Mercurial > repos > iuc > ribowaltz_process

diff ribowaltz_plot.R @ 1:042cab870a39 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
author iuc
date Mon, 23 Oct 2023 12:10:31 +0000
parents 6d4c94373bba
children
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line diff
--- a/ribowaltz_plot.R	Thu Sep 22 20:30:54 2022 +0000
+++ b/ribowaltz_plot.R	Mon Oct 23 12:10:31 2023 +0000
@@ -118,7 +118,7 @@
   print(metaprofile)
   sample_list <- list()
   for (sample_name in names(reads_psite_list)) {
-  sample_list[[sample_name]] <- c(sample_name)
+    sample_list[[sample_name]] <- c(sample_name)
   }
   metaheatmap <- metaheatmap_psite(
     reads_psite_list,
@@ -138,15 +138,15 @@
   pdf("codon_usage.pdf", height = 6, width = 16)
   json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite)
   for (sample_name in names(reads_psite_list)) {
-  cu_barplot <- codon_usage_psite(
-    reads_psite_list,
-    annotation_dt,
-    sample = sample_name,
-    fastapath = json_codon_usage_psite$fastapath,
-    fasta_genome = FALSE,
-    frequency_normalization = json_codon_usage_psite$frequency
-  )
-  print(cu_barplot[["plot"]])
+    cu_barplot <- codon_usage_psite(
+      reads_psite_list,
+      annotation_dt,
+      sample = sample_name,
+      fastapath = json_codon_usage_psite$fastapath,
+      fasta_genome = FALSE,
+      frequency_normalization = json_codon_usage_psite$frequency
+    )
+    print(cu_barplot[["plot"]])
   }
   dev.off()
 }