0.8.1

gseapy/__init__.py

@@ -3,6 +3,6 @@
 from .enrichr import enrichr
 from .parser import get_library_name
 
-__version__='0.8.0'
+__version__='0.8.1'
 
 

gseapy/__main__.py

@@ -12,7 +12,7 @@
 # or args = argparser.parse_args() will throw bugs!!!
 
 
-__version__ = '0.8.0'
+__version__ = '0.8.1'
 
 def main():
     """The Main function/pipeline for GSEAPY."""

gseapy/gsea.py

@@ -92,14 +92,12 @@ def _plotting(self, rank_metric, results, res2d,
 
         for gs in top_term:
             hit = results.get(gs)['hit_index']
-            gs = gs.replace('/','_').replace(":","_")
             """
             gsea_plot(rank_metric=rank_metric, enrich_term=gs, hit_ind=hit,
                       nes=results.get(gs)['nes'], pval=results.get(gs)['pval'], fdr=results.get(gs)['fdr'],
                       RES=results.get(gs)['rank_ES'], phenoPos=phenoPos, phenoNeg=phenoNeg, figsize=figsize,
                       format=format, outdir=outdir, module=module)
             """
-            #return fig obj to save.
             pool.apply_async(gsea_plot, args=(rank_metric, gs, hit, results.get(gs)['nes'],
                                               results.get(gs)['pval'],results.get(gs)['fdr'],
                                               results.get(gs)['rank_ES'],
@@ -121,7 +119,6 @@ def _plotting(self, rank_metric, results, res2d,
             #no values need to be returned
             for gs in top_term:
                 hit = results.get(gs)['hit_index']
-                gs = gs.replace('/','_').replace(":","_")
                 pool_heat.apply_async(heatmap, args=(datAB.iloc[hit], gs, outdir, 0,
                                                     (width, len(hit)/2), format))
                 #heatmap(datAB.iloc[hit], gs, outdir, 0, (width, len(hit)/2), format)
@@ -151,7 +148,7 @@ def _save_results(self, zipdata, outdir, module, gmt, rank_metric, permutation_t
             rdict['hit_index'] = ind
             res[gs] = rdict
 
-        res_df = DataFrame.from_dict(res, orient='index')
+        res_df = pd.DataFrame.from_dict(res, orient='index')
         res_df.index.name = 'Term'
         res_df.sort_values(by='fdr', inplace=True)
         res_df.drop(['rank_ES','hit_index'], axis=1, inplace=True)
@@ -492,7 +489,7 @@ def run(self):
                                    weighted_score_type=self.weighted_score_type,
                                    correl_vector=correl_vector)[2]
             #plotting
-            fig = gsea_plot(rank_metric, enrich_term, hit_ind, nes, pval,
+            gsea_plot(rank_metric, enrich_term, hit_ind, nes, pval,
                             fdr, RES, phenoPos, phenoNeg, self.figsize,
                             self.format, self.outdir, self.module)
 

gseapy/plot.py

@@ -93,6 +93,7 @@ def heatmap(df, term, outdir, axis=0, figsize=(5,5), format='png'):
         ax.spines[side].set_visible(False)
         cbar.ax.spines[side].set_visible(False)
     #cbar.ax.set_title('',loc='left')
+    term = term.replace('/','_').replace(":","_")
     canvas.print_figure("{a}/{b}.heatmap.{c}".format(a=outdir, b=term, c=format),
                         bbox_inches='tight')
 
@@ -197,6 +198,7 @@ def gsea_plot(rank_metric, enrich_term, hit_ind, nes, pval, fdr, RES,
     fig.subplots_adjust(hspace=0)
     #fig.tight_layout()
     #plt.close(fig)
+    enrich_term = enrich_term.replace('/','_').replace(":","_")
     canvas.print_figure('{0}/{1}.{2}.{3}'.format(outdir, enrich_term, module, format), 
                          bbox_inches='tight', dpi=300,)
     return 

setup.py

@@ -2,10 +2,10 @@
 import sys, os
 from setuptools import setup
 
-__version__='0.8.0'
+__version__='0.8.1'
 
 if sys.argv[-1] == 'publish':
-    os.system("python setup.py sdist bdist_egg register upload")
+    os.system("python setup.py sdist bdist_wheel register upload")
     print("You probably want to also tag the version now:")
     print("  git tag -a %s -m 'version %s'" % (__version__,__version__))
     print("  git push --tags")