some fixes

R/aggregate_fun.R

@@ -85,7 +85,7 @@ aggregate_fun <- function(data = data, metacoder = NULL, deseq = NULL, mgseq = N
       mgseqT <- read.table(paste(mgseq,"/signtab_",column1,"_",combinaisons[1,col],"_vs_",combinaisons[2,col],".csv",sep=""), h=TRUE,sep="\t")
     } else{
       if(file.exists(paste(mgseq,"/signtab_",column1,"_",combinaisons[2,col],"_vs_",combinaisons[1,col],".csv",sep=""))){
-        mgseqT <- read.table(paste(mgseq,"/signtab_",column1,"_",combinaisons[1,col],"_vs_",combinaisons[2,col],".csv",sep=""), h=TRUE,sep="\t")
+        mgseqT <- read.table(paste(mgseq,"/signtab_",column1,"_",combinaisons[2,col],"_vs_",combinaisons[1,col],".csv",sep=""), h=TRUE,sep="\t")
       }
       else{
         flog.warn('File does not exists.')

R/csv2phyloseq_fun.R

@@ -76,7 +76,7 @@ print(head(sequences1))
     flog.info('Done.')
     tree <- fitGTR$tree
 
-    data <- phyloseq(otu_table(otable, taxa_are_rows=TRUE), sample_data(mtable), tax_table(ttable), sequences1, tree) # phy_tree(tree),
+    data <- phyloseq(otu_table(otable, taxa_are_rows=TRUE), sample_data(mtable), tax_table(as.matrix(ttable)), sequences1, tree) # phy_tree(tree),
   }else{
     flog.info('Phyloseq object...')
     data <- phyloseq(otu_table(otable, taxa_are_rows=TRUE), sample_data(mtable), tax_table(as.matrix(ttable)), sequences1)

R/diversity_alpha_fun.R

@@ -168,7 +168,8 @@ diversity_alpha_fun <- function(data = data, output = "./plot_div_alpha/", colum
         # print(round(wilcox_res1$p.value,3))
         wilcox_col1 <- round(wilcox_res1$p.value,3)
         fun <- glue("resAlpha[[\"{m}\"]] <- list(anova = aov1, wilcox_col1 = wilcox_col1)")
-        write.table(wilcox_col1, paste(output,"/anovatable.csv", sep=""), sep="\t", row.names=FALSE)
+        write.table(wilcox_col1, paste(output,"/anovatable.csv", sep=""), sep="\t", col.names=NA)
+        # write.table(aov1, paste(output,"/anovatable.csv", sep=""), sep="\t", col.names=NA)  # need output for aov
         # print(fun)
         eval(parse(text=fun))