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 every 8 hours.
# 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 every 8 hours.
# Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
# generated.

unnamed-chunk-3-1.png

Session info:

sessionInfo()
# R Under development (unstable) (2025-10-21 r88958)
# Platform: x86_64-apple-darwin20
# Running under: macOS Ventura 13.7.8
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRblas.0.dylib 
# LAPACK: /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
# 
# locale:
# [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
# 
# time zone: America/New_York
# tzcode source: internal
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] phyloseq_1.55.0  igraph_2.2.1     Matrix_1.7-4     SpiecEasi_1.99.3
# [5] BiocStyle_2.39.0
# 
# loaded via a namespace (and not attached):
#  [1] gtable_0.3.6        shape_1.4.6.1       xfun_0.54          
#  [4] bslib_0.9.0         ggplot2_4.0.1       rhdf5_2.55.8       
#  [7] Biobase_2.71.0      lattice_0.22-7      rhdf5filters_1.23.0
# [10] vctrs_0.6.5         tools_4.6.0         generics_0.1.4     
# [13] biomformat_1.39.0   stats4_4.6.0        parallel_4.6.0     
# [16] tibble_3.3.0        cluster_2.1.8.1     pkgconfig_2.0.3    
# [19] huge_1.3.5          data.table_1.17.8   RColorBrewer_1.1-3 
# [22] S7_0.2.1            S4Vectors_0.49.0    lifecycle_1.0.4    
# [25] farver_2.1.2        compiler_4.6.0      stringr_1.6.0      
# [28] Biostrings_2.79.2   tinytex_0.57        Seqinfo_1.1.0      
# [31] codetools_0.2-20    permute_0.9-8       htmltools_0.5.8.1  
# [34] sass_0.4.10         yaml_2.3.10         glmnet_4.1-10      
# [37] pillar_1.11.1       crayon_1.5.3        jquerylib_0.1.4    
# [40] MASS_7.3-65         cachem_1.1.0        vegan_2.7-2        
# [43] magick_2.9.0        iterators_1.0.14    foreach_1.5.2      
# [46] nlme_3.1-168        tidyselect_1.2.1    digest_0.6.38      
# [49] stringi_1.8.7       dplyr_1.1.4         reshape2_1.4.5     
# [52] bookdown_0.45       labeling_0.4.3      splines_4.6.0      
# [55] ade4_1.7-23         fastmap_1.2.0       grid_4.6.0         
# [58] cli_3.6.5           magrittr_2.0.4      dichromat_2.0-0.1  
# [61] survival_3.8-3      ape_5.8-1           withr_3.0.2        
# [64] scales_1.4.0        rmarkdown_2.30      XVector_0.51.0     
# [67] multtest_2.67.0     pulsar_0.3.11       VGAM_1.1-13        
# [70] evaluate_1.0.5      knitr_1.50          IRanges_2.45.0     
# [73] mgcv_1.9-4          rlang_1.1.6         Rcpp_1.1.0         
# [76] glue_1.8.0          BiocManager_1.30.27 BiocGenerics_0.57.0
# [79] jsonlite_2.0.0      R6_2.6.1            Rhdf5lib_1.33.0    
# [82] plyr_1.8.9