minor fixes

R/bars_fun.R

@@ -16,7 +16,7 @@
 rarefaction <- function(data = data, col = NULL, step = 100, ggplotly = TRUE){
   plot_rare <- ggrare(data, step = step, color = col, plot = FALSE)
   plot_rare <- plot_rare + facet_wrap(col, ncol = 4) + theme_bw() +
-              theme(axis.text.x = element_text(angle = 45)) + theme(legend.position = "none")
+              theme(axis.text.x = element_text(angle = 45, hjust=1)) + theme(legend.position = "none")
   if(ggplotly){
     return(ggplotly(plot_rare))
   }else{

R/diversity_alpha_fun.R

@@ -15,7 +15,7 @@ alphaPlot <- function(data = data, col1 = "", col2 = "", measures = c("Shannon")
   }
   p$layers <- p$layers[-1]
   p <- p + ggtitle('Alpha diversity indexes') +  geom_boxplot(alpha = 1, outlier.shape = NA) +
-    theme_bw() + theme(axis.text.x = element_text(angle = 45)) + theme(legend.position = "none")
+    theme_bw() + theme(axis.text.x = element_text(angle = 45, hjust=1)) + theme(legend.position = "none")
   flog.info('Done.')
   return(p)
 }

R/generate_phyloseq_fun.R

@@ -24,7 +24,7 @@
 
 # Generate Phyloseq
 
-generate_phyloseq_fun <- function(dada_res = dada_res, tax.table = tax.table, tree = tree, metadata = "",
+generate_phyloseq_fun <- function(dada_res = dada_res, tax.table = tax.table, tree = NULL, metadata = "",
                                   output = "./phyloseq/", verbose = 1, returnval = TRUE){
 
 

README.md

@@ -35,7 +35,7 @@ installation.
 ## Tutorial
 
 Visit [the rANOMALY
-wikipage](https://forgemia.inra.fr/umrf/ranomaly/-/wikis/rANOMALY-wiki)
+wikipage](https://forgemia.inra.fr/umrf/ranomaly/-/wikis/home)
 
 ## Ressources