Changed normed to density in Matplotlib hist plots.

Ecogenomics · May 4, 2020 · b08edd7 · b08edd7
1 parent 6438d9a
commit b08edd7
Show file tree

Hide file tree

Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/checkm/plot/codingDensityPlots.py b/checkm/plot/codingDensityPlots.py
@@ -98,7 +98,7 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaCD):
             bins.append(binEnd)
             binEnd += binWidth
 
-        axesHist.hist(data, bins=bins, normed=True, color=(0.5, 0.5, 0.5))
+        axesHist.hist(data, bins=bins, density=True, color=(0.5, 0.5, 0.5))
         axesHist.set_xlabel('% coding density')
         axesHist.set_ylabel('% windows (' + str(self.options.cd_window_size) + ' bp)')
 

diff --git a/checkm/plot/gcPlots.py b/checkm/plot/gcPlots.py
@@ -86,7 +86,7 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaGC):
             bins.append(binEnd)
             binEnd += binWidth
 
-        axesHist.hist(data, bins=bins, normed=True, color=(0.5, 0.5, 0.5))
+        axesHist.hist(data, bins=bins, density=True, color=(0.5, 0.5, 0.5))
         axesHist.set_xlabel('% GC')
         axesHist.set_ylabel('% windows (' + str(self.options.gc_window_size) + ' bp)')
 

diff --git a/checkm/plot/tetraDistPlots.py b/checkm/plot/tetraDistPlots.py
@@ -91,7 +91,7 @@ def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDe
             bins.append(binEnd)
             binEnd += binWidth
 
-        axesHist.hist(data, bins=bins, normed=True, color=(0.5, 0.5, 0.5))
+        axesHist.hist(data, bins=bins, density=True, color=(0.5, 0.5, 0.5))
         axesHist.set_xlabel(r'$\Delta$ TD')
         axesHist.set_ylabel('% windows (' + str(self.options.td_window_size) + ' bp)')
 

diff --git a/scripts/simEvaluateBiasHistograms.py b/scripts/simEvaluateBiasHistograms.py
@@ -93,8 +93,8 @@ def plot(self):
     def plotOnAxes(self, axes, beforeCorrection, afterCorrection, xMin, xMax, yMin, yMax, bXLabel):  
         numBins = 100
 
-        n, bins, patches = axes.hist(beforeCorrection, numBins, normed=1, facecolor='blue', alpha=0.25, label='before correction')
-        n, bins, patches = axes.hist(afterCorrection, numBins, normed=1, facecolor='green', alpha=0.25, label='after correction')
+        n, bins, patches = axes.hist(beforeCorrection, numBins, density=1, facecolor='blue', alpha=0.25, label='before correction')
+        n, bins, patches = axes.hist(afterCorrection, numBins, density=1, facecolor='green', alpha=0.25, label='after correction')
 
         y = mlab.normpdf(bins, np.mean(beforeCorrection), np.std(beforeCorrection))
         axes.plot(bins, y, 'b--')