def _run(goea_results, flds):
"""Get string representations of P-value data floats ."""
obj = MgrNtGOEAs(goea_results)
pval_flds = set("s_" + k[2:] for k in flds if k[:2] == "p_")
nts = obj.get_nts_strpval()
fmts = ["{FLD}={{{FLD}}}".format(FLD=f) for f in pval_flds]
fmt = "{N} {NS} {GO} " + " ".join(fmts) + " {name}"
for idx, ntd in enumerate(nts):
print(fmt.format(N=idx, **ntd._asdict()))
print("FORMAT", fmt)
def _run(goea_results, flds):
"""Get string representations of P-value data floats ."""
obj = MgrNtGOEAs(goea_results)
pval_flds = set("s_" + k[2:] for k in flds if k[:2] == "p_")
nts = obj.get_nts_strpval()
fmts = ["{FLD}={{{FLD}}}".format(FLD=f) for f in pval_flds]
fmt = "{N} {NS} {GO} " + " ".join(fmts) + " {name}"
for idx, ntd in enumerate(nts):
print(fmt.format(N=idx, **ntd._asdict()))
print("FORMAT", fmt)
def test_example():
"""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)
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 test_example(prt=sys.stdout):
"""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)
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 = lambda nt: [
getattr(nt, 'namespace'),
getattr(nt, 'enrichment'),
getattr(nt, 'p_uncorrected'),
getattr(nt, 'depth'),
getattr(nt, 'GO')
]
nts_goea = sorted(nts_goea, key=sortby)
wr_py_nts(fout_py, nts_goea, docstring, var_name)
def get_ns2nts(results, fldnames=None, **kws):
"""Get namedtuples of GOEA results, split into BP, MF, CC."""
ns2nts = cx.defaultdict(list)
nts = MgrNtGOEAs(results).get_goea_nts_all(fldnames, **kws)
for ntgoea in nts:
ns2nts[ntgoea.NS].append(ntgoea)
return ns2nts
def wr_xlsx(self, fout_xlsx, goea_results, **kws):
"""Write a xlsx file."""
# kws: prt_if indent itemid2name(study_items)
objprt = PrtFmt()
prt_flds = kws.get('prt_flds', self.objprtres.get_prtflds_default(goea_results))
xlsx_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
if 'fld2col_widths' not in kws:
kws['fld2col_widths'] = {f:objprt.default_fld2col_widths.get(f, 8) for f in prt_flds}
RPT.wr_xlsx(fout_xlsx, xlsx_data, **kws)
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 prt_txt(self, prt, goea_results, prtfmt=None, **kws):
"""Print GOEA results in text format."""
if prtfmt is None:
prtfmt = (
"{GO} {NS} {p_uncorrected:5.2e} {ratio_in_study:>6} {ratio_in_pop:>9} "
"{depth:02} {name:40} {study_items}\n")
prtfmt = self.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 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 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 prt_txt(self, 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 = " ".join([objprt.default_fld2fmt[f] for f in flds])
#### prtfmt = ("{GO} {NS} {p_uncorrected:5.2e} {ratio_in_study:>6} {ratio_in_pop:>9} "
#### "{depth:02} {name:40} {study_items}\n")
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_objaart(goea_results, **kws):
"""Return a AArtGeneProductSetsOne object."""
nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
def wr_tsv(self, fout_tsv, goea_results, **kws):
"""Write tab-separated table data to file"""
prt_flds = kws.get('prt_flds', self.get_prtflds_default(goea_results))
tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.wr_tsv(fout_tsv, tsv_data, **kws)
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_go2nt(self, goea_results):
"""Return go2nt with added formatted string versions of the P-values."""
go2obj = self.objaartall.grprdflt.gosubdag.go2obj
# Add string version of P-values
goea_nts = MgrNtGOEAs(goea_results).get_nts_strpval()
return {go2obj[nt.GO].id: nt for nt in goea_nts if nt.GO in go2obj}
def prt_tsv(self, prt, goea_results, **kws):
"""Write tab-separated table data"""
prt_flds = kws.get('prt_flds', self.objprtres.get_prtflds_default(goea_results))
tsv_data = MgrNtGOEAs(goea_results).get_goea_nts_prt(prt_flds, **kws)
RPT.prt_tsv(prt, tsv_data, **kws)