In stefpeschel/NetCoMi: Network Construction and Comparison for Microbiome Data

# Suppress title check warning
options(rmarkdown.html_vignette.check_title = FALSE)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(NetCoMi)

Here is the code for reproducing the network plot shown on the landing page.

data("soilrep")

soil_warm_yes <- phyloseq::subset_samples(soilrep, warmed == "yes")
soil_warm_no  <- phyloseq::subset_samples(soilrep, warmed == "no")

net_seas_p <- netConstruct(soil_warm_yes, soil_warm_no,
                           filtTax = "highestVar",
                           filtTaxPar = list(highestVar = 500),
                           zeroMethod = "pseudo",
                           normMethod = "clr",
                           measure = "pearson",
                           verbose = 0)

netprops1 <- netAnalyze(net_seas_p, clustMethod = "cluster_fast_greedy")

nclust <- as.numeric(max(names(table(netprops1$clustering$clust1))))

col <- c(topo.colors(nclust), rainbow(6))

pdf("soilrep_networks.pdf", width = 29, height = 16)

plot(netprops1, 
     sameLayout = TRUE, 
     layoutGroup = "union", 
     colorVec = col,
     borderCol = "gray40", 
     nodeSize = "degree", 
     cexNodes = 0.9, 
     nodeSizeSpread = 3, 
     edgeTranspLow = 80, 
     edgeTranspHigh = 50,
     groupNames = c("Warming", "Non-warming"), 
     showTitle = TRUE, 
     cexTitle = 2.8,
     mar = c(1,1,3,1), 
     repulsion = 0.9, 
     labels = FALSE, 
     rmSingles = "inboth",
     nodeFilter = "clustMin", 
     nodeFilterPar = 10, 
     nodeTransp = 50, 
     hubTransp = 30)

dev.off()