What does R represent

[chestnzu1]

Hello:
Currently, I am using go_plot.ply to create a hierarchical graph, I notice inside the rectangle, there are some descriptions like the GOID, the depth, and descendant count, But I can not find the explanation for R. Can you tell me what does 'R' represent? Thanks in advance.

  best,
   Yi

[dvklopfenstein]

Hello,

Thank you for your interest in GOATOOLS and thanks for the great question.

R is depth when taking into account optional relationships, like part_of.

Depth is the length of the longest path from the root term, like cellular_component, to the term of interest.

So in this plot:

The bottom term's title is:

GO:0043231 D3 R4 d0

D3 means that the longest path from the root, cellular_component, to the bottom term is 3 edges, when using only the is_a required relationships.

R4 means that the longest path from the root, cellular_component, to the bottom term is 3 edges, when using both the is_a relationships (black arrows) and the optional part_of relationships (dashed orange arrows).

[dvklopfenstein]

Check out the new section at the top of this Python notebook added to better help other researchers understand D and R:

https://github.com/tanghaibao/goatools/blob/main/notebooks/get_isa_and_partof.ipynb

Thanks again for the terrific question