removing warnings

methylcheck/qc_plot.py

@@ -184,6 +184,7 @@ def qc_signal_intensity(data_containers=None, path=None, meth=None, unmeth=None,
     if return_fig:
         return fig
     plt.show()
+    plt.close('all')
     # print list of bad samples for user
     if len(bad_samples) > 0:
         print('List of Bad Samples')
@@ -431,6 +432,8 @@ def plot_M_vs_U(data_containers_or_path=None, meth=None, unmeth=None, poobah=Non
             return sns_scatterplot.get_figure()
         else:
             sb.scatterplot(x=sx, y=sy, s=3)
+        plt.show()
+        plt.close('all')
     else:
         return {'meth_median': meth.median(), 'unmeth_median': unmeth.median()}
 
@@ -543,6 +546,9 @@ def plot_beta_by_type(beta_df, probe_type='all', return_fig=False, silent=False,
 
     if return_fig:
         return figs
+    plt.show()
+    plt.close('all')
+
 
 def plot_controls(path=None, subset='all', return_fig=False):
     """internal array QC controls (available with the `--save_control` or `--all` methylprep process option)
@@ -740,6 +746,8 @@ def plot_controls(path=None, subset='all', return_fig=False):
 
     if return_fig and figs != []:
         return figs
+    plt.show()
+    plt.close('all')
 
 
 def _qc_plotter(stain_red, stain_green, color_dict=None, columns=None, ymax=None, xticks='show',
@@ -821,3 +829,4 @@ def _qc_plotter(stain_red, stain_green, color_dict=None, columns=None, ymax=None
     if return_fig:
         return fig
     plt.show()
+    plt.close('all')

methylcheck/samples/postprocessQC.py

@@ -63,6 +63,7 @@ def mean_beta_plot(df, verbose=False, save=False, silent=False):
         plt.savefig('mean_beta.png')
     if not silent:
         plt.show()
+        plt.close('all')
     else:
         plt.close(fig)
 
@@ -218,6 +219,7 @@ def beta_density_plot(df, verbose=False, save=False, silent=False, reduce=0.1, p
     if not silent:
         #plt.tight_layout()
         plt.show()
+        plt.close('all')
     else:
         plt.clf()
         plt.cla()

tests/samples/test_sample.py

@@ -88,3 +88,25 @@ def test_plot_mouse_betas_from_pickle(self):
         for saved_png in Path('.').rglob('./beta_mds_n=*.png'):
             print(saved_png)
             saved_png.unlink()
+
+
+def ignore_test():
+    with np.errstate(all='raise'):
+        df = methylcheck.load(Path(PATH,'beta_values.pkl'), verbose=False, silent=True)
+        methylcheck.sample_plot(df, silent=True, save=True)
+        methylcheck.beta_density_plot(df, silent=True)
+        methylcheck.sample_plot(df, silent=True)
+        methylcheck.mean_beta_plot(df, silent=True)
+        methylcheck.cumulative_sum_beta_distribution(df, silent=True)
+        methylcheck.beta_mds_plot(df, silent=True, save=False)
+        methylcheck.mean_beta_compare(df,df,silent=True)
+        #df = df0[['cm_value']]
+        #methylcheck.beta_density_plot(df, silent=True)
+        #df = df0[['m_value']]
+        #methylcheck.beta_density_plot(df, silent=True)
+        Path('./beta.png').unlink()
+        # Path('./beta_mds_n=*.png').unlink() -- causes error if this function doesn't create the file to remove
+        methylcheck.beta_mds_plot(df, silent=True, save=True)
+        for saved_png in Path('.').rglob('./beta_mds_n=*.png'):
+            print(saved_png)
+            saved_png.unlink()