Commit 3bb3619d authored by magali's avatar magali
Browse files

nouvelles stats family

parent 0a9e41b4
Pipeline #47882 passed with stage
in 3 minutes and 50 seconds
...@@ -211,6 +211,7 @@ p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Phylum",numberOfTaxa = ...@@ -211,6 +211,7 @@ p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Phylum",numberOfTaxa =
p<- p + facet_wrap(~Group, scales = "free_x", nrow = 1) + p<- p + facet_wrap(~Group, scales = "free_x", nrow = 1) +
theme(strip.text.x = element_text(size = 14, color = "black")) + theme(strip.text.x = element_text(size = 14, color = "black")) +
scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank()) scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank())
p <- p + ggtitle("Phylum Composition")
plot(p) plot(p)
``` ```
...@@ -315,7 +316,7 @@ sample_data(frogs.data.2)$Group <- factor(sample_data(frogs.data.2)$Group, label ...@@ -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") my.palette <- c("#FC8385", "#71C749", "#55CDD3", "#f7dc6f")
p1 <- plot_composition(frogs.data.2 , 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_fill_manual(name = NULL, values = my.palette) +
scale_color_manual(name = NULL, values = my.palette) + scale_color_manual(name = NULL, values = my.palette) +
theme(legend.position = "bottom", axis.text.x = element_blank())+ theme(legend.position = "bottom", axis.text.x = element_blank())+
...@@ -425,11 +426,38 @@ levels = correct.order) ...@@ -425,11 +426,38 @@ levels = correct.order)
p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Family",numberOfTaxa = 10, fill = "Family") p <- plot_composition(frogs.data, "Kingdom", "Bacteria", "Family",numberOfTaxa = 10, 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")
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) plot(p)
``` ```
```{r 07-composition-family merged,fig.width=6,fig.height=5, eval=TRUE} ```{r 07-composition-family 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)
...@@ -593,6 +621,36 @@ filter(data.phylum, Family == "Streptococcaceae") %>% ...@@ -593,6 +621,36 @@ filter(data.phylum, Family == "Streptococcaceae") %>%
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 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} ### Zoom au niveau Family dans chacun des Phylums {.tabset}
...@@ -609,7 +667,7 @@ p <- plot_composition(frogs.data, "Phylum", "Actinobacteria", "Family",numberOfT ...@@ -609,7 +667,7 @@ p <- plot_composition(frogs.data, "Phylum", "Actinobacteria", "Family",numberOfT
p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)+ p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)+
theme(strip.text.x = element_text(size = 14, color = "black")) + theme(strip.text.x = element_text(size = 14, color = "black")) +
scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank()) scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank())
p <- p + ggtitle("Composition within Actinobacteria")
plot(p) plot(p)
``` ```
...@@ -635,7 +693,7 @@ p <- plot_composition(frogs.data, "Phylum", "Bacteroidetes", "Family",numberOfTa ...@@ -635,7 +693,7 @@ p <- plot_composition(frogs.data, "Phylum", "Bacteroidetes", "Family",numberOfTa
p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)+ p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)+
theme(strip.text.x = element_text(size = 14, color = "black")) + theme(strip.text.x = element_text(size = 14, color = "black")) +
scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank()) scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank())
p <- p + ggtitle("Composition within Bacteroidetes")
plot(p) plot(p)
``` ```
...@@ -647,7 +705,7 @@ correct.order <- c("STDD-H2O","HFD-H2O","HFD-AB") ...@@ -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, sample_data(frogs.data.merged)$Group <- factor(sample_data(frogs.data.merged)$Group,
levels = correct.order) 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()) p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1) + theme(axis.text.x = element_blank())
plot(p) plot(p)
...@@ -657,11 +715,11 @@ plot(p) ...@@ -657,11 +715,11 @@ plot(p)
```{r 17-composition-firmicutes,fig.width=9,fig.height=5, eval=TRUE} ```{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)+ p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)+
theme(strip.text.x = element_text(size = 14, color = "black")) + theme(strip.text.x = element_text(size = 14, color = "black")) +
scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank()) scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank())
p <- p + ggtitle("Composition within Firmicutes")
plot(p) plot(p)
``` ```
...@@ -673,7 +731,7 @@ correct.order <- c("STDD-H2O","HFD-H2O","HFD-AB") ...@@ -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, sample_data(frogs.data.merged)$Group <- factor(sample_data(frogs.data.merged)$Group,
levels = correct.order) 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()) p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1) + theme(axis.text.x = element_blank())
plot(p) plot(p)
...@@ -683,11 +741,11 @@ plot(p) ...@@ -683,11 +741,11 @@ plot(p)
```{r 19-composition-proteobacteria,fig.width=9,fig.height=5, eval=TRUE} ```{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)+ p <- p + facet_wrap(~Group, scales = "free_x", nrow = 1)+
theme(strip.text.x = element_text(size = 14, color = "black")) + theme(strip.text.x = element_text(size = 14, color = "black")) +
scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank()) scale_y_continuous(label = scales::percent)+ theme(axis.text.x = element_blank())
p <- p + ggtitle("Composition within Proteobacteria")
plot(p) plot(p)
``` ```
......
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