Options to control vertical axis range.

create_metagene_profile.py

@@ -5,6 +5,9 @@ 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?
 # deeptools.countReadsPerBin.CountReadsPerBin, using:
 # - bedFile, with the gene spans
@@ -217,6 +220,7 @@ PARAMETER_INFO = "\n".join(DEFAULT_PARAMETERS.keys())
 
 
 def is_prof_param(key):
+    """Determine if *key* corresponds to a valid parameter for a *Profile*."""
     return key in {
         "plot_title", "y_axis_label", "y_min", "y_max", "averagetype",
         "reference_point_label", "start_label", "end_label",
@@ -315,6 +319,14 @@ def main():
         "-t", "--plot_title",
         default="Metagene profile",
         help="Title to use for the metagene plot.")
+    parser.add_argument(
+        "--yMin",
+        default=None,
+        help="Minimum value for the Y-axis")
+    parser.add_argument(
+        "--yMax",
+        default=None,
+        help="Maximum value for the Y-axis")
     parser.add_argument(
         "-e", "--extra_parameters",
         help="Path to a yaml file containing parameters for the "
@@ -330,6 +342,10 @@ def main():
         extra_parameters["group_labels"] = [args.plot_title]
     if args.library_labels:
         extra_parameters["sample_labels"] = args.library_labels
+    if args.yMin is not None:
+        extra_parameters["y_min"] = [float(args.yMin)]
+    if args.yMax is not None:
+        extra_parameters["y_max"] = [float(args.yMax)]
     if args.profile_plot:
         check_options_msg = "Use only one among options -c and -g."
         if args.gene_list: