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()