rmd et html males corrigé

202106_Obeglu/report_Obeglu_M.Rmd

@@ -678,8 +678,17 @@ Principe courbes de rarefaction : Compter le nombre d'OTU pour un ensemble de so
 
 ```{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))
+
+
 p <- p + facet_wrap(~Group) + geom_vline(xintercept = rare.level, color = "Gray60")+
   xlab("Sample Size (nb de séquences)") + ylab("Species Richness (nb d'OTU)")
 plot(p)
@@ -690,7 +699,7 @@ plot(p)
 
 ```{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)
 
@@ -699,9 +708,9 @@ plot(p)
 #### Richness Table
 
 ```{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 <- cbind(richness.table, sample_data(frogs.data.rare))
-richness.table$Depth <- sample_sums(frogs.data.rare)
+richness.table <- estimate_richness(frogs.data, measures = c("Observed", "Chao1", "Shannon", "Simpson", "InvSimpson", "Fisher"))
+richness.table <- cbind(richness.table, sample_data(frogs.data))
+richness.table$Depth <- sample_sums(frogs.data)
 richness.table %>% DT::datatable(extensions = 'Buttons', 
                                         options = list(dom = 'Bfrtip', 
                                                        pageLength = 10,
@@ -719,8 +728,8 @@ richness.table %>% DT::datatable(extensions = 'Buttons',
 Analyse de la variance, compare les moyennes d'échantillons.
 
 ```{r 33-anova, message = FALSE, eval=TRUE}
-div_data <- cbind(estimate_richness(frogs.data.rare, measures = "Observed"),  
-                  sample_data(frogs.data.rare))
+div_data <- cbind(estimate_richness(frogs.data, measures = "Observed"),  
+                  sample_data(frogs.data))
 model <- aov(Observed ~ 0 + Group, data = div_data)
 anova(model)
                  
@@ -770,8 +779,8 @@ comparison_data
 
 ```{r 39-create-richness-table, eval=TRUE}
 
-div_data <- cbind(estimate_richness(frogs.data.rare, measures = "Chao1"),  
-                  sample_data(frogs.data.rare))
+div_data <- cbind(estimate_richness(frogs.data, measures = "Chao1"),  
+                  sample_data(frogs.data))
 model <- aov(Chao1 ~ 0 + Group, data = div_data)
 anova(model)
                   
@@ -804,8 +813,8 @@ TukeyHSD(model)
 
 ```{r 43-create-richness-table, eval=TRUE}
 
-div_data <- cbind(estimate_richness(frogs.data.rare, measures = "Shannon"),  
-                  sample_data(frogs.data.rare))
+div_data <- cbind(estimate_richness(frogs.data, measures = "Shannon"),  
+                  sample_data(frogs.data))
 model <- aov(Shannon ~ 0 + Group, data = div_data)
 anova(model)
                   
@@ -839,8 +848,8 @@ TukeyHSD(model)
 
 ```{r 49-create-richness-table, eval=TRUE}
 
-div_data <- cbind(estimate_richness(frogs.data.rare, measures = "InvSimpson"),  
-                  sample_data(frogs.data.rare))
+div_data <- cbind(estimate_richness(frogs.data, measures = "InvSimpson"),  
+                  sample_data(frogs.data))
 model <- aov(InvSimpson ~ 0 + Group, data = div_data)
 anova(model)
                   
@@ -873,8 +882,8 @@ TukeyHSD(model)
 
 ```{r 55-create-richness-table, eval=TRUE}
 
-div_data <- cbind(estimate_richness(frogs.data.rare, measures = "Fisher"),  
-                  sample_data(frogs.data.rare))
+div_data <- cbind(estimate_richness(frogs.data, measures = "Fisher"),  
+                  sample_data(frogs.data))
 model <- aov(Fisher ~ 0 + Group, data = div_data)
 anova(model)