Commit d40fd287 authored by magali's avatar magali
Browse files

rmd et html males corrigé

parent c55b21f6
Pipeline #44681 passed with stage
in 3 minutes and 59 seconds
...@@ -678,8 +678,17 @@ Principe courbes de rarefaction : Compter le nombre d'OTU pour un ensemble de so ...@@ -678,8 +678,17 @@ Principe courbes de rarefaction : Compter le nombre d'OTU pour un ensemble de so
```{r ggrare, message=FALSE, eval = TRUE} ```{r ggrare, message=FALSE, eval = TRUE}
p <- ggrare(frogs.data, step = 100, color = "Group", plot = FALSE) if(file.exists("frogs.data.courbes.rare_M.rds")){
p <- readRDS("frogs.data.courbes.rare_M.rds")
}else{
p <- ggrare(frogs.data, step = 100, color = "Group", plot = FALSE)
saveRDS(p, file = "frogs.data.courbes.rare_M.rds")
}
rare.level <- min(sample_sums(frogs.data)) rare.level <- min(sample_sums(frogs.data))
p <- p + facet_wrap(~Group) + geom_vline(xintercept = rare.level, color = "Gray60")+ p <- p + facet_wrap(~Group) + geom_vline(xintercept = rare.level, color = "Gray60")+
xlab("Sample Size (nb de séquences)") + ylab("Species Richness (nb d'OTU)") xlab("Sample Size (nb de séquences)") + ylab("Species Richness (nb d'OTU)")
plot(p) plot(p)
...@@ -690,7 +699,7 @@ plot(p) ...@@ -690,7 +699,7 @@ plot(p)
```{r 30-plot-richness, eval = TRUE} ```{r 30-plot-richness, eval = TRUE}
p <- plot_richness(frogs.data.rare, color = "Group",measures = c("Observed", "Chao1", "Shannon", "InvSimpson", "Fisher"),x = "Group", title = "Alpha diversity Comparaison microbiote") +theme_bw() + geom_boxplot(aes(fill = Group)) + geom_point() + theme(axis.text.x = element_blank()) p <- plot_richness(frogs.data, color = "Group",measures = c("Observed", "Chao1", "Shannon", "InvSimpson", "Fisher"),x = "Group", title = "Alpha diversity Comparaison microbiote") +theme_bw() + geom_boxplot(aes(fill = Group)) + geom_point() + theme(axis.text.x = element_blank())
plot(p) plot(p)
...@@ -699,9 +708,9 @@ plot(p) ...@@ -699,9 +708,9 @@ plot(p)
#### Richness Table #### Richness Table
```{r 12-create-richness-table, message = FALSE, eval = TRUE} ```{r 12-create-richness-table, message = FALSE, eval = TRUE}
richness.table <- estimate_richness(frogs.data.rare, measures = c("Observed", "Chao1", "Shannon", "Simpson", "InvSimpson", "Fisher")) richness.table <- estimate_richness(frogs.data, measures = c("Observed", "Chao1", "Shannon", "Simpson", "InvSimpson", "Fisher"))
richness.table <- cbind(richness.table, sample_data(frogs.data.rare)) richness.table <- cbind(richness.table, sample_data(frogs.data))
richness.table$Depth <- sample_sums(frogs.data.rare) richness.table$Depth <- sample_sums(frogs.data)
richness.table %>% DT::datatable(extensions = 'Buttons', richness.table %>% DT::datatable(extensions = 'Buttons',
options = list(dom = 'Bfrtip', options = list(dom = 'Bfrtip',
pageLength = 10, pageLength = 10,
...@@ -719,8 +728,8 @@ richness.table %>% DT::datatable(extensions = 'Buttons', ...@@ -719,8 +728,8 @@ richness.table %>% DT::datatable(extensions = 'Buttons',
Analyse de la variance, compare les moyennes d'échantillons. Analyse de la variance, compare les moyennes d'échantillons.
```{r 33-anova, message = FALSE, eval=TRUE} ```{r 33-anova, message = FALSE, eval=TRUE}
div_data <- cbind(estimate_richness(frogs.data.rare, measures = "Observed"), div_data <- cbind(estimate_richness(frogs.data, measures = "Observed"),
sample_data(frogs.data.rare)) sample_data(frogs.data))
model <- aov(Observed ~ 0 + Group, data = div_data) model <- aov(Observed ~ 0 + Group, data = div_data)
anova(model) anova(model)
...@@ -770,8 +779,8 @@ comparison_data ...@@ -770,8 +779,8 @@ comparison_data
```{r 39-create-richness-table, eval=TRUE} ```{r 39-create-richness-table, eval=TRUE}
div_data <- cbind(estimate_richness(frogs.data.rare, measures = "Chao1"), div_data <- cbind(estimate_richness(frogs.data, measures = "Chao1"),
sample_data(frogs.data.rare)) sample_data(frogs.data))
model <- aov(Chao1 ~ 0 + Group, data = div_data) model <- aov(Chao1 ~ 0 + Group, data = div_data)
anova(model) anova(model)
...@@ -804,8 +813,8 @@ TukeyHSD(model) ...@@ -804,8 +813,8 @@ TukeyHSD(model)
```{r 43-create-richness-table, eval=TRUE} ```{r 43-create-richness-table, eval=TRUE}
div_data <- cbind(estimate_richness(frogs.data.rare, measures = "Shannon"), div_data <- cbind(estimate_richness(frogs.data, measures = "Shannon"),
sample_data(frogs.data.rare)) sample_data(frogs.data))
model <- aov(Shannon ~ 0 + Group, data = div_data) model <- aov(Shannon ~ 0 + Group, data = div_data)
anova(model) anova(model)
...@@ -839,8 +848,8 @@ TukeyHSD(model) ...@@ -839,8 +848,8 @@ TukeyHSD(model)
```{r 49-create-richness-table, eval=TRUE} ```{r 49-create-richness-table, eval=TRUE}
div_data <- cbind(estimate_richness(frogs.data.rare, measures = "InvSimpson"), div_data <- cbind(estimate_richness(frogs.data, measures = "InvSimpson"),
sample_data(frogs.data.rare)) sample_data(frogs.data))
model <- aov(InvSimpson ~ 0 + Group, data = div_data) model <- aov(InvSimpson ~ 0 + Group, data = div_data)
anova(model) anova(model)
...@@ -873,8 +882,8 @@ TukeyHSD(model) ...@@ -873,8 +882,8 @@ TukeyHSD(model)
```{r 55-create-richness-table, eval=TRUE} ```{r 55-create-richness-table, eval=TRUE}
div_data <- cbind(estimate_richness(frogs.data.rare, measures = "Fisher"), div_data <- cbind(estimate_richness(frogs.data, measures = "Fisher"),
sample_data(frogs.data.rare)) sample_data(frogs.data))
model <- aov(Fisher ~ 0 + Group, data = div_data) model <- aov(Fisher ~ 0 + Group, data = div_data)
anova(model) anova(model)
......
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