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This will provide you a summary of sequence reads per sample (minimum, maximum, average, etc) and the number and percentage of ASVs resolved to each taxonomic level.

6b. Taxonomic abundance bar plots

This section generates stacked bar plots showing the proportion of taxa per sample, for each taxonomic level.

First, you can output the raw ASV abundance data as a csv file. You can add this as supplemental data to a manuscript or use it in other plotting or statistical programs:

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tiff_exp <- paste0("community_tax_abund_bar_plot_", taxgroup, "_samples_.tiff")
ggsave(file = tiff_exp, dpi = 300, compression = "lzw", device = "tiff", plot = p, width = 20, height = 20, units = "cm")
pdf_exp <- paste0("community_tax_abund_bar_plot_", taxgroup, "_samples_.pdf")
ggsave(file = pdf_exp, device = "pdf", plot = p, width = 20, height = 20, units = "cm")

6c. Taxonomic abundance box and whisker plots

This section contains box and whisker plots for each taxonomic level (phylum … species).

As with the bar plots in the previous section, these B&W plots show the relative abundance (in %) of taxa. But whereas heatmaps show the mean %, box and whisker plots show the interquartile range between samples (max, min, median, quartiles), thus providing additional statistical information.

Choose the taxonomic level you want to plot (Choose from Phylum, Class, Order, Family, Genus, Species)

taxgroup <- "Order"

Generate the plot (and modify the attributes as you like)

Note the tax_show = 10 attribute. This says to show the top 10 taxa. Change this as desired.

p <- amp_boxplot(ampvisdata, tax_aggregate = taxgroup, tax_empty = "remove", tax_show = 10) +
theme_bw() +
theme(text = element_text(size = 18), axis.text.x = element_text(size=16), axis.text.y = element_text(size=14)) +
labs(x = taxgroup)
p

Export the plots as tiff and pdf:

tiff_exp <- paste0("community_tax_abund_BW_plot_", taxgroup, "_samples_.tiff")
ggsave(file = tiff_exp, dpi = 300, compression = "lzw", device = "tiff", plot = p, width = 20, height = 20, units = "cm")
pdf_exp <- paste0("community_tax_abund_BW_plot_", taxgroup, "_samples_.pdf")
ggsave(file = pdf_exp, device = "pdf", plot = p, width = 20, height = 20, units = "cm")

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