correct quote in metadata

metagenlab · Jul 6, 2020 · 51641fd · 51641fd
1 parent d18b701
commit 51641fd
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/ressources/r_scripts/importation/create_phyloseq_from_metadata.R b/ressources/r_scripts/importation/create_phyloseq_from_metadata.R
@@ -37,6 +37,6 @@ create_phyloseq_fct <- function(physeq_name = "physeq", melted_df_name = "physeq
   save(physeq_obj, file = "physeq_object")
 
   ### Write this table in a tsv file since it is ground for coming analysis and slow to compute
-  write.table(x = physeq_df, file = "physeq_df.tsv", append = F, quote = F, sep = "\t", eol = "\n", row.names = F, col.names = T )
+  write.table(x = physeq_df, file = "physeq_df.tsv", append = F, sep = "\t", eol = "\n", row.names = F, col.names = T )
 
 }
diff --git a/rules/4_post_processing/scripts/physeq_export.R b/rules/4_post_processing/scripts/physeq_export.R
@@ -41,7 +41,7 @@ ape::write.tree(tree, tree_path)
 metadata <- (sample_data(phyloseq_obj))
 metadata$Sample <- rownames(metadata)
 metadata <- metadata %>% select(Sample, everything())
-write.table(metadata, meta_path , sep="\t", quote=F, row.names = FALSE)
+write.table(metadata, meta_path , sep="\t", row.names = FALSE)
 
 ## Write the taxonomy table of the phyloseq object
 taxa_df<- as.data.frame(tax_table(phyloseq_obj), stringsAsFactors = F)

diff --git a/rules/4_post_processing/scripts/physeq_melt_table.R b/rules/4_post_processing/scripts/physeq_melt_table.R
@@ -29,4 +29,4 @@ phyloseq_obj <- prune_taxa(taxa_sums(phyloseq_obj) > 0, phyloseq_obj) ## Removes
 physeq_df <- psmelt(phyloseq_obj)
 
 ### Write this table in a tsv format
-write.table(x = physeq_df, file = phyloseq_melted_table, append = F, quote = F, sep = "\t", eol = "\n", row.names = F, col.names = T )
+write.table(x = physeq_df, file = phyloseq_melted_table, append = F, sep = "\t", eol = "\n", row.names = F, col.names = T )
diff --git a/rules/4_post_processing/scripts/transpose_and_add_meta_count_table.R b/rules/4_post_processing/scripts/transpose_and_add_meta_count_table.R
@@ -20,7 +20,7 @@
 
 ## Load the phyloseq phyloseq_object
     table <- read.table(count_table,  sep = "\t", header = TRUE)
-    meta <- read.table(meta,  sep = "\t", header = TRUE)
+    meta <- read.table(meta,  sep = "\t", header = TRUE, na.strings = "NA")
 
 ## Tranpose table
     table_t <- t(table)