Chapter 6 Shotgun metagenomic sequencing: Evaluate genes of interest (figure 5, supplement figure 10)
6.1 BSH
6.1.1 Evaluate BSH abundance at peri-GVHD onset
%>%
BSH_metalphlan left_join(cohort_BAS) %>%
filter(later=="Y") %>%
ggplot(aes(x=GI_GVHD, y=log10(cpm+0.55), color=GI_GVHD))+
geom_boxplot(width=0.2, lwd=0.8, outlier.shape = NA) +
geom_jitter(width=0.3, alpha=0.3, size=2.5)+
ylab("log10(BSH)")+
xlab("")+
theme_classic()+
stat_compare_means(comparisons=list(c("Y", "N")),
method="wilcox.test",
correct=FALSE)+
scale_color_manual(values=c("dodgerblue4", "red3"))+
theme(legend.position="none")
6.1.2 Evaluate BSH abundance at peri-engraftment time point
%>%
BSH_metalphlan left_join(cohort_BAS) %>%
filter(periengr=="Y") %>%
ggplot(aes(x=GI_GVHD, y=log10(cpm+0.05), color=GI_GVHD))+
geom_boxplot(width=0.2, lwd=0.8, outlier.shape = NA) +
geom_jitter(width=0.3, alpha=0.3, size=2.5)+
ylab("log10(BSH)")+
xlab("")+
theme_classic()+
stat_compare_means(comparisons=list(c("Y", "N")),
method="wilcox.test",
correct=FALSE)+
scale_color_manual(values=c("dodgerblue4", "red3"))+
theme(legend.position="none")
6.2 Bai operon gene
6.2.1 Evaluate correlation of bai operon gene sum and nonUDCA secondary BAs
%>%
bai_genes_clean distinct(sampleid, bai_operon_sum ) %>%
inner_join(both_conc_pools_final) %>%
ggplot(aes(x=log(secondary_nonUDCA), y=log(bai_operon_sum+0.05)))+
geom_point(alpha=0.6)+
stat_cor(method="pearson")+
geom_smooth(method="lm")+
theme_classic()+
ylab("bai operon log10(cpm)")+
xlab("SBAs* log10(pmol/mg)")
6.2.2 Bai operon gene sum in peri-GVHD onset
%>%
bai_genes_clean distinct(sampleid, bai_operon_sum ) %>%
inner_join(cohort_BAS %>% select(sampleid, GI_GVHD, later, ursodiol) %>% filter(later=="Y")) %>%
ggplot(aes(x=GI_GVHD, y=log(bai_operon_sum+0.01), color=GI_GVHD))+
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_operon_sum)") +
xlab("") +
theme_classic() +
stat_compare_means(comparisons=list(c("Y", "N")),
method="wilcox.test",
correct=FALSE)+
scale_color_manual(values=c("dodgerblue4", "red3")) +
theme(legend.position="none")
6.2.3 Bai operon individual gene abundance
%>%
bai_genes_clean inner_join(cohort_BAS %>% select(sampleid, GI_GVHD, later) %>% filter(later=="Y")) %>%
ggplot(aes(x=GI_GVHD, y=log(cpm+0.01), color=GI_GVHD))+
geom_boxplot(width=0.2, lwd=0.8, outlier.shape = NA) +
geom_jitter(width=0.3, alpha=0.3, size=2.5)+
ylab("log10(cpm)")+
xlab("")+
theme_classic()+
stat_compare_means(comparisons=list(c("Y", "N")),
method="wilcox.test",
correct=FALSE)+
scale_color_manual(values=c("dodgerblue4", "red3"))+
theme(legend.position="none")+
facet_grid(.~gene)