Chapter 8 Diversity, bai operon and domination

8.1 Evaluate correlation of a-diversity and bai operon sum

data_ba<- asv_alpha_all %>%  
  inner_join(bai_genes_clean %>% distinct(sampleid, bai_operon_sum)) %>% 
  left_join(cohort_BAS) %>% 
  filter(ursodiol=="Y")

data_ba %>% 
ggplot(aes(x=log10(simpson_reciprocal), y=log10(bai_operon_sum+0.01)))+
  geom_point(alpha=0.6)+
  stat_cor(method="pearson")+
  geom_smooth(method="lm")+
  theme_classic()+
  ylab("bai operon log10(cpm)")+
  xlab("a-diversity")

8.2 Identify patients with monodomination by 16S

#create dataset with asv
samples_asv<-cohort_BAS %>% 
  filter(later=="Y") %>% 
  select(sampleid) %>% 
  inner_join(counts_samples %>% 
               select(sampleid, asv_key, count, count_total)) %>% 
  inner_join(asv_annotation_blast_ag %>% 
               select(asv_key, kingdom, phylum, class, ordr, family, genus)) %>%
  mutate(relab=count/count_total) %>% 
  group_by(sampleid, genus)

pathogens_pre<- samples_asv %>% 
  filter(genus=="Enterococcus"|genus=="Streptococcus"|phylum=="Proteobacteria") %>% 
  mutate(enterococcus=ifelse(genus=="Enterococcus", relab, 0)) %>% 
  mutate(streptococcus=ifelse(genus=="Streptococcus", relab, 0)) %>% 
  mutate(proteobacteria=ifelse(phylum=="Proteobacteria", relab, 0)) %>% 
  mutate(enterococcus_dom=ifelse(enterococcus>=0.3, "Y", "N")) %>% 
  mutate(streptococcus_dom=ifelse(streptococcus>=0.3, "Y", "N")) %>% 
   mutate(proteobacteria_dom=ifelse(proteobacteria>=0.3, "Y", "N")) %>% 
  mutate(any_dom=ifelse(enterococcus_dom=="Y"|streptococcus_dom=="Y"|proteobacteria_dom=="Y", "Y", "N")) %>% 
  group_by(sampleid) %>% 
  arrange(desc(any_dom)) %>% slice(1)

8.3 Domination and a-diversity

pathogens_pre %>% inner_join(asv_alpha_all) %>% 
  ggplot(aes(x=any_dom, y=simpson_reciprocal, color=any_dom))+
   geom_boxplot(width=0.2, lwd=0.8, outlier.shape = NA) +
  geom_jitter(width=0.3, alpha=0.3, size=2.5)+
  ylab("log10(a-div)")+
  xlab("domination")+
  theme_classic()+
  stat_compare_means(comparisons=list(c("Y", "N")),
                     method="wilcox.test",
                     correct=FALSE)+
  scale_color_manual(values=c("turquoise4","darkviolet"))+
  theme(legend.position="none")

8.4 Domination and bai operon

pathogens_pre %>% inner_join(bai_genes_clean %>% distinct(sampleid, bai_operon_sum)) %>% 
  ggplot(aes(x=any_dom, y=log10(bai_operon_sum+0.01),  color=any_dom))+
   geom_boxplot(width=0.2, lwd=0.8, outlier.shape = NA) +
  geom_jitter(width=0.3, alpha=0.3, size=2.5)+
  ylab("log10(bai sum)")+
  xlab("domination")+
  theme_classic()+
  stat_compare_means(comparisons=list(c("Y", "N")),
                     method="wilcox.test",
                     correct=FALSE)+
  scale_color_manual(values=c("turquoise4","darkviolet"))+
  theme(legend.position="none")

8.5 SBAs and domination

pathogens_pre %>% inner_join(later_pools_final) %>% 
  ggplot(aes(x=any_dom, y=log10(secondary_nonUDCA), color=any_dom))+
   geom_boxplot(width=0.2, lwd=0.8, outlier.shape = NA) +
  geom_jitter(width=0.3, alpha=0.3, size=2.5)+
  ylab("log10(SBAs*)")+
  xlab("domination")+
  theme_classic()+
  stat_compare_means(comparisons=list(c("Y", "N")),
                     method="wilcox.test",
                     correct=FALSE)+
  scale_color_manual(values=c("turquoise4","darkviolet"))+
  theme(legend.position="none")