Figure 3B BB Ordinate

Load packages

library("ampvis")

Load data

data(DNAext_1.0)

Subset to the bead-beating related samples and rarefy

bb_time <- subset_samples(V13, Exp.beadbeating == "YES" | (Exp.time == "YES" & Date != "2012-10-31")) %>% 
  rarefy_even_depth(sample.size = 25000, rngseed = 712) %>%
  filter_taxa(function(x) max(x) >= 10, TRUE)

Figure 3B: Bead beating compared with time

amp_ordinate(data = bb_time, 
             plot.color.order = c("20s4ms","20s6ms","80s4ms","40s6ms","80s6ms","160s6ms","400s6ms"),
             plot.color = "Beadbeating", 
             plot.point.size = 2,
             plot.theme = "clean",
             plot.shape = "Date"
             ) +
  scale_shape_discrete(name = "Sampling date", 
                       labels=c("12-10-17","12-10-31","12-11-14", 
                                "12-12-12","13-01-16","13-03-25")) +
  scale_color_discrete(name = "Bead beating", 
                       labels=c("  20s at 4m/s","  20s at 6m/s","  80s at 4m/s",
                                "  40s at 6m/s","  80s at 6m/s","160s at 6m/s","400s at 6m/s")) +  
  theme(axis.text = element_blank(),
        legend.key.height = unit(3, "mm"),
        legend.key = element_blank()
        )

Save the plot

ggsave("plots/Fig1B.eps", width = 95, height = 70, units = "mm")