Commit 64f00514 authored by Etienne Rifa's avatar Etienne Rifa
Browse files

some fixes

parent 80c69c00
Pipeline #38542 passed with stage
in 15 seconds
......@@ -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.')
......
......@@ -76,7 +76,7 @@ print(head(sequences1))
flog.info('Done.')
tree <- fitGTR$tree
data <- phyloseq(otu_table(otable, taxa_are_rows=TRUE), sample_data(mtable), tax_table(ttable), sequences1, tree) # phy_tree(tree),
data <- phyloseq(otu_table(otable, taxa_are_rows=TRUE), sample_data(mtable), tax_table(as.matrix(ttable)), sequences1, tree) # phy_tree(tree),
}else{
flog.info('Phyloseq object...')
data <- phyloseq(otu_table(otable, taxa_are_rows=TRUE), sample_data(mtable), tax_table(as.matrix(ttable)), sequences1)
......
......@@ -168,7 +168,8 @@ diversity_alpha_fun <- function(data = data, output = "./plot_div_alpha/", colum
# print(round(wilcox_res1$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))
......
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