APE package on phylogenetic tree plot
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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 -- Sent via the guest posting facility at bioconductor.org.
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