add shannon diversity

metagenome-atlas · Oct 5, 2023 · 96db777 · 96db777
1 parent 3436fce
commit 96db777
Showing 1 changed file with 11 additions and 0 deletions.
diff --git a/R/Analyze_genecatalog.Rmd b/R/Analyze_genecatalog.Rmd
@@ -274,6 +274,10 @@ non_singleton_genes <- gene_stats %>%
   dplyr::pull(GeneNr)
 
 
+# take a subset to speed up caluclation !!!! remove this line
+non_singleton_genes <- non_singleton_genes[1:1000]
+
+
 cat("Select", length(non_singleton_genes), "non singleton genes from total", dim(gene_stats)[1], "genes.")
 
 
@@ -282,3 +286,10 @@ gene_coverage <- load_subset_of_genes(abundance_file, non_singleton_genes)
 ```
 
 
+```{r}
+shannon_diversity <- vegan::diversity(t(gene_coverage), index = "shannon")
+
+hist(shannon_diversity)
+```
+
+