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If you want to analyse another variable here, go back to the previous section, choose another variable and re-run the code from that point.

Choose the taxonomic level you want to plot (Choose from Phylum, Class, Order, Family, Genus, Species). This applies to both the heatmaps and B&W plots below.

taxgroup <- "Order"

Heatmaps

This section contains heatmaps for each taxonomic level (class - species) for your selected variable. The number in each cell is the relative proportion (in %) of taxa per group.

There are a variety of attributes you can modify:

Note the tax_show = 10 attribute. This says to show the top 10 taxa.

The plot_values_size = defines the size of the text in the heatmap cells.

The tax_add = NULL adds an additional taxonomic group to the taxa names (e.g. changing this to tax_add = "Phylum" and plotting Genus will name the taxa as 'phylum:genus' but leaving it as tax_add = NULL will just give the genus name.

showRemainingTaxa = T will aggregate, in a single row, the remaining taxa not shown on this heatmap. Change to F if you don't want to see this.

color_vector = NULL uses the default colour range (orange -> blue). You can change this by providing your own colour range, e.g. color_vector = c("red", "green"). You can choose from the huge number of R colours here: http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf

Generate the plot:

p <- amp_heatmap(ampvisdata, tax_show = 10, plot_values_size = 4, tax_add = NULL, showRemainingTaxa = T, color_vector = NULL, group_by = group, tax_aggregate = taxgroup, tax_empty = "remove")
p

Add some additional plot modifications. Change or remove these as desired (or add your own modifications)

p <- p +
theme_bw() +
theme(text = element_text(size = 18), axis.text.x = element_text(angle = 90, size=16), axis.text.y = element_text(size=14)) +
labs(y = taxgroup)
p

Export as pdf and tiff

tiff_exp <- paste0("community_tax_abund_heatmap_", group, "_", 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_heatmap_", group, "_", taxgroup, "_samples_.pdf")
ggsave(file = pdf_exp, device = "pdf", plot = p, width = 20, height = 20, units = "cm")

Box and whisker plots

This section contains B&W plots for each taxonomic level (class - species) for your selected variable. This is similar to the heatmaps you generated in section 6, but separates the B&W into groups per variable, thus enabling an examination of how the variable groups differ in terms of taxonomic abundance.

Again, there are a variety of attributes you can modify:

Note the tax_show = 7 attribute. This says to show the top 7 taxa (Tip: to look at specific taxa you can provide a vector of taxa names, e.g. tax_show = c("Bacteroidales", "Fibrobacterales")).

The tax_add = NULL adds an additional taxonomic group to the taxa names (e.g. changing this to tax_add = "Phylum" and plotting Genus will name the taxa as 'phylum:genus' but leaving it as tax_add = NULL will just give the genus name.

Generate the plot:

p <- amp_boxplot(ampvisdata, tax_show = 7, tax_add = NULL, tax_aggregate = taxgroup, tax_empty = "remove", group_by = group)
p

You can change additional properties of the plot here:

p$mapping$fill <- as.name(".Group")
p <- p + theme_bw() +
scale_color_manual(values=c("Red", "Green", "Blue")) + scale_fill_manual(values=c("Red", "Green", "Blue")) +
labs(fill = group, x = taxgroup) +
theme(text = element_text(size = 18), axis.text.x = element_text(size=18), axis.text.y = element_text(size=16)) +
guides(color = "none")
p

Export as pdf and tiff

tiff_exp <- paste0("community_tax_abund_BW_", group, "_", 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_", group, "_", taxgroup, "_samples_.pdf")
ggsave(file = pdf_exp, device = "pdf", plot = p, width = 20, height = 20, units = "cm")