes
a vector of character specifying the node label. If the tree calculated from count matrix or other case, the node label will generated by ape::makeNodeLabel function. And the Most Recent Common Ancestors(MRCA) node will be named with weighted group information, if the parameter group is not null.