Created
April 5, 2018 16:43
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geom_hilight() does not work
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| library(ggtree) | |
| # load a tree | |
| # tree <- treeio::read.tree("phylotree.nwk") | |
| # this is eqivalent to: | |
| tree <- structure(list(edge = structure(c(14L, 15L, 16L, 15L, 17L, 17L, | |
| 17L, 15L, 18L, 18L, 18L, 15L, 19L, 15L, 20L, 15L, 15L, 15L, 14L, | |
| 21L, 15L, 16L, 1L, 17L, 2L, 3L, 4L, 18L, 5L, 6L, 7L, 19L, 8L, | |
| 20L, 9L, 10L, 11L, 12L, 21L, 13L), .Dim = c(20L, 2L)), Nnode = 8L, | |
| node.label = c("Root", "k__Bacteria", "p__Bacteroidetes", | |
| "p__Firmicutes", "p__Proteobacteria", "p__Actinobacteria", | |
| "p__Fusobacteria", "k__Viruses"), tip.label = c("c__Bacteroidia", | |
| "c__Negativicutes", "c__Bacilli", "c__Clostridia", "c__Betaproteobacteria", | |
| "c__Gammaproteobacteria", "c__Epsilonproteobacteria", "c__Actinobacteria", | |
| "c__Fusobacteriia", "p__Spirochaetes", "p__Candidatus_Saccharibacteria", | |
| "p__Synergistetes", "p__Viruses_noname")), .Names = c("edge", | |
| "Nnode", "node.label", "tip.label"), class = "phylo", order = "cladewise") | |
| # show internal nodes | |
| ggtree(tree, layout= "circular") + geom_text2(aes(subset=!isTip, label=node), hjust=-.3) + geom_tiplab() | |
| # why there is no highlight? | |
| ggtree(tree, layout= "circular") + geom_hilight(node = 16) | |
| # show internal nodes | |
| ggtree(tree) + geom_text2(aes(subset=!isTip, label=node), hjust=-.3) + geom_tiplab() | |
| # why there is no highlight? | |
| ggtree(tree) + geom_hilight(node = 16) | |
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r$> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
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] ggtree_1.10.5 treeio_1.2.2 ggplot2_2.2.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 lattice_0.20-35 ape_5.0 tidyr_0.8.0 grid_3.4.4 plyr_1.8.4 jsonlite_1.5 nlme_3.1-131.1 gtable_0.2.0 magrittr_1.5
[11] scales_0.5.0 pillar_1.2.1 rlang_0.2.0 lazyeval_0.2.1 rvcheck_0.0.9 labeling_0.3 glue_1.2.0 purrr_0.2.4 munsell_0.4.3 parallel_3.4.4
[21] compiler_3.4.4 colorspace_1.3-2 tibble_1.4.2