Tree building and visualization
Source:vignettes/articles/tree_visualization.Rmd
tree_visualization.RmdIn introduction, you can read the review of (zou2024?), entitled “Common Methods for Phylogenetic Tree Construction and Their Implementation in R“.
library("tidytree") # first load to disable warning about phylo class
library("MiscMetabar")
library("phangorn")
data(data_fungi)
df <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 9000)
df_tree <- quiet(build_phytree_pq(df, nb_bootstrap = 5))
data_fungi_tree <- merge_phyloseq(df, phyloseq::phy_tree(df_tree$ML$tree))
library("treeio")
library("ggtree")
ggtree(data_fungi_tree@phy_tree, layout = "ellipse") + geom_tiplab()
ggtree(as.treedata(df_tree$ML), layout = "slanted")
ggdensitree(df_tree$ML_bs, alpha = .3, colour = "steelblue") +
geom_tiplab(size = 3) + hexpand(.35)
ggtree(as.treedata(df_tree$ML)) +
geom_text(aes(x = branch, label = AA_subs, vjust = -.5), size = 1)
tax_tab <- as.data.frame(data_fungi_tree@tax_table)
tax_tab <- data.frame("OTU" = rownames(tax_tab), tax_tab)
p <- ggtree(as.treedata(data_fungi_tree@phy_tree)) %<+%
tax_tab
p + geom_tippoint(aes(color = Class, shape = Phylum)) +
geom_text(aes(label = Genus), hjust = -0.2, size = 2)
ggtree(as.treedata(data_fungi_tree@phy_tree), branch.length = "none") %<+%
tax_tab +
geom_tippoint(aes(color = Class, shape = Phylum), size = 2)
Session information
sessionInfo()
#> R version 4.4.3 (2025-02-28)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Debian GNU/Linux 12 (bookworm)
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.21.so; LAPACK version 3.11.0
#>
#> locale:
#> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
#> [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
#> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Europe/Paris
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] ggtree_3.12.0 treeio_1.28.0 phangorn_2.12.1 ape_5.8-1
#> [5] MiscMetabar_0.14.2 purrr_1.0.4 dplyr_1.1.4 dada2_1.34.0
#> [9] Rcpp_1.0.14 ggplot2_3.5.1 phyloseq_1.50.0 tidytree_0.4.6
#>
#> loaded via a namespace (and not attached):
#> [1] DBI_1.2.3 bitops_1.0-9
#> [3] deldir_2.0-4 permute_0.9-7
#> [5] rlang_1.1.5 magrittr_2.0.3
#> [7] ade4_1.7-22 matrixStats_1.5.0
#> [9] compiler_4.4.3 mgcv_1.9-1
#> [11] png_0.1-8 systemfonts_1.2.1
#> [13] vctrs_0.6.5 reshape2_1.4.4
#> [15] quadprog_1.5-8 stringr_1.5.1
#> [17] pwalign_1.0.0 pkgconfig_2.0.3
#> [19] crayon_1.5.3 fastmap_1.2.0
#> [21] XVector_0.44.0 labeling_0.4.3
#> [23] Rsamtools_2.20.0 rmarkdown_2.29
#> [25] UCSC.utils_1.0.0 ragg_1.3.3
#> [27] xfun_0.51 zlibbioc_1.50.0
#> [29] cachem_1.1.0 aplot_0.2.4
#> [31] GenomeInfoDb_1.40.1 jsonlite_1.9.1
#> [33] biomformat_1.32.0 rhdf5filters_1.16.0
#> [35] DelayedArray_0.30.1 Rhdf5lib_1.26.0
#> [37] BiocParallel_1.38.0 jpeg_0.1-10
#> [39] parallel_4.4.3 cluster_2.1.8
#> [41] R6_2.6.1 bslib_0.9.0
#> [43] stringi_1.8.4 RColorBrewer_1.1-3
#> [45] GenomicRanges_1.56.2 jquerylib_0.1.4
#> [47] SummarizedExperiment_1.34.0 iterators_1.0.14
#> [49] knitr_1.49 DECIPHER_3.2.0
#> [51] IRanges_2.38.1 Matrix_1.7-2
#> [53] splines_4.4.3 igraph_2.1.4
#> [55] tidyselect_1.2.1 abind_1.4-8
#> [57] yaml_2.3.10 vegan_2.6-10
#> [59] codetools_0.2-20 hwriter_1.3.2.1
#> [61] lattice_0.22-6 tibble_3.2.1
#> [63] plyr_1.8.9 Biobase_2.64.0
#> [65] withr_3.0.2 ShortRead_1.62.0
#> [67] evaluate_1.0.3 gridGraphics_0.5-1
#> [69] desc_1.4.3 survival_3.8-3
#> [71] RcppParallel_5.1.10 Biostrings_2.72.1
#> [73] pillar_1.10.1 MatrixGenerics_1.16.0
#> [75] foreach_1.5.2 stats4_4.4.3
#> [77] ggfun_0.1.8 generics_0.1.3
#> [79] S4Vectors_0.42.1 munsell_0.5.1
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#> [83] lazyeval_0.2.2 tools_4.4.3
#> [85] interp_1.1-6 data.table_1.17.0
#> [87] GenomicAlignments_1.40.0 fs_1.6.5
#> [89] fastmatch_1.1-6 rhdf5_2.48.0
#> [91] grid_4.4.3 tidyr_1.3.1
#> [93] latticeExtra_0.6-30 colorspace_2.1-1
#> [95] patchwork_1.3.0 nlme_3.1-167
#> [97] GenomeInfoDbData_1.2.12 cli_3.6.4
#> [99] textshaping_1.0.0 S4Arrays_1.4.1
#> [101] gtable_0.3.6 yulab.utils_0.2.0
#> [103] sass_0.4.9 digest_0.6.37
#> [105] BiocGenerics_0.50.0 ggplotify_0.1.2
#> [107] SparseArray_1.4.8 farver_2.1.2
#> [109] htmlwidgets_1.6.4 htmltools_0.5.8.1
#> [111] pkgdown_2.1.1 multtest_2.60.0
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#> [115] MASS_7.3-65