Moved plotting scripts to subdirectory.

create_metagene_profile.py → plotting_scripts/create_metagene_profile.py

@@ -5,7 +5,6 @@ This script reads bigwig files, and creates a metagene profile.
 
 The profiles can be restricted based on a list of gene identifiers.
 """
-# TODO: Set vertical scale ?
 # TODO: Set font size or graph width to avoid very large titles (also for the pipeline) ?
 
 # TODO: What about using deeptools?
@@ -196,6 +195,7 @@ def fix_none(param_value):
 DEFAULT_PARAMETERS = {
     "upstream": 0,
     "downstream": 0,
+    # TODO: change to 2000 ?
     "body": 500,
     "bin size": 10,
     "ref point": None,