Merge pull request #15 from GreenleafLab/master

sync with sarah

Author: curtisLayton

bin/findFmaxDist.py

@@ -293,9 +293,11 @@ def plotDist(vec, bounds):
     return
 
 
-def plotGammaFunction(vec, results=None, params=None, bounds=[0,5]):
+def plotGammaFunction(vec, results=None, params=None, bounds=None):
     """ Take vector and fit and plot distribution. """
-    # plot pdf 
+    # plot pdf
+    if bounds is None:
+        bounds = np.percentile(vec, [0,100])
     plotDist(vec, bounds)
     more_x = np.linspace(*bounds, num=100)
 

bin/singleClusterFits.py

@@ -172,11 +172,11 @@ def bindingSeriesByCluster(concentrations, bindingSeries,
     if fitParameters is None:
         fitParameters = getInitialFitParameters(concentrations)
 
-    # change fmin initial
-    initial_fluorescence = bindingSeries.sort([0]).dropna().iloc[::100, 0]
-    print "Fitting fmin initial..."
-    fitParameters.loc['initial', 'fmin'] = findFmaxDist.fitGammaDistribution(
-        initial_fluorescence, plot=True, set_offset=0).loc['mean']
+        # change fmin initial
+        initial_fluorescence = bindingSeries.sort([0]).dropna().iloc[::100, 0]
+        print "Fitting fmin initial..."
+        fitParameters.loc['initial', 'fmin'] = findFmaxDist.fitGammaDistribution(
+            initial_fluorescence, plot=True, set_offset=0).loc['mean']
 
     # sort by fluorescence in null_column to try to get groups of equal
     # distributions of binders/nonbinders