taxonomie plots en Venn diagrammen op basis van data gecorrigeerd voo…

…r aantal reads per staal, anders is denk ik bijvoorbeeld gedeelde en unieke OTUs per landgebruik, taxonomie, etc niet vergelijkbaar

source/rmarkdown/annelida_data_analyse.Rmd

@@ -127,13 +127,24 @@ veganobject <- psotu2veg(physeq)
 
 ```{r convert-tidytacos}
 tidy_physeq <- tidytacos::from_phyloseq(physeq)
+tidy_physeq_rarefied <- tidytacos::from_phyloseq(physeq_rarefied)
+
 tidy_physeq <- tidy_physeq %>%
   remove_empty_samples() %>%
   tidytacos::set_rank_names(
     rank_names = c("phylum", "class", "order", "family", "genus", "species")
   ) %>%
   tidytacos::add_alpha() %>%
   tidytacos::add_total_count()
+
+tidy_physeq_rarefied <- tidy_physeq_rarefied %>%
+  remove_empty_samples() %>%
+  tidytacos::set_rank_names(
+    rank_names = c("phylum", "class", "order", "family", "genus", "species")
+  ) %>%
+  tidytacos::add_alpha() %>%
+  tidytacos::add_total_count()
+
 ```
 
 
@@ -192,41 +203,44 @@ tidy_physeq$samples %>%
 ## OTU tabel
 
 ```{r verken-otu-data}
-glimpse(otu_table(physeq) %>% as.data.frame %>% as_tibble())
+physeq_rarefied <- rarefy_even_depth(physeq, sample.size = 30780)
+
+
+glimpse(otu_table(physeq_rarefied) %>% as.data.frame %>% as_tibble())
 ```
 
 ## Taxonomie tabel
 
 ```{r verken-taxonomie-data}
-glimpse(tax_table(physeq) %>% as.data.frame %>% as_tibble())
+glimpse(tax_table(physeq_rarefied) %>% as.data.frame %>% as_tibble())
 ```
 
 Unieke en gedeelde taxa per diepte:
 
 ```{r}
-tidy_physeq %>%
+tidy_physeq_rarefied %>%
   tidytacos::tacoplot_venn(Diepte)
 ```
 
 Unieke en gedeelde taxa per landgebruik:
 
 ```{r}
-tidy_physeq %>%
+tidy_physeq_rarefied %>%
   tidytacos::tacoplot_venn(Landgebruik_MBAG)
 ```
 
 ```{r}
-tidy_physeq %>%
+tidy_physeq_rarefied %>%
   tidytacos::tacoplot_stack()
 ```
 
 ```{r}
-tidy_physeq %>%
+tidy_physeq_rarefied %>%
   tidytacos::tacoplot_stack(x = Landgebruik_MBAG)
 ```
 
 ```{r}
-tidy_physeq %>%
+tidy_physeq_rarefied %>%
   tidytacos::tacoplot_stack(x = Diepte)
 ```