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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
The text was updated successfully, but these errors were encountered:
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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
I think the problem is that taxa_level eliminate the tax_table, or I'm doing something wrong ???
Thanks
The text was updated successfully, but these errors were encountered: