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

@@ -114,9 +114,9 @@ Start by getting the full processed dada data:
     $ cp /bioinf/home/tfrancis/marmic_NGS2020/16S_amplicons/demultiplexed/seqtab_final.rds .
     $ cp /bioinf/home/tfrancis/marmic_NGS2020/16S_amplicons/demultiplexed/taxa_final.rds .
 
-Then start R (any R, doesn't matter this time)
+Then R 
 
-    $ R
+    $ /home/tfrancis/R-3.6.2/bin/R
 
 load the data:
 
@@ -159,13 +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: