Aditional undesired sample
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sanrrone • 0
@sanrrone-10054
Last seen 5.7 years ago

 

Hi, doing the tutorial in plot_ordination examples, everything works, I can plot the GlobalPatterns data with plot_ordination, but in the example 3, specifically with biplot, additional figures, shape, and color appear named Samples (see this image https://www.dropbox.com/s/r3dtvh65io5a1yp/Rplot.png?dl=0). This occur with tutorial or not data. the code that I use was:

data(GlobalPatterns)
GP<-GlobalPatterns

wh0<-genefilter_sample(GP, filterfun_sample(function(x) x > 5), A = 0.5 * nsamples(GP))

GP1<- prune_taxa(wh0, GP)

phylum.sum = tapply(taxa_sums(GP1), tax_table(GP1)[, "Phylum"], sum, na.rm = TRUE)
top5phyla = names(sort(phylum.sum, TRUE))[1:5]
GP1 = prune_taxa((tax_table(GP1)[, "Phylum"] %in% top5phyla), GP1)
GP1 = transform_sample_counts(GP1, function(x) 1e+06 * x/sum(x))
GP.ord <- ordinate(GP1, "NMDS", "bray")

plot_ordination(GP1, GP.ord, type = "biplot", color = "Class", shape = "Phylum", title = "Biplot")

Thanks in advance

phyloseq • 664 views
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Entering edit mode
sanrrone • 0
@sanrrone-10054
Last seen 5.7 years ago

I'm wrong everything is ok, the additional samples must be in the graph.

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