def GOs_to_nx(goea_results, sig=0.05):
sig_go = [go for go in goea_results if go.p_fdr_bh <= sig]
godagsmall = OboToGoDagSmall(
goea_results=sig_go).godag
try:
import networkx as nx
except ImportError as e:
print('NetworkX not installed')
node_info = [(go.GO, {"depth": go.depth, "enrichment": go.enrichment,
"name": go.name, "p_uncorrected": go.p_uncorrected,
"p_fdr_bh": go.p_fdr_bh, "pop_count": go.pop_count,
"pop_items": go.pop_items, "pop_n": go.pop_n,
"ratio_in_pop": go.ratio_in_pop,
"ratio_in_study": go.ratio_in_study,
"study_count": go.study_count,
"study_items": go.study_items,
"study_n": go.study_n}) for go in sig_go]
conns = godagsmall.p_from_cs
edges = []
for k, v in dict(conns).items():
if 'GO' in str(k):
vals = list(v)
for g in vals:
edges.append((k, g))
G = nx.Graph()
G.add_nodes_from(node_info)
G.add_edges_from(edges)
return G
def plot_gos(fout_png, goids, obo_dag, *args, **kws):
"""Given GO ids and the obo_dag, create a plot of paths from GO ids."""
engine = kws['engine'] if 'engine' in kws else 'pydot'
godagsmall = OboToGoDagSmall(goids=goids, obodag=obo_dag).godag
# godagplot = GODagSmallPlot(godagsmall, *args, **kws)
godagplot = GODagSmallPlot(godagsmall, obo=obo_dag, *args, **kws) # add by gdq
godagplot.plt(fout_png, engine)
def plt_goea_results(fout_png, goea_results, *args, **kws):
"""Plot a single page."""
engine = kws['engine'] if 'engine' in kws else 'pydot'
godagsmall = OboToGoDagSmall(goea_results=goea_results).godag
godagplot = GODagSmallPlot(godagsmall,
*args,
goea_results=goea_results,
**kws)
godagplot.plt(fout_png, engine)
def plot_goid2goobj(fout_png, goid2goobj, *args, **kws):
"""Given a dict containing GO id and its goobj, create a plot of paths from GO ids."""
engine = kws['engine'] if 'engine' in kws else 'pydot'
godagsmall = OboToGoDagSmall(goid2goobj=goid2goobj).godag
godagplot = GODagSmallPlot(godagsmall, *args, **kws)
godagplot.plt(fout_png, engine)
def parent_terms(go_dag, go_id):
'''Return parent terms of `go_id` in a `go_dag`.
'''
sub_dag = OboToGoDagSmall(goids=[go_id], obodag=go_dag).godag
all_parents = list(sub_dag.go2obj.keys())
return all_parents
