Taxonomic Analysis
We want to know how many genera in the Order Enterobacteriaceae there are sequences for in the Greengenes 85% OTU database as well as how many sequences are assigned to each genera. We will first create a dataframe with the desired information then a plot to summarize the results.
## Per genus count data
gamma_df <- gamma_16S$taxa %>%
group_by(Genus) %>%
summarise(Count = n()) %>%
ungroup() %>%
mutate(Genus = fct_reorder(Genus, Count))
## Count info for text
total_otus <- sum(gamma_df$Count)
no_genus_assignment <- gamma_df$Count[gamma_df$Genus == "g__"]
escherichia_count <- gamma_df$Count[gamma_df$Genus == "g__Escherichia"]
## excluding unassigned genera and genera with only one assigned sequence
gamma_trim_df <- gamma_df %>% filter(Genus != "g__", Count > 1)For the Greengenes database there are a total of 247 OTUs assigned to 56 genera in the Class Gammaproteobacteria. The number of OTUs assigned to specific genera, range from 76 to 1 @ref(fig:generaCount). As this database is preclustered to 85% similarity the number of OTUs per genus is more of an indicator of genera diversity than how well the genera is represented in the database. For example no sequences present in the database are assigned to the genus Shigella and only 1 are assigned to Escherichia. OTUs only assigned to the family, g__, is the most abundant group, 154, many of which are likely from these two genera. Next we will use the phylogenetic information to evaluate this assumption.
ggplot(gamma_trim_df) +
geom_bar(aes(x = Genus, y = Count), stat = "identity") +
labs(y = "Number of OTUs") +
coord_flip() +
theme_bw() 
Number of seqeunces assigned to genera in the Class Gammaproteobacteria. Only Genera with more than one assigned sequence are shown.
