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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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PCoA Graphs #1139

Closed GlycineMax closed 3 years ago

GlycineMax commented 4 years ago

Hello, are there any scripts to build PCoA graphs using data from DADA2?

Could we integrate MicrobeR after DADA2? PCoA(METRIC="braycurtis", METADATA=experiment_metadata, FEATURES=otutable, TREE=ggtree, COLOR="Time", SHAPE="Group", SUBSAMPLE=TRUE, AXIS=c(1,2))

Thank you!

benjjneb commented 4 years ago

The tutorial demonstrates importing DADA2 ASV/taxonomy information into phyloseq, and then using phyloseq to perform and plot ordinations: https://benjjneb.github.io/dada2/tutorial.html#bonus-handoff-to-phyloseq

But you can integrate DADA2 output into any other microbiome analysis/viz package just as long as you understand how to hand the DADA2 objects (sequence table: numeric matrix, taxonomy table: character matrix) to that package correctly.