Code cleaning and documenting.

libhts/libhts.py

@@ -264,32 +264,32 @@ def plot_norm_correlations(correlations):
     #correlations.plot.kde(ax=ax1)
     #sns.violinplot(data=correlations, orient="h", ax=ax2)
     #ax2.set_xlabel("Pearson correlation coefficient")
-    ax = sns.violinplot(data=correlations, cut=0)
-    ax.set_ylabel("Pearson correlation coefficient")
+    axis = sns.violinplot(data=correlations, cut=0)
+    axis.set_ylabel("Pearson correlation coefficient")
 
 
 def plot_counts_distribution(data, xlabel):
     # TODO: try to plot with semilog x axis
-    #ax = data.plot.kde(legend=None)
-    #ax.set_xlabel(xlabel)
-    #ax.legend(ncol=len(REPS))
+    #axis = data.plot.kde(legend=None)
+    #axis.set_xlabel(xlabel)
+    #axis.legend(ncol=len(REPS))
     try:
-        ax = data.plot.kde()
+        axis = data.plot.kde()
     except ValueError as e:
         msg = "".join([
             "There seems to be a problem with the data.\n",
             "The data matrix has %d lines and %d columns.\n" % (len(data), len(data.columns))])
         warnings.warn(msg)
         raise
-    ax.set_xlabel(xlabel)
+    axis.set_xlabel(xlabel)
 
 
 def plot_boxplots(data, ylabel):
     fig = plt.figure(figsize=(6, 12))
-    ax = fig.add_subplot(111)
-    data.plot.box(ax=ax)
-    ax.set_ylabel(ylabel)
-    for label in ax.get_xticklabels():
+    axis = fig.add_subplot(111)
+    data.plot.box(ax=axis)
+    axis.set_ylabel(ylabel)
+    for label in axis.get_xticklabels():
         label.set_rotation(90)
     plt.tight_layout()
 
@@ -352,9 +352,9 @@ def plot_lfc_distribution(res, contrast, fold_type=None):
         fold_type = "log2FoldChange"
     lfc = getattr(res, fold_type).dropna()
     lfc.name = contrast
-    ax = sns.kdeplot(lfc)
-    ax.set_xlabel(fold_type)
-    ax.set_ylabel("frequency")
+    axis = sns.kdeplot(lfc)
+    axis.set_xlabel(fold_type)
+    axis.set_ylabel("frequency")
 
 
 def make_status2colour(down_statuses, up_statuses):