Commit d41f423e authored by magali's avatar magali
Browse files

corrections caec

parent 6c6a4040
Pipeline #44223 passed with stage
in 3 minutes and 38 seconds
......@@ -551,7 +551,8 @@ p3 <- p3 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test",
#Select groups
frogs.data_cinq <- subset_samples(frogs.data, Group %in% c("S-A_Caec","A_Caec"))
#Select groups
frogs.data_cinq <- subset_samples(frogs.data, Group %in% c("S-AG_Caec","AG_Caec"))
## Select only some families
families <- c("Atopobiaceae","Bacteroidaceae", "Bifidobacteriaceae", "Desulfovibrionaceae","Lachnospiraceae" , "Marinifilaceae", "Prevotellaceae", "Rikenellaceae","Ruminococcaceae", "Tannerellaceae")
......@@ -561,7 +562,7 @@ phy <- frogs.data_cinq %>% subset_taxa(Family %in% families) %>% tax_glom(taxran
depth <- sample_sums(frogs.data_cinq)[1]
plotdata<-psmelt(phy) %>%
mutate(Abundance = Abundance / depth,
Group = factor(Group, labels = c("S-A_Caec","A_Caec")))
Group = factor(Group, labels = c("S-AG_Caec","AG_Caec")))
p4 <- ggplot(plotdata,aes(x = Group,y=Abundance, color = Group, Group = Group)) +
stat_boxplot(geom = "errorbar", width = 0.5) +
......@@ -581,7 +582,6 @@ p4 <- p4 + stat_compare_means(aes(label = ..p.signif..), method = "wilcox.test",
fontface = "bold")
plot_grid(p3, p4, ncol = 1)
```
#### Kruskal test
......
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