Figure 3A Relative Beadbeating Heatmap

Load packages

library("ampvis")

Load data

data(DNAext_1.0)

Subset to the bead-beating related samples and normalise sample counts

bbn <- subset_samples(V13,Exp.beadbeating == "YES") %>%
  transform_sample_counts(function(x) x / sum(x) * 100)

Figure 3A: Relative bead beating

amp_heatmap(data = bbn,
            group = "Beadbeating",
            tax.aggregate = "Phylum",
            tax.empty = "remove",
            tax.class = "p__Proteobacteria",
            order.x = c("20s4ms","20s6ms","80s4ms","40s6ms","80s6ms","160s6ms","400s6ms"),
            order.y = "400s6ms",            
            plot.colorscale = "log10",
            plot.breaks = c(2,5,10,20), 
            scale.seq = 100,
            tax.show = 11,
            plot.text.size = 2,
            plot.theme = "clean"
            ) + 
  scale_x_discrete(labels = c("20s\n4m/s","20s\n6m/s","80s\n4m/s","40s\n6m/s",
                              "80s\n6m/s","160s\n6m/s","400s\n6m/s")) +
  theme(axis.text.x = element_text(angle = 0, hjust = 0.4, size = 8, color = "black"))

Save the plot

ggsave("plots/Fig3A.eps", width = 90, height = 70, units = "mm")