From b8a950fbc87e769a8507e7f32cbf2d73c88df69c Mon Sep 17 00:00:00 2001
From: Alexander Minges <alexander.minges@hhu.de>
Date: Fri, 8 Apr 2016 15:55:57 +0200
Subject: [PATCH] option to disable MM calculation; option to scale y and x
 axis in kinetics plot as log

---
 analyze-cli.py          | 45 ++++++++++++++++++++++++++++++++++++++---
 libkinetics/__init__.py |  9 +++++++--
 2 files changed, 49 insertions(+), 5 deletions(-)

diff --git a/analyze-cli.py b/analyze-cli.py
index cc477d3..9658172 100755
--- a/analyze-cli.py
+++ b/analyze-cli.py
@@ -42,9 +42,12 @@ class ExperimentHelper():
     Provides plotting and data output functionality for libkinetics.Experiment.
     """
 
-    def __init__(self, experiment, logger):
+    def __init__(self, experiment, logger, unit, logx=False, logy=False):
         self.exp = experiment
         self.logger = logger
+        self.logx = logx
+        self.logy = logy
+        self.unit = unit
 
     def linear_regression_function(self, slope, x, intercept):
         y = slope * x + intercept
@@ -83,9 +86,14 @@ class ExperimentHelper():
     def plot_kinetics(self, outpath):
         exp = self.exp
         fig, ax = plt.subplots()
-        ax.set_xlabel('c [mM]')
+        ax.set_xlabel('c [{}]'.format(self.unit))
         ax.set_ylabel('dA/dt [Au/s]')
         ax.set_title('Kinetics')
+        
+        if self.logx:
+            ax.set_xscale('log')
+        if self.logy:
+            ax.set_yscale('log')
 
         ax.errorbar(exp.raw_kinetic_data['x'],
                     exp.raw_kinetic_data['y'],
@@ -159,10 +167,22 @@ def parse_arguments():
                         '--replicates',
                         action='store_true',
                         help='fit kinetics to individual replicates')
+    parser.add_argument('-nm',
+                        '--no-michaelis',
+                        action='store_true',
+                        help='do not compute michaelis-menten kinetics')
     parser.add_argument('-wh',
                         '--hill',
                         action='store_true',
                         help='compute additional kinetics using Hill equation')
+    parser.add_argument('-lx',
+                        '--log-x',
+                        action='store_true',
+                        help='x axis in kinetics is log-scaled')
+    parser.add_argument('-ly',
+                        '--log-y',
+                        action='store_true',
+                        help='y axis in kinetics is log-scaled')
     parser.add_argument('start',
                         type=np.float64,
                         help='start of fitting window')
@@ -173,6 +193,9 @@ def parse_arguments():
     parser.add_argument('output',
                         type=str,
                         help='results will be written to this directory')
+    parser.add_argument('unit',
+                        type=str,
+                        help='unit of concentrations')
 
     args = parser.parse_args()
 
@@ -243,6 +266,21 @@ def main():
     logger = initialize_logger()
     # grab fitting window from provided arguments
     fitting_window = (args.start, args.end)
+    
+    if args.log_x:
+        logx = args.log_x
+    else:
+        logx = False
+        
+    if args.log_y:
+        logy = args.log_y
+    else:
+        logy = False
+    
+    if args.no_michaelis:
+        no_mm = args.no_michaelis
+    else:
+        no_mm = False
 
     if args.hill:
         do_hill = args.hill
@@ -278,9 +316,10 @@ def main():
             exp = libkinetics.Experiment(data_files,
                                          fitting_window,
                                          do_hill=do_hill,
+                                         no_mm=no_mm,
                                          logger=logger,
                                          fit_to_replicates=fit_to_replicates)
-            ehlp = ExperimentHelper(exp, logger)
+            ehlp = ExperimentHelper(exp, logger, args.unit, logx=logx, logy=logy)
             logger.info('Plotting linear fits')
             ehlp.plot_data(str(output_path))
             logger.info('Plotting kinetic fit(s)')
diff --git a/libkinetics/__init__.py b/libkinetics/__init__.py
index 627e1cd..0be8752 100644
--- a/libkinetics/__init__.py
+++ b/libkinetics/__init__.py
@@ -225,7 +225,7 @@ class Experiment():
             lower and upper bounds for calculating the v0 linear fit.
     """
 
-    def __init__(self, data_files, xlim, do_hill=False,
+    def __init__(self, data_files, xlim, do_hill=False, no_mm=False,
                  fit_to_replicates=False, logger=None):
         """
         Inits Experiment class with experimental parameters
@@ -240,6 +240,8 @@ class Experiment():
                 linear fitting of v0
             do_hill:  boolean to define whether to fit Hill-type kinetics in
                 addition to Michaelis-Menten kinetics. Defaults to False
+            no_mm: boolean to define whether the calculation of Michaelis-Menten
+                kinetics is supressed. Defaults to False
             fit_to_replicates: boolean to define wheter to fit to individual
                 replicates instead of the avarage slope. Defaults to False
             logger: logging.Logger instance. If not given, a new logger is
@@ -311,7 +313,10 @@ class Experiment():
                 self.raw_kinetic_data['yerr'].append(m.avg_slope_err)
 
         # calculate kinetics
-        self.mm = self.do_mm_kinetics()
+        if not no_mm:
+            self.mm = self.do_mm_kinetics()
+        else:
+            self.mm = None
         if do_hill:
             self.hill = self.do_hill_kinetics()
         else: