1 Working with phyloseq

SpiecEasi includes some convenience wrappers to work directly with phyloseq objects.

library(SpiecEasi)
library(phyloseq)
## Load round 2 of American gut project
data('amgut2.filt.phy')
se.mb.amgut2 <- spiec.easi(amgut2.filt.phy, method='mb', lambda.min.ratio=1e-2,
                           nlambda=20, pulsar.params=list(rep.num=50))
ig2.mb <- adj2igraph(getRefit(se.mb.amgut2),  vertex.attr=list(name=taxa_names(amgut2.filt.phy)))

The plot_network function provides an easy way to visualize networks with taxonomic information from phyloseq objects. You can specify different taxonomic ranks for coloring nodes and customize the visualization further.

plot_network(ig2.mb, amgut2.filt.phy, type='taxa', color="Rank3")
# Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
# ℹ Please use tidy evaluation idioms with `aes()`.
# ℹ See also `vignette("ggplot2-in-packages")` for more information.
# ℹ The deprecated feature was likely used in the phyloseq package.
#   Please report the issue at <https://github.com/joey711/phyloseq/issues>.
# This warning is displayed once per session.
# Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
# generated.
# Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
# ℹ Please use `linewidth` instead.
# ℹ The deprecated feature was likely used in the phyloseq package.
#   Please report the issue at <https://github.com/joey711/phyloseq/issues>.
# This warning is displayed once per session.
# Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
# generated.

unnamed-chunk-3-1.png

Session info:

sessionInfo()
# R version 4.6.0 alpha (2026-04-05 r89794)
# Platform: x86_64-pc-linux-gnu
# Running under: Ubuntu 24.04.4 LTS
# 
# Matrix products: default
# BLAS:   /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so 
# LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
# 
# locale:
#  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#  [3] LC_TIME=en_GB              LC_COLLATE=C              
#  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
# [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
# 
# time zone: America/New_York
# tzcode source: system (glibc)
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] phyloseq_1.55.2  igraph_2.2.3     Matrix_1.7-5     SpiecEasi_1.99.5
# [5] BiocStyle_2.39.0
# 
# loaded via a namespace (and not attached):
#  [1] ade4_1.7-24                 tidyselect_1.2.1           
#  [3] dplyr_1.2.1                 farver_2.1.2               
#  [5] Biostrings_2.79.5           S7_0.2.1                   
#  [7] fastmap_1.2.0               digest_0.6.39              
#  [9] lifecycle_1.0.5             cluster_2.1.8.2            
# [11] survival_3.8-6              magrittr_2.0.5             
# [13] compiler_4.6.0              rlang_1.2.0                
# [15] sass_0.4.10                 tools_4.6.0                
# [17] yaml_2.3.12                 data.table_1.18.2.1        
# [19] knitr_1.51                  labeling_0.4.3             
# [21] S4Arrays_1.11.1             DelayedArray_0.37.1        
# [23] plyr_1.8.9                  RColorBrewer_1.1-3         
# [25] abind_1.4-8                 withr_3.0.2                
# [27] BiocGenerics_0.57.0         grid_4.6.0                 
# [29] stats4_4.6.0                multtest_2.67.0            
# [31] biomformat_1.39.16          ggplot2_4.0.2              
# [33] scales_1.4.0                iterators_1.0.14           
# [35] MASS_7.3-65                 dichromat_2.0-0.1          
# [37] tinytex_0.59                SummarizedExperiment_1.41.1
# [39] cli_3.6.5                   rmarkdown_2.31             
# [41] vegan_2.7-3                 crayon_1.5.3               
# [43] generics_0.1.4              otel_0.2.0                 
# [45] pulsar_0.3.13               reshape2_1.4.5             
# [47] ape_5.8-1                   cachem_1.1.0               
# [49] stringr_1.6.0               splines_4.6.0              
# [51] parallel_4.6.0              BiocManager_1.30.27        
# [53] XVector_0.51.0              matrixStats_1.5.0          
# [55] vctrs_0.7.2                 glmnet_4.1-10              
# [57] jsonlite_2.0.0              VGAM_1.1-14                
# [59] bookdown_0.46               IRanges_2.45.0             
# [61] S4Vectors_0.49.1            magick_2.9.1               
# [63] foreach_1.5.2               jquerylib_0.1.4            
# [65] glue_1.8.0                  codetools_0.2-20           
# [67] stringi_1.8.7               shape_1.4.6.1              
# [69] gtable_0.3.6                GenomicRanges_1.63.2       
# [71] tibble_3.3.1                pillar_1.11.1              
# [73] htmltools_0.5.9             Seqinfo_1.1.0              
# [75] huge_1.5.1                  R6_2.6.1                   
# [77] evaluate_1.0.5              lattice_0.22-9             
# [79] Biobase_2.71.0              bslib_0.10.0               
# [81] Rcpp_1.1.1                  permute_0.9-10             
# [83] SparseArray_1.11.13         nlme_3.1-169               
# [85] mgcv_1.9-4                  xfun_0.57                  
# [87] MatrixGenerics_1.23.0       pkgconfig_2.0.3