Practical-3-Processing-16S-rRNA-amplicon-data.md

@@ -140,11 +140,14 @@ Like I said at the beginning, installation of DADA2 wasn't easy, and so in this
         theme_classic() +
         theme(axis.text.x=element_text(angle=45, hjust=1))
     }
-    pdf("Marmic-amplicon-plot.pdf")
-    plotTaxon(seqtab.nochim, taxa, "Bacteroidetes", 0.01, "Genus")
-    dev.off()
 
-Once you have your plot, you can open a new terminal and run: 
+So the bit above creates the function called `plotTaxon()`, which we can then use to generate the plots. We're going to create a pdf of the plot by first opening a pdf file with the `pdf()` command, then run the `plotTaxon()` function, then switch off the plotting device.
+
+    > pdf("Marmic-amplicon-plot.pdf")
+    > plotTaxon(seqtab.nochim, taxa, "Bacteroidetes", 0.01, "Genus")
+    > dev.off()
+
+Once you have your plot, you can open a new terminal (don't quit R because we will want to create different plots for different taxa - just change the file name for the pdf) and run: 
 
     $ atril Marmic-amplicon-plot.pdf