nouvelles stats family

202111_Obesite/report_Obesite.Rmd

@@ -211,6 +211,7 @@ p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Phylum",numberOfTaxa =
 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("Phylum Composition")
 
 plot(p)
 ```
@@ -315,7 +316,7 @@ sample_data(frogs.data.2)$Group <- factor(sample_data(frogs.data.2)$Group, label
 my.palette <- c("#FC8385", "#71C749", "#55CDD3", "#f7dc6f")
                                                        
 p1 <- plot_composition(frogs.data.2 , 
-                      "Kingdom", "Bacteria", "Phylum", fill = "Phylum", facet_grid = "~Group", x = "Name", numberOfTaxa = 6) + 
+                      "Kingdom", "Bacteria", "Phylum", fill = "Phylum", facet_grid = "~Group", x = "Name", numberOfTaxa = 5) + 
   scale_fill_manual(name = NULL, values = my.palette) + 
   scale_color_manual(name = NULL, values = my.palette) + 
   theme(legend.position = "bottom", axis.text.x = element_blank())+
@@ -425,11 +426,38 @@ levels = correct.order)
 
 p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Family",numberOfTaxa = 10, fill = "Family")
 p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)
+p <- p + ggtitle("Family Composition")
+plot(p)
+
+```
+
+```{r 06.2-composition-phylum,fig.width=10,fig.height=5, eval=TRUE}
+correct.order <- c("STDD-H2O","HFD-H2O","HFD-AB")
+sample_data(frogs.data)$Group <- factor(sample_data(frogs.data)$Group,
+levels = correct.order)
+
+
+p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Family",numberOfTaxa = 20, fill = "Family")
+p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)
+
+plot(p)
+
+```
+
+```{r 06.3-composition-phylum,fig.width=10,fig.height=5, eval=TRUE}
+correct.order <- c("STDD-H2O","HFD-H2O","HFD-AB")
+sample_data(frogs.data)$Group <- factor(sample_data(frogs.data)$Group,
+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)
 
 plot(p)
 
 ```
 
+
 ```{r 07-composition-family merged,fig.width=6,fig.height=5, eval=TRUE}
 frogs.data.merged<-merge_samples(frogs.data,group="Group")
 sample_data(frogs.data.merged)$Group <- sample_names(frogs.data.merged)
@@ -593,6 +621,36 @@ filter(data.phylum, Family == "Streptococcaceae") %>%
   dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh")
 ```
 
+Dunn Post-Hoc test sur le résultat Kruskall-Wallis de l'impact de `Group` sur les abondances Erysipelotrichaceae
+
+```{r Post-Hoc test Erysipelotrichaceae, eval=TRUE}
+
+filter(data.phylum, Family == "Erysipelotrichaceae") %>% 
+  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 Bifidobacteriaceae
+
+```{r Post-Hoc test Bifidobacteriaceae, eval=TRUE}
+
+filter(data.phylum, Family == "Bifidobacteriaceae") %>% 
+  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 Coriobacteriaceae
+
+```{r Post-Hoc test Coriobacteriaceae, eval=TRUE}
+
+filter(data.phylum, Family == "Coriobacteriaceae") %>% 
+  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 Alcaligenaceae
+
+```{r Post-Hoc test Alcaligenaceae, eval=TRUE}
+
+filter(data.phylum, Family == "Alcaligenaceae") %>% 
+  dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh")
+```
 
 ### Zoom au niveau Family dans chacun des Phylums {.tabset}  
 
@@ -609,7 +667,7 @@ p <- plot_composition(frogs.data, "Phylum", "Actinobacteria", "Family",numberOfT
 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 Actinobacteria")
 plot(p)
 ```
 
@@ -635,7 +693,7 @@ p <- plot_composition(frogs.data, "Phylum", "Bacteroidetes", "Family",numberOfTa
 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 Bacteroidetes")
 plot(p)
 ```
 
@@ -647,7 +705,7 @@ correct.order <- c("STDD-H2O","HFD-H2O","HFD-AB")
 sample_data(frogs.data.merged)$Group <- factor(sample_data(frogs.data.merged)$Group,
 levels = correct.order)
 
-p <- plot_composition(frogs.data.merged, "Phylum", "Bacteroidetes", "Family",numberOfTaxa = 5, fill = "Family")
+p <- plot_composition(frogs.data.merged, "Phylum", "Bacteroidetes", "Family",numberOfTaxa = 10, fill = "Family")
 p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1) +  theme(axis.text.x = element_blank())   
 plot(p)
 
@@ -657,11 +715,11 @@ plot(p)
 
 ```{r 17-composition-firmicutes,fig.width=9,fig.height=5, eval=TRUE}
 
-p <- plot_composition(frogs.data, "Phylum", "Firmicutes", "Family",numberOfTaxa = 5, fill = "Family")
+p <- plot_composition(frogs.data, "Phylum", "Firmicutes", "Family",numberOfTaxa = 10, 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)
 ```
 
@@ -673,7 +731,7 @@ correct.order <- c("STDD-H2O","HFD-H2O","HFD-AB")
 sample_data(frogs.data.merged)$Group <- factor(sample_data(frogs.data.merged)$Group,
 levels = correct.order)
 
-p <- plot_composition(frogs.data.merged, "Phylum", "Firmicutes", "Family",numberOfTaxa = 5, fill = "Family")
+p <- plot_composition(frogs.data.merged, "Phylum", "Firmicutes", "Family",numberOfTaxa = 10, fill = "Family")
 p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1) +  theme(axis.text.x = element_blank())   
 plot(p)
 
@@ -683,11 +741,11 @@ plot(p)
 
 ```{r 19-composition-proteobacteria,fig.width=9,fig.height=5, eval=TRUE}
 
-p <- plot_composition(frogs.data, "Phylum", "Proteobacteria", "Family",numberOfTaxa = 5, fill = "Family")
+p <- plot_composition(frogs.data, "Phylum", "Proteobacteria", "Family",numberOfTaxa = 10, 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 Proteobacteria")
 plot(p)
 ```