some fixes

fix message at ranomaly startup
add message when no significant features in aggregate

NAMESPACE

@@ -50,7 +50,6 @@ import(metagenomeSeq)
 import(mixOmics)
 import(pairwiseAdonis)
 import(phyloseq)
-import(plotly)
 import(psadd)
 import(reshape2)
 import(scales)
@@ -63,10 +62,13 @@ importFrom(DECIPHER,AlignSeqs)
 importFrom(DESeq2,DESeq)
 importFrom(DESeq2,results)
 importFrom(DESeq2,resultsNames)
+importFrom(dplyr,`%>%`)
 importFrom(dplyr,across)
+importFrom(dplyr,arrange)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_map)
 importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
 importFrom(ggpubr,ggtexttable)
 importFrom(ggpubr,text_grob)
 importFrom(ggpubr,ttheme)
@@ -95,7 +97,11 @@ importFrom(phangorn,NJ)
 importFrom(phangorn,dist.ml)
 importFrom(phangorn,phyDat)
 importFrom(phangorn,pml)
+importFrom(plotly,config)
 importFrom(plotly,ggplotly)
+importFrom(plotly,layout)
+importFrom(plotly,plot_ly)
+importFrom(plotly,subplot)
 importFrom(ranacapa,ggrare)
 importFrom(reshape2,melt)
 importFrom(tibble,rownames_to_column)

R/aggregate_fun.R

@@ -274,10 +274,9 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
 
 
   # print(TABfinal)
-  if(length(TABfinal) > 0){
+  if(length(TABfinal$ListAllOtu) > 0){
     flog.info('Building csv file...')
 
-
     TAX <- cbind(seqid = rownames(ttax[as.character(TABfinal$ListAllOtu),]),as.data.frame(ttax[as.character(TABfinal$ListAllOtu),]))
 
     sseq <- cbind(seqid = row.names(as.data.frame(sseq)), as.data.frame(sseq))
@@ -328,7 +327,7 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
     # save(data, file=paste(output,"/signif_phyloseq.rdata",sep=""))
     #
 
-  }
+  }else{flog.info("No significant results in the three methods...")}
 
 
 }

R/bars_fun.R

@@ -7,7 +7,7 @@
 #'
 #' @return A plotly graph.
 #'
-#' @import plotly
+#' @importFrom plotly ggplotly
 #' @importFrom ranacapa ggrare
 #'
 #' @export
@@ -73,10 +73,10 @@ aggregate_top_taxa <- function (x, top, level){
 #'
 #' @return Returns barplots in an interactive plotly community plot
 #'
-#' @import plotly
+#' @importFrom plotly ggplotly plot_ly layout subplot
 #' @importFrom reshape2 melt
 #' @importFrom gtools mixedsort
-#' @importFrom dplyr group_map group_by across
+#' @importFrom dplyr group_map group_by across `%>%` mutate arrange
 #'
 #'
 #' @export
@@ -221,8 +221,8 @@ if( all(Ord1 != sample_variables(data))){
     meltdat$sample.id = factor(meltdat$sample.id, levels = unique(meltdat$sample.id)) # keep sample ids order from metadata.
     }
 
-    p1 = meltdat  %>% arrange(across({Ord1})) %>% group_by(across({Ord1})) %>%
-        mutate(across(where(is.character), as.factor)) %>%
+    p1 = meltdat  %>% dplyr::arrange(across({Ord1})) %>% dplyr::group_by(across({Ord1})) %>%
+        dplyr::mutate(across(where(is.character), as.factor)) %>%
         dplyr::group_map(~ plot_ly(data=., x = ~sample.id, y = ~value, type = 'bar',
                                    name = ~variable,
                                    color = ~variable, legendgroup = ~variable,
@@ -230,13 +230,13 @@ if( all(Ord1 != sample_variables(data))){
                          keep = TRUE)  %>%
       subplot(nrows = 1, shareX = TRUE, shareY=TRUE, titleX = FALSE) %>%
       layout(title="",
-             xaxis = list(title = glue("{Ord1} = {levels(meltdat[, Ord1])[1]}")),
+             xaxis = list(title = glue("{Ord1} =\n{levels(meltdat[, Ord1])[1]}")),
              yaxis = list(title = ylab),
              barmode = 'stack')
 
     for (i in 2:length(unique(meltdat[, Ord1]))) {
       p1$x$layoutAttrs[[1]][[paste0("xaxis", i)]] = NULL
-      p1$x$layoutAttrs[[1]][[paste0("xaxis", i)]]$title <- glue("{Ord1} = {levels(meltdat[, Ord1])[i]}")
+      p1$x$layoutAttrs[[1]][[paste0("xaxis", i)]]$title <- glue("{Ord1} =\n{levels(meltdat[, Ord1])[i]}")
     }
     if(!is.null(outfile)){
       htmlwidgets::saveWidget(p1, outfile)

R/diversity_beta_light.R

@@ -20,7 +20,7 @@
 #' @import ggplot2
 #' @import pairwiseAdonis
 #' @import vegan
-#' @importFrom plotly ggplotly
+#' @importFrom plotly ggplotly config
 #'
 #' @export