How to use the goatools.rpt.goea_nt_xfrm.MgrNtGOEAs function in goatools

"""Test GoeaResults in plotting package."""
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    # Gene Ontology Enrichment Analysis (GOEA)
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    taxid = 10090 # Mouse study
    # Load ontologies, associations, and population ids
    geneids_pop = GeneID2nt_mus.keys()
    geneids2symbol_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    geneids_study = geneids2symbol_study.keys()
    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
    # Run GOEA on study
    goea_results_all = goeaobj.run_study(geneids_study)
    goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
    goea_results_nt = MgrNtGOEAs(goea_results_sig).get_goea_nts_all()
    # Test managing GOEA results
    objres = GoeaResults(goea_results_sig)
    run(objres, prt)
    objnts = GoeaResults(goea_results_nt)
    run(objnts, prt)
    # Plot GOEA results
    fout_img = os.path.join(REPO, "test_plot_objgoearesults_{NS}.png")
    plot_results(fout_img, goea_results_sig, id2symbol=geneids2symbol_study)

# --------------------------------------------------------------------
    # --------------------------------------------------------------------
    # Gene Ontology Enrichment Analysis (GOEA)
    # --------------------------------------------------------------------
    # --------------------------------------------------------------------
    taxid = 10090 # Mouse study
    # Load ontologies, associations, and population ids
    geneids_pop = GeneID2nt_mus.keys()
    geneids2symbol_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
    geneids_study = geneids2symbol_study.keys()
    goeaobj = get_goeaobj("fdr_bh", geneids_pop, taxid)
    go2obj = goeaobj.obo_dag
    # Run GOEA on study
    goea_results_all = goeaobj.run_study(geneids_study)
    goea_results_sig = [r for r in goea_results_all if r.p_fdr_bh < 0.05]
    goea_results_nt = MgrNtGOEAs(goea_results_sig).get_goea_nts_all()
    assert goea_results_nt
    ns2gos = get_ns2gos(goea_results_sig)
    # Test plotting GOEA results
    gosubdag = GoSubDag(set(r.GO for r in goea_results_sig), go2obj)
    plot_results("test_plot_goids_a_goea_{NS}.png", goea_results_sig,
                 id2symbol=geneids2symbol_study, parentcnt=True, childcnt=True)
    for nss, goids in ns2gos.items():
        plt_goids(gosubdag, "test_plot_goids_b_{NS}.png".format(NS=nss), goids)
        plot_gos("test_plot_goids_c_{NS}.png".format(NS=nss), goids, go2obj)

def wr_txt(self, fout_txt, goea_results, prtfmt=None, **kws):
        """Print GOEA results to text file."""
        if not goea_results:
            sys.stdout.write("      0 GOEA results. NOT WRITING {FOUT}\n".format(FOUT=fout_txt))
            return
        with open(fout_txt, 'w') as prt:
            if 'title' in kws:
                prt.write("{TITLE}\n".format(TITLE=kws['title']))
            data_nts = self.prt_txt(prt, goea_results, prtfmt, **kws)
            log = self.log if self.log is not None else sys.stdout
            log.write("  {N:>5} GOEA results for {CUR:5} study items. WROTE: {F}\n".format(
                N=len(data_nts),
                CUR=len(MgrNtGOEAs(goea_results).get_study_items()),
                F=fout_txt))

def get_sortobj(self, goea_results, **kws):
        """Return a Grouper object, given a list of GOEnrichmentRecord."""
        nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
        goids = set(nt.GO for nt in nts_goea)
        go2nt = {nt.GO:nt for nt in nts_goea}
        grprobj = Grouper("GOEA", goids, self.hdrobj, self.grprdflt.gosubdag, go2nt=go2nt)
        grprobj.prt_summary(sys.stdout)
        # hdrgo_prt", "section_prt", "top_n", "use_sections"
        sortobj = Sorter(grprobj, section_sortby=lambda nt: getattr(nt, self.pval_fld))
        return sortobj

def run_study_nts(self, study, **kws):
        """Run GOEA on study ids. Return results as a list of namedtuples."""
        goea_results = self.run_study(study, **kws)
        return MgrNtGOEAs(goea_results).get_goea_nts_all()

def get_goea_nts_prt(goea_results, **kws):
    """Get namedtuples containing user-specified (or default) data from GOATOOLS GOEA results."""
    return MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)

def wr_py_goea_results(self, fout_py, goea_results, **kws):
        """Save GOEA results into Python package containing list of namedtuples."""
        var_name = kws.get("var_name", "goea_results")
        docstring = kws.get("docstring", "")
        sortby = kws.get("sortby", None)
        if goea_results:
            from goatools.nt_utils import wr_py_nts
            nts_goea = goea_results
            # If list has GOEnrichmentRecords or verbose namedtuples, exclude some fields.
            if hasattr(goea_results[0], "_fldsdefprt") or hasattr(goea_results[0], 'goterm'):
                # Exclude some attributes from the namedtuple when saving results
                # to a Python file because the information is redundant or verbose.
                nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
            docstring = "\n".join([docstring, "# {VER}\n\n".format(VER=self.obo_dag.version)])
            assert hasattr(nts_goea[0], '_fields')
            if sortby is None:
                sortby = MgrNtGOEAs.dflt_sortby_objgoea
            nts_goea = sorted(nts_goea, key=sortby)
            wr_py_nts(fout_py, nts_goea, docstring, var_name)

def prt_txt(prt, goea_results, prtfmt=None, **kws):
        """Print GOEA results in text format."""
        objprt = PrtFmt()
        if prtfmt is None:
            flds = ['GO', 'NS', 'p_uncorrected',
                    'ratio_in_study', 'ratio_in_pop', 'depth', 'name', 'study_items']
            prtfmt = objprt.get_prtfmt_str(flds)
        prtfmt = objprt.adjust_prtfmt(prtfmt)
        prt_flds = RPT.get_fmtflds(prtfmt)
        data_nts = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
        RPT.prt_txt(prt, data_nts, prtfmt, prt_flds, **kws)
        return data_nts

def get_study_items(goea_results):
    """Get all study items found in a GOATOOLS GOEA (e.g., geneids)."""
    return MgrNtGOEAs(goea_results).get_study_items()