name_motifs: Labelling (by lowercase letters) of assemblages by assembly...
In functClust: Functional Clustering of Redundant Components of a System

Description Usage Arguments Details Value

Take a vector of component affectation by clusters, then look for the assemblages containing components that belong to the same clusters, finally label each set of assemblages by a different number.

1	name_motifs(affectElt, mOccur)

`affectElt`	a vector of integers. The vector contains the labels of the different functional groups to which each component belongs. Each functional group is labelled as an integer.
`mOccur`	a matrix of occurrence (occurrence of components). Its first dimension equals to `length(fct)`. Its second dimension equals to the number of components.

General:
A hierarchical tree is recorded as a list of matrix of component affectation and a vector of coefficients of determination. The matrix of component affectation is a square matrix. Its dimension is "number of leaves" = "number of components". The clusters of components are labelled by integers, an integer by cluster. The first line of the square matrix corresponds to the trivial cluster. The trivial cluster get together all the components: all components are thus labelled by one. The second line separates the trivial cluster into 2 sub-clusters: the components are labelled 1 or 2 according to the cluster to which they belong. The following lines separate the trivial cluster into n sub-clusters, labelled from 1 to the line numero. The last line separate each component in a singleton cluster.

A set of s components generates m = 2^s - 1 assembly motifs. The clusters of components are previously shifted by shift_affectElt, for sorting clusters from the most efficient cluster (labelled a, on the left), its size is generally smaller than the least efficient clusters, towards the least efficient clusters (labelled m' < m}, on the right). component clusters are thus labelled: \code{a, b, c, ... m' < m.

Each assembly motif is a combination of clusters. The assembly motifs are simply labelled as the combination of clusters that they contain: a, b, c, ..., ab, ac bc, ..., abc ....

The order of all vectors of strings is this of the input vector affectElt.

Return a list of vector of strings.

components: corresponds to colnames(mOccur),
clusters: corresponds to names of clusters of components,
assemblages: corresponds to rownames(mOccur),
motifs: corresponds to names of assembly motifs, termed as combinations of component clusters.