renamed run column

metagenlab · Aug 2, 2024 · a66778f · a66778f
1 parent b0485f3
commit a66778f
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/zamp/rules/In_silico/scripts/abundance_to_mismatches.R b/zamp/rules/In_silico/scripts/abundance_to_mismatches.R
@@ -18,7 +18,7 @@ count_table_path <- snakemake@input[["count_table_path"]]
     merged_mismatch_table_path <- snakemake@output[["merged_mismatch_table_path"]]
 
 ## Params
-    RUN <- snakemake@params["RUN"]
+    run <- snakemake@params["run"]
 
 ## Libraries
     library(dplyr)
@@ -39,7 +39,7 @@ mismatches_table$Query.id <- str_remove(string = mismatches_table$Query.id, patt
 
 merged_mismatch_table <- left_join(mismatches_table, count_table, by = c("Query.id"= "ID"))
 
-merged_mismatch_table$RUN <- head(as.character(RUN))
+merged_mismatch_table$run <- head(as.character(run))
 
 
 write.table(x = merged_mismatch_table, file = merged_mismatch_table_path, sep = "\t", row.names = FALSE)

diff --git a/zamp/rules/In_silico/scripts/compare_all_mismatches.R b/zamp/rules/In_silico/scripts/compare_all_mismatches.R
@@ -28,14 +28,14 @@
 # Merge data from multiple runs (if necessary)
 # Merge data from multiple runs (if necessary)
   if (length(mismatch_tables_path) == 1){
-    print("Unique RUN, no merging of seq_tabl")
+    print("Unique run, no merging of seq_tabl")
     st.all <- readRDS(seq_tab)
   }else{
-    print("Multiple RUN, merging")
+    print("Multiple run, merging")
     st.all <- do.call("rbind", lapply(mismatch_tables_path, read.table, header = TRUE, sep = "\t"))
   }
 
-  p <- ggplot(st.all, aes(x=Mismatches, fill=RUN, weight = Counts)) +
+  p <- ggplot(st.all, aes(x=Mismatches, fill=run, weight = Counts)) +
     geom_histogram( color="black", binwidth=1, position = position_dodge2(padding = 0.3, preserve = "single")) +
     theme_bw()
 

diff --git a/zamp/rules/In_silico/scripts/compare_mismatches.R b/zamp/rules/In_silico/scripts/compare_mismatches.R
@@ -22,10 +22,10 @@
 
 # Merge data from multiple runs (if necessary)
   if (length(mismatch_tables_path) == 1){
-    print("Unique RUN, no merging of seq_tabl")
+    print("Unique run, no merging of seq_tabl")
     st.all <- readRDS(seq_tab)
   }else{
-    print("Multiple RUN, merging")
+    print("Multiple run, merging")
     st.all <- do.call("rbind", lapply(mismatch_tables_path, read.table, header = TRUE, sep = "\t", row.names = 1))
   }