Commit 426505d9 authored by Etienne Rifa's avatar Etienne Rifa
Browse files

manual+namespace update

parent be723e90
......@@ -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)
......@@ -11,6 +11,7 @@ bars_fun(
Ord1 = NULL,
sample_labels = FALSE,
split = FALSE,
split_sid_order = FALSE,
relative = TRUE,
autoorder = TRUE,
ylab = "Abundance",
......
......@@ -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).}
......
......@@ -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.
......
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