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

@@ -106,6 +106,7 @@ Now lets save our results, so that we can use them again later without having to
 Now that we have these outputs, we need to make them useful! One way to do that is to use the R package phyloseq, which will integrate all kinds of fun things. You can check out the phyloseq/DADA2 interaction on the DADA2 website: https://benjjneb.github.io/dada2/tutorial.html
 
 For now though, we're just going to use a (relatively) simple plotting function to inspect the sequence diversity in our samples. If you get bored you can try and puzzle through what the plot function is doing and start changing things. But if you're not bothered, you still get some nice plots :) 
+Like I said at the beginning, installation of DADA2 wasn't easy, and so in this R installation we don't get plots appearing on screen, we have to write them to file and look at them separately. I know. 
 
     library(ggplot2)
     library(reshape2)
@@ -139,4 +140,12 @@ For now though, we're just going to use a (relatively) simple plotting function
         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: 
+
+    $ atril Marmic-amplicon-plot.pdf
+
+to view it. Happy plotting!