Chapter 3 Third break-out room

3.1 Barplot

ps1.com <- microbiome::transform(ps1, "compositional")

# filtering    0.001, 0.01,  
ps1.com.fil = filter_taxa(ps1.com, function(x) sum(x) > .01, TRUE)  

# Phylum - Family
ps.phylum = tax_glom(ps1.com.fil, taxrank="Phylum", NArm=FALSE)  
plot_bar(ps.phylum, fill="Phylum") + facet_wrap(~Pen, scales= "free_x", nrow=1)  

Try how filtering influence the barplot

3.2 Dendrogram

d <- distance(ps1, method = "bray")
#d <- distance(ps1, method = "jaccard", binary = TRUE)
#d <- distance(ps1, method = "unifrac")  
#d <- distance(ps1, method = "wunifrac")   #  distance


hpws <- hclust(d, method = "complete")
#hpws <- hclust(d, method = "ward.D2")

# add color 
library(dendextend)
dend <- as.dendrogram(hpws)
colors_to_use <- as.numeric(meta$Pen)
colors_to_use <- colors_to_use[order.dendrogram(dend)]
labels_colors(dend) <- colors_to_use

plot(as.dendrogram(dend, hang = -1, cex = 0.6)) 

Try how cluster type influence the dendrogram