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 4.6.1 (2026-06-24)
# Platform: x86_64-pc-linux-gnu
# Running under: Ubuntu 26.04 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-r0.3.32.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_1.57.0  SpiecEasi_2.1.1  BiocStyle_2.41.0
# 
# loaded via a namespace (and not attached):
#  [1] gtable_0.3.6         shape_1.4.6.1        xfun_0.60           
#  [4] bslib_0.11.0         ggplot2_4.0.3        Biobase_2.73.1      
#  [7] lattice_0.22-9       vctrs_0.7.3          tools_4.6.1         
# [10] generics_0.1.4       biomformat_1.41.0    stats4_4.6.1        
# [13] parallel_4.6.1       cluster_2.1.8.2      pkgconfig_2.0.3     
# [16] Matrix_1.7-5         huge_1.6             data.table_1.18.4   
# [19] RColorBrewer_1.1-3   S7_0.2.2             S4Vectors_0.51.5    
# [22] lifecycle_1.0.5      compiler_4.6.1       farver_2.1.2        
# [25] stringr_1.6.0        Biostrings_2.81.5    Seqinfo_1.3.0       
# [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_5.0           crayon_1.5.3        
# [37] jquerylib_0.1.4      MASS_7.3-66          cachem_1.1.0        
# [40] vegan_2.7-5          iterators_1.0.14     foreach_1.5.2       
# [43] nlme_3.1-170         digest_0.6.39        stringi_1.8.7       
# [46] reshape2_1.4.5       labeling_0.4.3       maketools_1.3.2     
# [49] splines_4.6.1        ade4_1.7-24          fastmap_1.2.0       
# [52] grid_4.6.1           cli_3.6.6            magrittr_2.0.5      
# [55] survival_3.8-9       ape_5.8-1            withr_3.0.3         
# [58] scales_1.4.0         rmarkdown_2.31       XVector_0.53.0      
# [61] multtest_2.69.0      igraph_2.3.3         otel_0.2.0          
# [64] pulsar_0.3.13        VGAM_1.1-14          evaluate_1.0.5      
# [67] knitr_1.51           IRanges_2.47.2       mgcv_1.9-4          
# [70] rlang_1.3.0          Rcpp_1.1.2           glue_1.8.1          
# [73] BiocManager_1.30.27  BiocGenerics_0.59.10 jsonlite_2.0.0      
# [76] R6_2.6.1             plyr_1.8.9