genomewalker
4/11/2016 - 1:49 PM

plot_map.R

mapWorld <- borders("world", colour="#0a0c2a", fill="#0a0c2a") # create a layer of borders
    myPalette <- colorRampPalette((brewer.pal(11, "Spectral")))
    sc <- scale_colour_gradientn(colours = myPalette(100))
    mapWorld <- borders("world", colour="#0a0c2a", fill="#0a0c2a") # create a layer of borders
    
    zp1 <- ggplot(all_edges) + mapWorld  # Pretty simple plot code
    zp1 <- zp1 + geom_path(aes(x = y, y = x, group = Group,  # Edges with gradient
                               colour = Similarity, size = -Sequence/20000000))  # and taper
    zp1 <- zp1 + scale_size(range = c(1, 5), guide = "none")  # Customize taper
    zp1 <- zp1 + scale_colour_gradientn(colours = ( myPalette(100)), name="dissimilarity")
    
    zp1 <- zp1 + theme(panel.background = element_rect(fill = "white", colour = "black"), 
                       panel.grid.major = element_blank(),
                       panel.grid.minor = element_blank(),
                       axis.ticks = element_blank(), 
                       axis.text.x = element_text (size = 12, vjust = 0), 
                       axis.text.y = element_text (size = 12, hjust = 1.3)) + 
      coord_cartesian() + 
      labs(y="",x="") 
    zp1 <- zp1+ scale_fill_gradientn(colours = rev(viridis(256)))
    
    zp1<-zp1 + geom_point(data = metadata ,  
                          aes(x = longitude, y = latitude, fill = eigcent, size = eigcent), shape = 21) # Customize gradient v
    zp1 <- zp1 + theme_bw() + coord_equal(ratio=1) + theme(legend.position="right") +
      xlab("") + ylab("") + scale_x_continuous(breaks=c(-100,0,100)) +
      ggtitle(bquote(atop(.(name), atop(italic(.(name)), "")))) #