r spaghetti.R

Posted 2021-05-24

plotSpaghetti<-function(X){
  
  fill <- color <- "meow_realm"
  #Spaghetti plots
  colourCount = length(unique(X$meow_realm))
  getPalette = colorRampPalette(brewer.pal(9, "Set1"))
  
  g <- ggplot(X, aes(x = x, y = y, colour = meow_realm)) + 
    geom_point(aes(x = x, y = y, colour = meow_realm), 
               size = 2, data = subset(X, method == "observed")) 

  g <- g + geom_ribbon(aes(ymin = y.lwr, ymax = y.upr, 
                           fill = meow_realm, colour = NULL, group = label), 
                       alpha = 0.2, data = X)
  
  g <- g + geom_line(aes(x = x, y = y, fill = meow_realm, group = label),
                   size = 0.5, linetype=1, data = subset(X, method == "interpolated" ))
  
  g <- g + 
    geom_line(aes(x = x, y = y, fill = meow_realm, group = label),
                   size = 0.5, linetype=2, data = subset(X, method == "extrapolated" )) + 
    theme_bw() + 
    guides(col=guide_legend(nrow=2),linetype = guide_legend(title = "Method"),
           colour = guide_legend(title = "Order"), fill = guide_legend(title = "Order"),
           shape = guide_legend(title = "Site")) +
    theme(legend.position = "bottom", text = element_text(size = 8))
  
  g <- g + 
    scale_colour_manual(guide = guide_legend(title = ""),
                        values = colorRampPalette(brewer.pal(9, "Set1"))(colourCount)) +
    scale_fill_manual(guide = guide_legend(title = ""), 
                      values = colorRampPalette(brewer.pal(9, "Set1"))(colourCount)) +
    guides(fill=F) + 
    theme(legend.key = element_rect(fill = "white"))  + 
    theme(legend.position="bottom") +
    xlab("Number of sequences sampled") + 
    ylab("Species diversity") 
  
  g <- g + 
    facet_grid(order~meow_realm, scale="free") + 
    theme(legend.key.size = unit(0.5, "cm")) + 
    guides(col = guide_legend(nrow = 2, byrow = TRUE))
  
  return(g)
}


plotSpaghetti(inext_est_raw_rar %>% filter(water_depth <= 5, !is.na(meow_realm)))