RScelestial (version 1.0.4)

distance.matrix.tree: Calculates distance matrix for a nodes on a tree.

Description

It is used for internal purposes.

Usage

distance.matrix.tree(graph, cell.names, tree.nodes, normalize = TRUE)

Value

A matrix with equal number of rows and columns, a row/column for each cell. Elements of matrix represent distance between cells on the graph.

Arguments

graph

The tree

cell.names

Name of the cells to be the row and column name of the resulting matrix

tree.nodes

For each cell.names a tree node is stored in tree.nodes.

normalize

If TRUE the resulting matrix is normalized.

Examples

## Synthesise an evolution
S = synthesis(10, 5, 20, seed=7)
## Run Scelestial
SC = scelestial(as.ten.state.matrix(S$seqeunce))
## Calculate the distance matrix
vertices <- rownames(SC$input);
distance.matrix.tree(SC$tree, vertices, vertices, normalize = TRUE)
#              C1         C10          C2          C3          C4
# C1  0.000000000 0.003512891 0.015222451 0.014051472 0.008196692
# C10 0.003512891 0.000000000 0.011709560 0.010538580 0.004683800
# C2  0.015222451 0.011709560 0.000000000 0.010538627 0.007025759
# C3  0.014051472 0.010538580 0.010538627 0.000000000 0.005854780
# C4  0.008196692 0.004683800 0.007025759 0.005854780 0.000000000
# C5  0.011709560 0.008196668 0.003512891 0.007025736 0.003512868
# C6  0.023419213 0.019906322 0.019906368 0.009367741 0.015222521
# C7  0.018735342 0.015222451 0.015222498 0.004683871 0.010538651
# C8  0.015222474 0.011709583 0.014051542 0.012880562 0.007025783
# C9  0.010538627 0.007025736 0.009367695 0.008196715 0.002341935
# C5          C6          C7          C8          C9
# C1  0.011709560 0.023419213 0.018735342 0.015222474 0.010538627
# C10 0.008196668 0.019906322 0.015222451 0.011709583 0.007025736
# C2  0.003512891 0.019906368 0.015222498 0.014051542 0.009367695
# C3  0.007025736 0.009367741 0.004683871 0.012880562 0.008196715
# C4  0.003512868 0.015222521 0.010538651 0.007025783 0.002341935
# C5  0.000000000 0.016393477 0.011709606 0.010538651 0.005854803
# C6  0.016393477 0.000000000 0.004683871 0.022248304 0.017564457
# C7  0.011709606 0.004683871 0.000000000 0.017564433 0.012880586
# C8  0.010538651 0.022248304 0.017564433 0.000000000 0.004683847
# C9  0.005854803 0.017564457 0.012880586 0.004683847 0.000000000