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Last seen 9.6 years ago
Hello R users,
I tried to used both APE and apTreeshape to plot the phylogenetic tree
from the generated tree or OTU table. I have the tree file generated
from Qiime, but when I use the following command to read the tree, it
has the following error message:
> t <- read.nexus("rep_phylo.tre")
Error in start:end : NA/NaN argument
I checked the tree as below:
coveragePerOrigin
1 2 3 4 5 6 7 8 9 10
11 12 13 14
11788 13073 14150 13739 14212 14555 14498 15879 16634 17753
19651 23185 28858 109511
It seems that the tree is not the format required by APE or something.
Any input would be appreciated.
Thanks a lot for the help.
-- output of sessionInfo():
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] apTreeshape_1.4-5 ape_3.0-11
loaded via a namespace (and not attached):
[1] grid_3.0.1 lattice_0.20-15 nlme_3.1-110 quantreg_5.05
SparseM_1.03 tools_3.0.1
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