Commit 70bbcdf9 authored by Magali Monnoye's avatar Magali Monnoye
Browse files

nouvelles stats familly obésité

parent 835947fa
...@@ -452,7 +452,7 @@ levels = correct.order) ...@@ -452,7 +452,7 @@ levels = correct.order)
p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Family",numberOfTaxa = 30, fill = "Family") p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Family",numberOfTaxa = 30, fill = "Family")
p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1) p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)
p <- p + ggtitle("Family Composition")+ theme(axis.text.x = element_blank())
plot(p) plot(p)
``` ```
...@@ -652,6 +652,47 @@ filter(data.phylum, Family == "Alcaligenaceae") %>% ...@@ -652,6 +652,47 @@ filter(data.phylum, Family == "Alcaligenaceae") %>%
dunn.test::dunn.test(x = .$Abundance, g = .$Group, method = "bh") 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} ### 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. 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") ...@@ -723,6 +764,17 @@ p <- p + ggtitle("Composition within Firmicutes")
plot(p) 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} ```{r 18-composition-Firmicutes merged,fig.width=6,fig.height=5, eval=TRUE}
frogs.data.merged<-merge_samples(frogs.data,group="Group") frogs.data.merged<-merge_samples(frogs.data,group="Group")
sample_data(frogs.data.merged)$Group <- sample_names(frogs.data.merged) sample_data(frogs.data.merged)$Group <- sample_names(frogs.data.merged)
......
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