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

@@ -159,11 +159,13 @@ then do the plotting :)
         theme(axis.text.x=element_text(angle=45, hjust=1))
     }
 
+    plotTaxon(seqtab.nochim, taxa, "Bacteroidetes", 0.01, "Genus")
+
 # Ignore this bit about making pdfs
 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: