Example pipeline for running SpiecEasi on biom files

AGSEdemo.R

library('devtools')
install_github('zdk123/SpiecEasi')
library(SpiecEasi)
library(phyloseq)

url <- "https://github.com/zdk123/SpiecEasi/blob/master/inst/extdata/study_1925_closed_reference_otu_table.biom"
download.file(url, desfile='AG1.biom' method='wget') ## download method is system dependent

amgut1 <- import_biom('AG1.biom')
## filter taxa that appear in fewer than 30% of the samples
amgut1.filt <- prune_taxa(rowSums(sign(amgut1@otu_table@.Data)) > nsamples(amgut1)*.3, amgut1)

ig.mb <- graph.adjacency(se.mb.amgut$refit, mode='undirected')
vsize <- exp(colMeans(se.mb.amgut$data)/2)+2

## filter edges that we are less confidence of (i.e. by StARS 'merge' estimate)
highconfnet <- se.mb.amgut$refit * (se.mb.amgut$merge[[se.mb.amgut$opt.index]] > .9)
ig.hc <- graph.adjacency(highconfnet, mode='undirected')
am.coord <- layout.fruchterman.reingold(ig.mb)

## plot
par(mfrow=c(1,2))
plot(ig.mb, layout=am.coord, vertex.size=vsize, vertex.label=NA, main="MB")
plot(ig.hc,  layout=am.coord,  vertex.size=vsize, vertex.label=NA, main="High Confidence edges")