Updated intermediate R data visualization materials

intermediate-r-data-visualization/2. nucleotide_resolution.R

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+library(ggplot2)
+
+#Following library will be used to reformat data for plotting.
+library(reshape2)
+
+#Load the data for plotting.
+load("nucleotide_resolution.RData")
+
+#Open a pdf file for plotting.
+pdf("Nucleotide_resolution.pdf")
+
+#Loop through all genes.
+for (i in 1:length(dat)) {
+  
+  #Get data for this gene.
+  this_dat <- dat[[i]]
+  
+  #Reformat data for plotting.
+  this_dat <- melt(this_dat, id.vars = "Position")
+  
+  #Store the plot in a variable.
+  p <- ggplot(this_dat, aes(x = Position, y = value)) +
+    geom_bar(stat = "identity") +
+    facet_grid(variable ~ .)+
+    scale_y_continuous(breaks = c(0, 0.5, 1))+
+    ylab("Signal")+
+    annotate(geom = "rect",
+             xmin = to_annotate$Start[i],
+             xmax = to_annotate$End[i], 
+             ymin = -Inf,
+             ymax = Inf, fill = "red",
+             color = NA, 
+             alpha = 0.3) +
+    ggtitle(names(dat)[i])
+  
+  #Print plot to file.
+  print(p)
+}
+
+#Close file.
+dev.off()