manual+namespace update

NAMESPACE

@@ -66,6 +66,7 @@ importFrom(DESeq2,resultsNames)
 importFrom(dplyr,across)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_map)
+importFrom(dplyr,left_join)
 importFrom(ggpubr,ggtexttable)
 importFrom(ggpubr,text_grob)
 importFrom(ggpubr,ttheme)
@@ -97,4 +98,5 @@ importFrom(phangorn,pml)
 importFrom(plotly,ggplotly)
 importFrom(ranacapa,ggrare)
 importFrom(reshape2,melt)
+importFrom(tibble,rownames_to_column)
 importFrom(venn,venn)

man/bars_fun.Rd

@@ -11,6 +11,7 @@ bars_fun(
   Ord1 = NULL,
   sample_labels = FALSE,
   split = FALSE,
+  split_sid_order = FALSE,
   relative = TRUE,
   autoorder = TRUE,
   ylab = "Abundance",

man/diversity_alpha_fun.Rd

@@ -20,7 +20,7 @@ diversity_alpha_fun(
 
 \item{output}{Output directory}
 
-\item{column1}{Column name of first factor to test (covariable in ANOVA).}
+\item{column1}{Column name of first factor to test (covariable in ANOVA), or principal factor if only one factor to test.}
 
 \item{column2}{Column name of second factor to test (last factor in ANOVA).}
 

man/diversity_beta_light.Rd

@@ -14,7 +14,8 @@ diversity_beta_light(
   output = "./plot_div_beta/",
   axes = c(1, 2),
   tests = TRUE,
-  verbose = 2
+  verbose = 2,
+  ellipse = TRUE
 )
 }
 \arguments{
@@ -37,6 +38,8 @@ diversity_beta_light(
 \item{tests}{Whether to compute tests or not (TRUE/FALSE)}
 
 \item{verbose}{Verbose level. (1: quiet, 2: print infos, 3: print infos + debug)}
+
+\item{ellipse}{Plot ellipse (TRUE)}
 }
 \value{
 Return specific plots and tests in list and output them in the output directory.