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taxa_level problem #48

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cabraham03 opened this issue Aug 3, 2020 · 0 comments
Open

taxa_level problem #48

cabraham03 opened this issue Aug 3, 2020 · 0 comments

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@cabraham03
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I'm trying to make a plot to correlate the environmental variables, so I'm using the next manual:
http://userweb.eng.gla.ac.uk/umer.ijaz/projects/microbiomeSeq_Tutorial.html#intro

the problem is taxa_level, when I merge otus table at Phylum level:

physeq <- taxa_level(physeq, "Phylum")
the result file present the otu_table and sample_data, but the tax_table is absent !!!

phyloseq-class experiment-level object
otu_table() OTU Table: [ 66 taxa and 26 samples ]
sample_data() Sample Data: [ 26 samples by 7 sample variables ]

so when I try to plot

env.taxa.cor <- taxa.env.correlation(physeq, grouping_column = "Country", method = "pearson",
pvalue.threshold = 0.05, padjust.method = "BH", adjustment = 5, num.taxa = 50,
select.variables = NULL)
plot_taxa_env(env.taxa.cor)

the generated plot present the otus names as labels (left side) instead the taxon names,
the env.taxa.cor data.frame is like

     Taxa        Env  Correlation       Pvalue Type    AdjPvalue Significance
1   C1161         pH -0.444485235 1.570246e-02    T 2.774101e-01             
2   C1161         pH -0.035147154 8.046258e-01    V 8.953632e-01             
3   C1161       Temp -0.266526616 1.622375e-01    T 7.098855e-01             
4   C1161       Temp -0.247116381 7.736761e-02    V 7.098855e-01

I think the problem is that taxa_level eliminate the tax_table, or I'm doing something wrong ???
Thanks

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