PCoA plot with phyla abundance

Question

[Bioinfonext]

Hi,

could anyone please help me how to make PCoA plot with phyla abundance as shown in below link from amplicon sequencing data.

Thanks

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

[Bioinfonext]

ok, sorry for that,

I have changed above image link.

[Ram]

Did you read the post? It has instructions on how to add the image. Pasting the URL directly is not the optimal way of doing it.

[Asaf]

Where are you struggling? Do you have the abundance in the phylum level already?

[Bioinfonext]

Hi Asaf,

Yes I do have relative abundance at phyla level. currently I am using below phyloseq code for PCoA plot but not sure how to insert bacterial abundance in this plot at phyla level.

physeqN3 = filter_taxa(physeqN2, function(x) sum(x > 5) > (0.2*length(x)), TRUE)
phyloseq_prop = transform_sample_counts(physeqN3, function(x) 1E6 * x/sum(x))
phyloseq_prop_bray <- ordinate(phyloseq_prop, "PCoA", "bray")
p=plot_ordination(phyloseq_prop,phyloseq_prop_bray, color = "Region", shape="Region")
p = p + geom_point(size = 4, alpha = 0.75)
p + ggtitle("PCoA root-dry season data,genus-Bray distance ")

many thanks nabiyogesh

[Asaf]

Not sure how to do this with phyloseq. You can extract the abundance table and try with https://github.com/vqv/ggbiplot

[Bioinfonext]

Yes, I do have relative abundance table and metadata file but not sure how should I proceed after this, could you please share the R code for ggbiplot.