gseapy/gsea.py
def run(self):
        """GSEA main procedure"""

        assert self.permutation_type in ["phenotype", "gene_set"]
        assert self.min_size <= self.max_size

        # Start Analysis
        self._logger.info("Parsing data files for GSEA.............................")
        # phenotype labels parsing
        phenoPos, phenoNeg, cls_vector = gsea_cls_parser(self.classes)
        # select correct expression genes and values.
        dat = self.load_data(cls_vector)
        # data frame must have length > 1
        assert len(dat) > 1
        # ranking metrics calculation.
        dat2 = ranking_metric(df=dat, method=self.method, pos=phenoPos, neg=phenoNeg,
                              classes=cls_vector, ascending=self.ascending)
        self.ranking = dat2
        # filtering out gene sets and build gene sets dictionary
        gmt = self.load_gmt(gene_list=dat2.index.values, gmt=self.gene_sets)

        self._logger.info("%04d gene_sets used for further statistical testing....."% len(gmt))
        self._logger.info("Start to run GSEA...Might take a while..................")
        # cpu numbers
        self._set_cores()
        # compute ES, NES, pval, FDR, RES
        dataset = dat if self.permutation_type =='phenotype' else dat2
        gsea_results,hit_ind,rank_ES, subsets = gsea_compute_tensor(data=dataset, gmt=gmt, n=self.permutation_num,
                                                             weighted_score_type=self.weighted_score_type,
                                                             permutation_type=self.permutation_type,
                                                             method=self.method,
                                                             pheno_pos=phenoPos, pheno_neg=phenoNeg,
                                                             classes=cls_vector, ascending=self.ascending,
                                                             processes=self._processes, seed=self.seed)
        
        self._logger.info("Start to generate GSEApy reports and figures............")
        res_zip = zip(subsets, list(gsea_results), hit_ind, rank_ES)
        self._save_results(zipdata=res_zip, outdir=self.outdir, module=self.module,
                                   gmt=gmt, rank_metric=dat2, permutation_type=self.permutation_type)

        # reorder datarame for heatmap
        self._heatmat(df=dat.loc[dat2.index], classes=cls_vector, 
                      pheno_pos=phenoPos, pheno_neg=phenoNeg)
        # Plotting
        if not self._noplot:
            self._plotting(rank_metric=dat2, results=self.results,
                           graph_num=self.graph_num, outdir=self.outdir,
                           figsize=self.figsize, format=self.format,
                           pheno_pos=phenoPos, pheno_neg=phenoNeg)

        self._logger.info("Congratulations. GSEApy ran successfully.................\n")
        if self._outdir is None:
            self._tmpdir.cleanup()

        return
def run(self):
        assert self.permutation_type in ["phenotype", "gene_set"]
        assert self.min_size <= self.max_size

        # Start Analysis
        self._logger.info("Parsing data files for GSEA.............................")
        # phenotype labels parsing
        phenoPos, phenoNeg, cls_vector = gsea_cls_parser(self.classes)
        # select correct expression genes and values.
        dat = self.load_data(cls_vector)
        # data frame must have length > 1
        assert len(dat) > 1
        # ranking metrics calculation.
        dat2 = ranking_metric(df=dat, method=self.method, pos=phenoPos, neg=phenoNeg,
                              classes=cls_vector, ascending=self.ascending)
        self.ranking = dat2
        # filtering out gene sets and build gene sets dictionary
        gmt = self.load_gmt(gene_list=dat2.index.values, gmt=self.gene_sets)

        self._logger.info("%04d gene_sets used for further statistical testing....."% len(gmt))
        self._logger.info("Start to run GSEA...Might take a while..................")
        # cpu numbers
        self._set_cores()
        # compute ES, NES, pval, FDR, RES
        dataset = dat if self.permutation_type =='phenotype' else dat2
        gsea_results,hit_ind,rank_ES, subsets = gsea_compute_tensor(data=dataset, gmt=gmt, n=self.permutation_num,
                                                             weighted_score_type=self.weighted_score_type,
                                                             permutation_type=self.permutation_type,
                                                             method=self.method,
                                                             pheno_pos=phenoPos, pheno_neg=phenoNeg,
                                                             classes=cls_vector, ascending=self.ascending,
                                                             processes=self._processes, seed=self.seed)
        
