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PCoA plot with phyla abundance

Hi,

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

enter image description here

Thanks

r vegan phyloseq
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written by Bioinfonext 48

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)

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written by Ram 4.5K

ok, sorry for that,

I have changed above image link.

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written by Bioinfonext 48

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.

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written by Ram 4.5K

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

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written by Asaf 1.0K

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

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written by Bioinfonext 48

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.

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written by Bioinfonext 48

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