def _plt_gogrouped(self, goids, go2color_usr, **kws):
"""Plot grouped GO IDs."""
fout_img = self.get_outfile(kws['outfile'], goids)
sections = read_sections(kws['sections'], exclude_ungrouped=True)
print("KWWSSSSSSSS", kws)
# kws_plt = {k:v for k, v in kws.items if k in self.kws_plt}
grprobj_cur = self._get_grprobj(goids, sections)
# GO: purple=hdr-only, green=hdr&usr, yellow=usr-only
# BORDER: Black=hdr Blu=hdr&usr
grpcolor = GrouperColors(
grprobj_cur) # get_bordercolor get_go2color_users
grp_go2color = grpcolor.get_go2color_users()
grp_go2bordercolor = grpcolor.get_bordercolor()
for goid, color in go2color_usr.items():
grp_go2color[goid] = color
objcolor = Go2Color(self.gosubdag,
objgoea=None,
go2color=grp_go2color,
go2bordercolor=grp_go2bordercolor)
go2txt = GrouperPlot.get_go2txt(grprobj_cur, grp_go2color,
grp_go2bordercolor)
objplt = GoSubDagPlot(self.gosubdag,
Go2Color=objcolor,
go2txt=go2txt,
**kws)
objplt.prt_goids(sys.stdout)
objplt.plt_dag(fout_img)
sys.stdout.write("{N:>6} sections read\n".format(
N="NO" if sections is None else len(sections)))
return fout_img
def _get_objpltg(self, goids, go2color_usr, **kws):
"""Plot grouped GO IDs."""
#### fout_img = self.get_outfile(kws['outfile'], goids)
sections = read_sections(kws['sections'], exclude_ungrouped=True)
# print ("KWWSSSSSSSS", kws)
# kws_plt = {k:v for k, v in kws.items if k in self.kws_plt}
grprobj_cur = self._get_grprobj(goids, sections)
# GO: purple=hdr-only, green=hdr&usr, yellow=usr-only
# BORDER: Black=hdr Blu=hdr&usr
grpcolor = GrouperColors(
grprobj_cur) # get_bordercolor get_go2color_users
grp_go2color = grpcolor.get_go2color_users()
grp_go2bordercolor = grpcolor.get_bordercolor()
for goid, color in go2color_usr.items():
grp_go2color[goid] = color
objcolor = Go2Color(self.gosubdag,
objgoea=None,
go2color=grp_go2color,
go2bordercolor=grp_go2bordercolor)
go2txt = GrouperPlot.get_go2txt(grprobj_cur, grp_go2color,
grp_go2bordercolor)
return GoSubDagPlot(self.gosubdag,
Go2Color=objcolor,
go2txt=go2txt,
**kws)
def test_grouper_d2(do_plot=False):
"""Group depth-02 GO terms under their most specific depth-01 GO parent(s)."""
# Get GOs to be grouped
# Since no "Grouping GOs" were provided, depth-01 GOs are used for grouping.
grprdflt = GrouperDflts()
hdrobj = HdrgosSections(grprdflt.gosubdag,
grprdflt.hdrgos_dflt,
sections=None,
hdrgos=None)
grprobj = Grouper("Transient Increase",
get_data0(),
hdrobj,
grprdflt.gosubdag,
go2nt=None)
objwr = WrSections(grprobj)
objwr.wr_txt_section_hdrgos("transient_increase_hdrgos.txt")
objwr.wr_txt_grouping_gos()
if do_plot:
# Don't run in Travis-CI because it does not contain 'dot'
from goatools.grouper.grprplt import GrouperPlot
GrouperPlot(grprobj).plot_groups_unplaced()
chk_hdrs(grprobj)
def test_dflthdrs(prt=sys.stdout, do_plt=False):
"""Group depth-02 GO terms under their most specific depth-01 GO parent(s)."""
