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toNewick() returns wrong branch length #159

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Lan-h opened this issue Jan 3, 2022 · 1 comment
Open

toNewick() returns wrong branch length #159

Lan-h opened this issue Jan 3, 2022 · 1 comment

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@Lan-h
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Lan-h commented Jan 3, 2022

Hi,
I tried to follow the vignette to convert a dataframe to Newick format, but I the branch length in the output are wrong, although the overall shape of the tree is correct.
This is my current data.tree object:
`

population = FromDataFrameTable(myTable, pathName = "LineageTracing", colLevels = c("TimeBranching") , na.rm = FALSE)
print(population,"TimeBranching")
levelName TimeBranching
1 1 0
2 ¦--2 1
3 ¦--3 5
4 ¦--4 9
5 ¦ °--6 1
6 °--5 10
and the way I tried to convert it to Newick format:
ToNewick(population, heightAttribute = "TimeBranching")
"(2:-1,3:-5,(6:8)4:-9,5:-10)1;"
`
the output should be "(2:1,3:5,(6:1)4:9,5:10)1;" instead.

Is there a way to fix this issue ? Thank you in advance!

@gluc
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gluc commented Nov 11, 2023

Hey, sorry for the late reply. Could you please provide a reproducible example (specifically: what is myTable)? Thx.

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