Warning message: In estimate_richness(physeq, split = TRUE, measures = measures) : The data you have provided does not have any singletons. This is highly suspicious. Results of richness estimates (for example) are probably unreliable, or wrong, if you have already trimmed low-abundance taxa from the data. We recommended that you find the un-trimmed data and retry.

Table Phylum prevalence (raw data) <br><br> Phylum id <br> Column 1 = Media read counts per Phylum <br> Column 2 = Total counts per Phylum <br> Column 3 = Proportion of taxa per samples (Column 2 / samples number) <br><br><br> Quality filtering and data wrangling <br><br> Sample and Taxas that met the following filters were retained for further analysis. <br><br> 1) Phylum with n total counts number equal or above 5. <br> 2) Taxa mean read_counts n equal or above 1e-5. <br> 3) Taxa total read_counts above n (n=2) in at least 10% of the samples. <br> 4) Samples with >= 100 reads. <br> 4.2) Rarefaction by minimal sum sample (Optional). <br> 5) Taxa total read_counts above-defined prevalences threshold (5%). <br> 6) Transform count to percentage. <br> 7) Filter count under threshold (0.1%). <br> <br><br>

plot_richness(gp, x= 'Group', color = 'Group', measures = c("Observed", "Chao1", "Shannon")) + geom_boxplot() + scale_x_discrete(limits= level_order)

rarecurve(t(otu_table(physeq1)), step = 50, cex= 0.5)