# Initialize GoSubDag for grouping use once, since it takes a few seconds to initialize
grprdflt = _get_grprdflt()
# Get GOs to be grouped
data = get_data0()
# This may need to be updated if default hdrgos are changed
exp_hdrs0 = set([
"GO:0050789", # BP 11,095 L01 D01 B regulation of biological process
"GO:0044848", # BP 62 L01 D01 S biological phase
"GO:0050794", # BP 8,031 L02 D02 AB regulation of cellular process
"GO:0019222", # BP 3,227 L02 D02 AB regulation of metabolic process
"GO:0048583", # BP 2,377 L02 D02 AB regulation of response to stimulus
"GO:0050793", # BP 1,789 L02 D02 AB regulation of developmental process
"GO:0023051", # BP 1,364 L02 D02 AB regulation of signaling
"GO:0002682", # BP 1,183 L02 D02 AB regulation of immune system process
"GO:0007155", # BP 165 L02 D02 P cell adhesion
"GO:0080134", # BP 940 L03 D03 AB regulation of response to stress
"GO:0007165", # BP 717 L03 D03 AB signal transduction
"GO:0050877", # BP 96 L03 D03 K neurological system process
"GO:0007267"
]) # BP 99 L03 D04 CDR cell-cell signaling
# Since no "GO group headers" (None) were provided, depth-01 GOs are used for grouping.
hdrobj0 = HdrgosSections(grprdflt.gosubdag,
grprdflt.hdrgos_dflt,
sections=None,
hdrgos=None)
grprobj0 = Grouper("dflt", data, hdrobj0, grprdflt.gosubdag, go2nt=None)
_, _, nts0_go, act_hdrs0 = run(grprobj0, hdrobj0, exp_hdrs0)
# Grouping GOs are provided, these are added to the depth-01 defaults GOs are used for grouping.
hdrgos = set([
"GO:0099536", # BP 40 L04 D05 CDR regulation of response to stimulus
"GO:0051239", # BP 2,532 L02 D02 AB regulation of multicellular organismal process
"GO:0048519", # BP 3,293 L02 D02 AB negative regulation of biological process
"GO:0048518"
]) # BP 3,353 L02 D02 AB positive regulation of biological process
exp_hdrs1 = exp_hdrs0.union(hdrgos)
name = "usrhdrs4"
hdrobj1 = HdrgosSections(grprdflt.gosubdag,
grprdflt.hdrgos_dflt,
sections=None,
hdrgos=hdrgos)
grprobj1 = Grouper(name, data, hdrobj1, grprdflt.gosubdag, go2nt=None)
sortobj1, _, nts1_go, act_hdrs1 = run(grprobj1, hdrobj1, exp_hdrs1)
if do_plt:
from goatools.grouper.grprplt import GrouperPlot
prt.write("\nPLOT DAG\n")
GrouperPlot(grprobj1).plot_grouped_gos()
# GO:0099536 was a "middle" term (neither usrgo, not hdrgo) in run0, but is a hdrgo in run1
# print "THIS"
# grprdflt.gosubdag.prt_goids(nts1_go)
# print "MINUS"
# grprdflt.gosubdag.prt_goids(nts0_go)
# print "EQUALS"
# print nts1_go.difference(nts0_go)
assert nts1_go.difference(nts0_go) == set(["GO:0099536"])
assert act_hdrs1.difference(act_hdrs0) == set(hdrgos)
hdrgo_prt = False
sys.stdout.write("\n{NAME}: PRINT GOs hdrgo_prt({H}):\n".format(
H=hdrgo_prt, NAME=name))
sortobj1.prt_gos(hdrgo_prt=hdrgo_prt)
nts2 = sortobj1.get_nts_flat(hdrgo_prt)
nts2_go = set([nt.GO for nt in nts2])
assert len(nts1_go) > len(nts2_go)
assert nts1_go.intersection(data) == nts2_go
assert nts2_go == data