gseapy/gsea.py
def _plotting(self, rank_metric, results, graph_num, outdir, 
                  format, figsize, pheno_pos='', pheno_neg=''):
        """ Plotting API.
            :param rank_metric: sorted pd.Series with rankings values.
            :param results: self.results
            :param data: preprocessed expression table

        """
        
        # no values need to be returned
        if self._outdir is None: return
        #Plotting
        top_term = self.res2d.index[:graph_num]
        # multi-threading
        pool = Pool(self._processes)
        for gs in top_term:
            hit = results.get(gs)['hits_indices']
            NES = 'nes' if self.module != 'ssgsea' else 'es'
            term = gs.replace('/','_').replace(":","_")
            outfile = '{0}/{1}.{2}.{3}'.format(self.outdir, term, self.module, self.format)
            # gseaplot(rank_metric=rank_metric, term=term, hits_indices=hit,
            #           nes=results.get(gs)[NES], pval=results.get(gs)['pval'], 
            #           fdr=results.get(gs)['fdr'], RES=results.get(gs)['RES'],
            #           pheno_pos=pheno_pos, pheno_neg=pheno_neg, figsize=figsize,
            #           ofname=outfile)
            pool.apply_async(gseaplot, args=(rank_metric, term, hit, results.get(gs)[NES],
                                              results.get(gs)['pval'],results.get(gs)['fdr'],
                                              results.get(gs)['RES'],
                                              pheno_pos, pheno_neg, 
                                              figsize, 'seismic', outfile))
            if self.module == 'gsea':
                outfile2 = "{0}/{1}.heatmap.{2}".format(self.outdir, term, self.format)
                # heatmap(df=self.heatmat.iloc[hit, :], title=term, ofname=outfile2, 
                #         z_score=0, figsize=(self._width, len(hit)/2))
                pool.apply_async(heatmap, args=(self.heatmat.iloc[hit, :], 0, term, 
                                               (self._width, len(hit)/2+2), 'RdBu_r',
                                                True, True, outfile2))
        pool.close()
        pool.join()
def _plotting(self, rank_metric, results, graph_num, outdir, 
                  format, figsize, pheno_pos='', pheno_neg=''):
        """ Plotting API.
            :param rank_metric: sorted pd.Series with rankings values.
            :param results: self.results
            :param data: preprocessed expression table

        """
        
        # no values need to be returned
        if self._outdir is None: return
        #Plotting
        top_term = self.res2d.index[:graph_num]
        # multi-threading
        pool = Pool(self._processes)
        for gs in top_term:
            hit = results.get(gs)['hits_indices']
            NES = 'nes' if self.module != 'ssgsea' else 'es'
            term = gs.replace('/','_').replace(":","_")
            outfile = '{0}/{1}.{2}.{3}'.format(self.outdir, term, self.module, self.format)
            # gseaplot(rank_metric=rank_metric, term=term, hits_indices=hit,
            #           nes=results.get(gs)[NES], pval=results.get(gs)['pval'], 
            #           fdr=results.get(gs)['fdr'], RES=results.get(gs)['RES'],
            #           pheno_pos=pheno_pos, pheno_neg=pheno_neg, figsize=figsize,
            #           ofname=outfile)
            pool.apply_async(gseaplot, args=(rank_metric, term, hit, results.get(gs)[NES],
                                              results.get(gs)['pval'],results.get(gs)['fdr'],
                                              results.get(gs)['RES'],
                                              pheno_pos, pheno_neg, 
                                              figsize, 'seismic', outfile))
            if self.module == 'gsea':
                outfile2 = "{0}/{1}.heatmap.{2}".format(self.outdir, term, self.format)
                # heatmap(df=self.heatmat.iloc[hit, :], title=term, ofname=outfile2, 
                #         z_score=0, figsize=(self._width, len(hit)/2))
                pool.apply_async(heatmap, args=(self.heatmat.iloc[hit, :], 0, term, 
                                               (self._width, len(hit)/2+2), 'RdBu_r',
                                                True, True, outfile2))
        pool.close()
        pool.join()
def _plotting ( self , rank_metric , results , graph_num , outdir , format , figsize , pheno_pos = '' , pheno_neg = '' ) : # no values need to be returned if self . _outdir is None : return #Plotting top_term = self . res2d . index [ : graph_num ] # multi-threading pool = Pool ( self . _processes ) for gs in top_term : hit = results . get ( gs ) [ 'hits_indices' ] NES = 'nes' if self . module != 'ssgsea' else 'es' term = gs . replace ( '/' , '_' ) . replace ( ":" , "_" ) outfile = '{0}/{1}.{2}.{3}' . format ( self . outdir , term , self . module , self . format ) # gseaplot(rank_metric=rank_metric, term=term, hits_indices=hit, #           nes=results.get(gs)[NES], pval=results.get(gs)['pval'],  #           fdr=results.get(gs)['fdr'], RES=results.get(gs)['RES'], #           pheno_pos=pheno_pos, pheno_neg=pheno_neg, figsize=figsize, #           ofname=outfile) pool . apply_async ( gseaplot , args = ( rank_metric , term , hit , results . get ( gs ) [ NES ] , results . get ( gs ) [ 'pval' ] , results . get ( gs ) [ 'fdr' ] , results . get ( gs ) [ 'RES' ] , pheno_pos , pheno_neg , figsize , 'seismic' , outfile ) ) if self . module == 'gsea' : outfile2 = "{0}/{1}.heatmap.{2}" . format ( self . outdir , term , self . format ) # heatmap(df=self.heatmat.iloc[hit, :], title=term, ofname=outfile2,  #         z_score=0, figsize=(self._width, len(hit)/2)) pool . apply_async ( heatmap , args = ( self . heatmat . iloc [ hit , : ] , 0 , term , ( self . _width , len ( hit ) / 2 + 2 ) , 'RdBu_r' , True , True , outfile2 ) ) pool . close ( ) pool . join ( )
Plotting API.
            :param rank_metric: sorted pd.Series with rankings values.
            :param results: self.results
            :param data: preprocessed expression table
Plotting API . : param rank_metric : sorted pd . Series with rankings values . : param results : self . results : param data : preprocessed expression table