nouvelles stats familly obésité

202111_Obesite/report_Obesite.Rmd

@@ -452,7 +452,7 @@ levels = correct.order)
 
 p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Family",numberOfTaxa = 30, fill = "Family")
 p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)
-
+p <- p + ggtitle("Family Composition")+  theme(axis.text.x = element_blank())   
 plot(p)
 
 ```
@@ -652,6 +652,47 @@ filter(data.phylum, Family == "Alcaligenaceae") %>%
   dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh")
 ```
 
+Dunn Post-Hoc test sur le résultat Kruskall-Wallis de l'impact de `Group` sur les abondances Christensenellacaea
+
+```{r Post-Hoc test Christensenellacaea, eval=TRUE}
+
+filter(data.phylum, Family == "Christensenellaceae") %>% 
+  dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh")
+```
+
+Dunn Post-Hoc test sur le résultat Kruskall-Wallis de l'impact de `Group` sur les abondances Chlostridiaceae
+
+```{r Post-Hoc test Chlostridiaceae, eval=TRUE}
+
+filter(data.phylum, Family == "Clostridiaceae 1") %>% 
+  dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh")
+```
+
+Dunn Post-Hoc test sur le résultat Kruskall-Wallis de l'impact de `Group` sur les abondances Enterocccaceae
+
+```{r Post-Hoc test Enterocccaceae, eval=TRUE}
+
+filter(data.phylum, Family == "Enterobacteriaceae") %>% 
+  dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh")
+```
+
+Dunn Post-Hoc test sur le résultat Kruskall-Wallis de l'impact de `Group` sur les abondances Lactobacillaceae
+
+```{r Post-Hoc test Lactobacillaceae, eval=TRUE}
+
+filter(data.phylum, Family == "Lactobacillaceae") %>% 
+  dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh")
+```
+
+Dunn Post-Hoc test sur le résultat Kruskall-Wallis de l'impact de `Group` sur les abondances Peptostreptococcaceae
+
+```{r Post-Hoc test Peptostreptococcaceae, eval=TRUE}
+
+filter(data.phylum, Family == "Peptostreptococcaceae") %>% 
+  dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh")
+```
+
+
 ### Zoom au niveau Family dans chacun des Phylums {.tabset}  
 
 Les 4 phylums d'intérêts sont les Actinobacteriota, les Bacteroidota, les Desulfobacterota, les Fibrobacterota, les Firmicutes et les Proteobacteria.
@@ -723,6 +764,17 @@ p <- p + ggtitle("Composition within Firmicutes")
 plot(p)
 ```
 
+```{r 17bis-composition-firmicutes,fig.width=9,fig.height=5, eval=TRUE}
+
+p <- plot_composition(frogs.data, "Phylum", "Firmicutes", "Family",numberOfTaxa = 15, fill = "Family")
+p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)+
+    theme(strip.text.x = element_text(size = 14, color = "black"))  +
+      scale_y_continuous(label = scales::percent)+  theme(axis.text.x = element_blank())
+p <- p + ggtitle("Composition within Firmicutes")
+plot(p)
+```
+
+
 ```{r 18-composition-Firmicutes merged,fig.width=6,fig.height=5, eval=TRUE}
 frogs.data.merged<-merge_samples(frogs.data,group="Group")
 sample_data(frogs.data.merged)$Group <- sample_names(frogs.data.merged)