Question: splatter simulating paths
0
gravatar for nikolaspapadop
14 months ago by
nikolaspapadop10 wrote:

I am trying to use splatter to simulate certain topologies - let's say I want to simulate a differentiation whose Newick tree would look like (B,(D,E)C)A; How do I implement this as a path for splatSimulate? It is not clear to me how to set up the path.from parameter.

single cell splatter • 264 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by nikolaspapadop10
Answer: splatter simulating paths
2
gravatar for nikolaspapadop
14 months ago by
nikolaspapadop10 wrote:

ok had to go into the code, but I think i figured it out:

when you define path.from, you specify at which points the branch starts. The end point of the branch you defined is always the position you are at:

path.from <- c(0, 1, 1, 2, 2)
               |  |  |  |  |
               1  2  3  4  5

this defines a tree that looks like this:

    ┌---3
0---1   ┌---4
    └---2        
        └---5

would be great if the authors can confirm/deny :)

ADD COMMENTlink modified 14 months ago • written 14 months ago by nikolaspapadop10
Hi @nikolaspapadop That is correct. I like your diagram, I might look at including that in the help page for the function.
ADD REPLYlink written 14 months ago by luke.zappia50

thank you for the verification! Maybe it can save someone else some time :)

ADD REPLYlink written 14 months ago by nikolaspapadop10
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