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 4.5.2 (2025-10-31)
# Platform: x86_64-pc-linux-gnu
# Running under: Ubuntu 24.04.3 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=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: Etc/UTC
# tzcode source: system (glibc)
# 
# 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_0.56          
#  [4] bslib_0.9.0         ggplot2_4.0.1       rhdf5_2.55.12      
#  [7] Biobase_2.71.0      lattice_0.22-7      vctrs_0.7.0        
# [10] rhdf5filters_1.23.3 tools_4.5.2         generics_0.1.4     
# [13] biomformat_1.39.0   stats4_4.5.2        parallel_4.5.2     
# [16] cluster_2.1.8.1     pkgconfig_2.0.3     huge_1.3.5         
# [19] data.table_1.18.0   RColorBrewer_1.1-3  S7_0.2.1           
# [22] S4Vectors_0.49.0    lifecycle_1.0.5     compiler_4.5.2     
# [25] farver_2.1.2        stringr_1.6.0       Biostrings_2.79.4  
# [28] Seqinfo_1.1.0       codetools_0.2-20    permute_0.9-8      
# [31] htmltools_0.5.9     sys_3.4.3           buildtools_1.0.0   
# [34] sass_0.4.10         yaml_2.3.12         glmnet_4.1-10      
# [37] crayon_1.5.3        jquerylib_0.1.4     MASS_7.3-65        
# [40] cachem_1.1.0        vegan_2.7-2         iterators_1.0.14   
# [43] foreach_1.5.2       nlme_3.1-168        digest_0.6.39      
# [46] stringi_1.8.7       reshape2_1.4.5      labeling_0.4.3     
# [49] maketools_1.3.2     splines_4.5.2       ade4_1.7-23        
# [52] fastmap_1.2.0       grid_4.5.2          cli_3.6.5          
# [55] magrittr_2.0.4      survival_3.8-6      ape_5.8-1          
# [58] withr_3.0.2         scales_1.4.0        rmarkdown_2.30     
# [61] XVector_0.51.0      multtest_2.67.0     pulsar_0.3.11      
# [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] Rhdf5lib_1.33.0     plyr_1.8.9