Tree building and visualization

library("tidytree") # first load to disable warning about phylo class
#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : 
#>   object 'type_sum.accel' not found
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 4.4.2 (2024-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Debian GNU/Linux 12 (bookworm)
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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_0.12.0 purrr_1.0.2        dplyr_1.1.4        dada2_1.34.0      
#>  [9] Rcpp_1.0.13-1      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_1.1.4                 magrittr_2.0.3             
#>   [7] ade4_1.7-22                 matrixStats_1.4.1          
#>   [9] compiler_4.4.2              mgcv_1.9-1                 
#>  [11] png_0.1-8                   systemfonts_1.1.0          
#>  [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_0.49                   zlibbioc_1.50.0            
#>  [29] cachem_1.1.0                aplot_0.2.3                
#>  [31] GenomeInfoDb_1.40.1         jsonlite_1.8.9             
#>  [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_4.4.2              cluster_2.1.6              
#>  [41] R6_2.5.1                    bslib_0.8.0                
#>  [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_1.7-1               
#>  [53] splines_4.4.2               igraph_2.1.2               
#>  [55] tidyselect_1.2.1            abind_1.4-8                
#>  [57] yaml_2.3.10                 vegan_2.6-8                
#>  [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_1.0.1              gridGraphics_0.5-1         
#>  [69] desc_1.4.3                  survival_3.7-0             
#>  [71] RcppParallel_5.1.9          Biostrings_2.72.1          
#>  [73] pillar_1.10.0               MatrixGenerics_1.16.0      
#>  [75] foreach_1.5.2               stats4_4.4.2               
#>  [77] ggfun_0.1.8                 generics_0.1.3             
#>  [79] S4Vectors_0.42.1            munsell_0.5.1              
#>  [81] scales_1.3.0                glue_1.8.0                 
#>  [83] lazyeval_0.2.2              tools_4.4.2                
#>  [85] interp_1.1-6                data.table_1.16.4          
#>  [87] GenomicAlignments_1.40.0    fs_1.6.5                   
#>  [89] fastmatch_1.1-4             rhdf5_2.48.0               
#>  [91] grid_4.4.2                  tidyr_1.3.1                
#>  [93] latticeExtra_0.6-30         colorspace_2.1-1           
#>  [95] patchwork_1.3.0             nlme_3.1-166               
#>  [97] GenomeInfoDbData_1.2.12     cli_3.6.3                  
#>  [99] textshaping_0.4.1           S4Arrays_1.4.1             
#> [101] gtable_0.3.6                yulab.utils_0.1.8          
#> [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            
#> [113] lifecycle_1.0.4             httr_1.4.7                 
#> [115] MASS_7.3-61