R/clustering_kos.R

In mirnavazquez/InsectMicrobiome: Analize amplicon sequences from insects.

clustering_kos<-function(databiomKO, estadio){
  y <- read_biom("ko_predictions.biom")
  otumaty = as(biom_data(y), "matrix")
  OTUy = otu_table(otumaty, taxa_are_rows=TRUE)
  taxmaty = as.matrix(observation_metadata(y), rownames.force=TRUE)
  TAXy = tax_table(taxmaty)
  path_1 = phyloseq(OTUy, TAXy, map)
  wh0Ko = genefilter_sample(path_1, filterfun_sample(function(x) x > 5), A=0.5*nsamples(path_1))
  GP1Ko = prune_taxa(wh0Ko, path_1)
  GP1Ko = transform_sample_counts(GP1Ko, function(x) 1E6 * x/sum(x))
  kO1 <- subset_samples(GP1Ko, SampleType == "Larvae")
  pdf("KOclustering.pdf", width=10, height=10)
  orduKo = ordinate(kO1, "PCoA", "bray")
  pKo = plot_ordination(kO1, orduKo, color="Host")
  pKo = pKo + geom_point(size=3, alpha=0.75)
  pKo = pKo + scale_colour_brewer(type="qual", palette="Set1")
  pKo + ggtitle("MDS/PCoA on Bray distance, KOs")
  dev.off()
}