Update analysis.R

files/analysis.R

@@ -59,13 +59,17 @@ biom_metagenome
 # phylum, class, order, family, genus, species.
 
 # We can view the otu_table with:
-View(biom_metagenome@tax_table)
+View(biom_metagenome@otu_table)
 # This will open a view of the table in the same pane as your script.
 
-# This table has the OTU identity in the row names and the samples in the 
+# This table has the OTU identity in the row names and the samples in the
 # columns. The values in the columns are the abundance of that OTU in that
 # sample.
 
+# We can view the tax_table with:
+View(biom_metagenome@tax_table)
+# This gives the rank for each taxa
+
 # k__ kingdom/domain (note a letter, two underscores)
 # p__ phylum
 # c__ class
@@ -449,4 +453,4 @@ abundance_of_taxa_wide %>%
 # guessed from that graph that Proteobacteria had a higher relative abundance in 
 # one sample than the other, because the bars were very large. But we probably 
 # wouldn't have been able to tell which sample Chlamydiae was more abundant in - 
-# its relative proportion in both is too small to see in the bar chart. 
+# its relative proportion in both is too small to see in the bar chart.