Random DAGs

Random trees

dag_random_tree() generates a random tree. By default it generates a binary tree where all leaf terms have depth = 9.

library(simona)
set.seed(123)
tree1 = dag_random_tree()
tree1

## An ontology_DAG object:
##   Source: dag_random_tree 
##   1023 terms / 1022 relations / a tree
##   Root: 1 
##   Terms: 1, 10, 100, 1000, ...
##   Max depth: 9 
##   Aspect ratio: 56.89:1

dag_circular_viz(tree1)

Strictly speaking, tree1 is not random. The tree is growing from the root. In dag_random_tree(), there are several arguments that can be used for generating random trees.

• n_children: Number of child terms. It can be a single value where each term will the same number of child terms. The value can also be a range, then the number of child terms will be randomly picked in that range.
• p_stop: A branch can stop growing based on this probability. On a certain step of the tree growing, let’s denote the set of leaf terms as L, then, in the next round, floor(length(L)*p_stop) leaf terms will stop growing, while the remaining leaf terms will continue to grow. If a leaf term continues to grow, it will be linked to n_children child terms if n_children is a single value, or pick a number from the range of [n_children[1], n_children[2]].

The tree growing stops when the number of total terms exceeds max.

So the default call of dag_random_tree() is identical to:

dag_random_tree(n_children = 2, p_stop = 0, max = 2^10 - 1)

We can change these arguments to some other values, such as:

tree2 = dag_random_tree(n_children = c(2, 6), p_stop = 0.5, max = 2000)
tree2

## An ontology_DAG object:
##   Source: dag_random_tree 
##   1999 terms / 1998 relations / a tree
##   Root: 1 
##   Terms: 1, 10, 100, 1000, ...
##   Max depth: 7 
##   Aspect ratio: 105.71:1

dag_circular_viz(tree2)

Random DAGs

A more general random DAG is generated based on the random tree. Taking tree1 which is already generated, the function dag_add_random_children() adds more random children to terms in tree1.

dag1 = dag_add_random_children(tree1)
dag1

## An ontology_DAG object:
##   Source: dag_add_random_children 
##   1023 terms / 1115 relations
##   Root: 1 
##   Terms: 1, 10, 100, 1000, ...
##   Max depth: 9 
##   Avg number of parents: 1.09
##   Avg number of children: 1.03
##   Aspect ratio: 56.89:1 (based on the longest distance from root)
##                 52.78:1 (based on the shortest distance from root)

dag_circular_viz(dag1)