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)))

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.

sessionInfo()
# R version 4.5.3 (2026-03-11)
# Platform: x86_64-pc-linux-gnu
# Running under: Ubuntu 24.04.4 LTS
# 
# 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-r0.3.26.so;  LAPACK version 3.12.0
# 
# locale:
#  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#  [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: Etc/UTC
# tzcode source: system (glibc)
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] phyloseq_1.55.2  SpiecEasi_1.99.5 BiocStyle_2.39.0
# 
# loaded via a namespace (and not attached):
#  [1] gtable_0.3.6        shape_1.4.6.1       xfun_0.57          
#  [4] bslib_0.10.0        ggplot2_4.0.2       Biobase_2.71.0     
#  [7] lattice_0.22-9      vctrs_0.7.2         tools_4.5.3        
# [10] generics_0.1.4      biomformat_1.39.16  stats4_4.5.3       
# [13] parallel_4.5.3      cluster_2.1.8.2     pkgconfig_2.0.3    
# [16] Matrix_1.7-5        huge_1.5.1          data.table_1.18.2.1
# [19] RColorBrewer_1.1-3  S7_0.2.1            S4Vectors_0.49.1   
# [22] lifecycle_1.0.5     compiler_4.5.3      farver_2.1.2       
# [25] stringr_1.6.0       Biostrings_2.79.5   Seqinfo_1.1.0      
# [28] codetools_0.2-20    permute_0.9-10      htmltools_0.5.9    
# [31] sys_3.4.3           buildtools_1.0.0    sass_0.4.10        
# [34] yaml_2.3.12         glmnet_4.1-10       crayon_1.5.3       
# [37] jquerylib_0.1.4     MASS_7.3-65         cachem_1.1.0       
# [40] vegan_2.7-3         iterators_1.0.14    foreach_1.5.2      
# [43] nlme_3.1-169        digest_0.6.39       stringi_1.8.7      
# [46] reshape2_1.4.5      labeling_0.4.3      maketools_1.3.2    
# [49] splines_4.5.3       ade4_1.7-24         fastmap_1.2.0      
# [52] grid_4.5.3          cli_3.6.5           magrittr_2.0.5     
# [55] survival_3.8-6      ape_5.8-1           withr_3.0.2        
# [58] scales_1.4.0        rmarkdown_2.31      XVector_0.51.0     
# [61] multtest_2.67.0     igraph_2.2.2        pulsar_0.3.13      
# [64] VGAM_1.1-14         evaluate_1.0.5      knitr_1.51         
# [67] IRanges_2.45.0      mgcv_1.9-4          rlang_1.1.7        
# [70] Rcpp_1.1.1          glue_1.8.0          BiocManager_1.30.27
# [73] BiocGenerics_0.57.0 jsonlite_2.0.0      R6_2.6.1           
# [76] plyr_1.8.9