        self._logger.info("Start to generate GSEApy reports and figures............")
        res_zip = zip(subsets, list(gsea_results), hit_ind, rank_ES)
        self._save_results(zipdata=res_zip, outdir=self.outdir, module=self.module,
                                   gmt=gmt, rank_metric=dat2, permutation_type=self.permutation_type)

        # reorder datarame for heatmap
        self._heatmat(df=dat.loc[dat2.index], classes=cls_vector, 
                      pheno_pos=phenoPos, pheno_neg=phenoNeg)
        # Plotting
        if not self._noplot:
            self._plotting(rank_metric=dat2, results=self.results,
                           graph_num=self.graph_num, outdir=self.outdir,
                           figsize=self.figsize, format=self.format,
                           pheno_pos=phenoPos, pheno_neg=phenoNeg)

        self._logger.info("Congratulations. GSEApy ran successfully.................\n")
        if self._outdir is None:
            self._tmpdir.cleanup()

        return
def run ( self ) : assert self . permutation_type in [ "phenotype" , "gene_set" ] assert self . min_size <= self . max_size # Start Analysis self . _logger . info ( "Parsing data files for GSEA............................." ) # phenotype labels parsing phenoPos , phenoNeg , cls_vector = gsea_cls_parser ( self . classes ) # select correct expression genes and values. dat = self . load_data ( cls_vector ) # data frame must have length > 1 assert len ( dat ) > 1 # ranking metrics calculation. dat2 = ranking_metric ( df = dat , method = self . method , pos = phenoPos , neg = phenoNeg , classes = cls_vector , ascending = self . ascending ) self . ranking = dat2 # filtering out gene sets and build gene sets dictionary gmt = self . load_gmt ( gene_list = dat2 . index . values , gmt = self . gene_sets ) self . _logger . info ( "%04d gene_sets used for further statistical testing....." % len ( gmt ) ) self . _logger . info ( "Start to run GSEA...Might take a while.................." ) # cpu numbers self . _set_cores ( ) # compute ES, NES, pval, FDR, RES dataset = dat if self . permutation_type == 'phenotype' else dat2 gsea_results , hit_ind , rank_ES , subsets = gsea_compute_tensor ( data = dataset , gmt = gmt , n = self . permutation_num , weighted_score_type = self . weighted_score_type , permutation_type = self . permutation_type , method = self . method , pheno_pos = phenoPos , pheno_neg = phenoNeg , classes = cls_vector , ascending = self . ascending , processes = self . _processes , seed = self . seed ) self . _logger . info ( "Start to generate GSEApy reports and figures............" ) res_zip = zip ( subsets , list ( gsea_results ) , hit_ind , rank_ES ) self . _save_results ( zipdata = res_zip , outdir = self . outdir , module = self . module , gmt = gmt , rank_metric = dat2 , permutation_type = self . permutation_type ) # reorder datarame for heatmap self . _heatmat ( df = dat . loc [ dat2 . index ] , classes = cls_vector , pheno_pos = phenoPos , pheno_neg = phenoNeg ) # Plotting if not self . _noplot : self . _plotting ( rank_metric = dat2 , results = self . results , graph_num = self . graph_num , outdir = self . outdir , figsize = self . figsize , format = self . format , pheno_pos = phenoPos , pheno_neg = phenoNeg ) self . _logger . info ( "Congratulations. GSEApy ran successfully.................\n" ) if self . _outdir is None : self . _tmpdir . cleanup ( ) return
GSEA main procedure
GSEA main procedure