misc changes

R/aggregate_fun.R

@@ -84,7 +84,6 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
       flog.warn('File does not exists.')
       deseqT <- data.frame()
     }
-    # print(head(deseqT))
     flog.info('MetagenomeSeq.')
     if(file.exists(paste(mgseq,"/signtab_",column1,"_",combinaisons[1,col],"_vs_",combinaisons[2,col],".csv",sep=""))){
       mgseqT <- read.table(paste(mgseq,"/signtab_",column1,"_",combinaisons[1,col],"_vs_",combinaisons[2,col],".csv",sep=""), h=TRUE,sep="\t")

R/diversity_beta_light.R

@@ -10,6 +10,7 @@
 #' @param ord0 Currently supported method options are: c("DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA")
 #' @param output The output file directory.
 #' @param tests Whether to compute tests or not (TRUE/FALSE)
+#' @param verbose Verbose level. (1: quiet, 2: print infos, 3: print infos + debug)
 #'
 #' @return Return specific plots and tests in list and output them in the output directory.
 #'
@@ -24,7 +25,18 @@
 
 # Decontam Function
 
-diversity_beta_light <- function(psobj, rank = "ASV", col = NULL, cov = NULL, dist0 = "bray", ord0 = "MDS", output="./plot_div_beta/", tests = TRUE) {
+diversity_beta_light <- function(psobj, rank = "ASV", col = NULL, cov = NULL, dist0 = "bray", ord0 = "MDS", output="./plot_div_beta/", tests = TRUE, verbose = 2) {
+
+  if(verbose == 3){
+  invisible(flog.threshold(DEBUG))
+  }
+  if(verbose == 2){
+    invisible(flog.threshold(INFO))
+  }
+  if(verbose == 1){
+    invisible(flog.threshold(ERROR))
+  }
+
 
   if(!dir.exists(output)){
     dir.create(output, recursive=TRUE)

R/generate_phyloseq_fun.R

@@ -56,7 +56,7 @@ generate_phyloseq_fun <- function(dada_res = dada_res, tax.table = tax.table, tr
     data <- phyloseq(dada_res$otu.table, tax_table(as.matrix(tax.table)), sample.metadata, DNAStringSet(sequences))
   } else{
     flog.info('Building phyloseq object with tree...')
-    data <- phyloseq(dada_res$otu.table, tax.table, sample.metadata, phy_tree(tree), DNAStringSet(sequences))
+    data <- phyloseq(dada_res$otu.table, tax_table(as.matrix(tax.table)), sample.metadata, phy_tree(tree), DNAStringSet(sequences))
   }
   flog.info('Done.')
   data_rel <- transform_sample_counts(data, function(x) x / sum(x) )

R/heatmap_fun.R

@@ -17,8 +17,6 @@
 #' @export
 
 
-# Decontam Function
-
 heatmap_fun <- function(data = data, column1 = "", top = 20, output = "./plot_heatmap/", rank = "Species", relative = TRUE, aggregate = TRUE, legend = "Abundance"){
   LL = list()
 
@@ -28,6 +26,8 @@ heatmap_fun <- function(data = data, column1 = "", top = 20, output = "./plot_he
   }
   flog.info('Done.')
 
+  if( is.na(match(column1, sample_variables(data))) ){stop("This factor is not in sample_variables(data).")}
+
   ps.glom.rel <- psobj.top <- dataglom <- data
 
   if(!is.null(rank)){