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():
"""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 run_2(gosubdag):
"""Test GO colors at high and low levels of hierarchy."""
goids = [
'GO:0002682', # GO:0002682 1,127 D03 A regulation of immune system process
'GO:0002726'
] # GO:0002726 2 D09 A +reg of T cell cytokine production
gosubdag.prt_goids(goids)
go2color = {
'GO:0002682': '#b1fc99', # pale light green
'GO:0002726': '#f6cefc'
} # very light purple
plt_goids(gosubdag,
"test_get_parents2.png",
goids,
go2color=go2color,
mark_alt_id=True)
assert 'GO:0002682' in gosubdag.rcntobj.go2parents
def run_1(gosubdag_all):
"""Test that using an Alt ID to color a parent in the middle does color."""
# Main ID: GO:0035556 135 L04 D04 AB intracellular signal transduction
# Alt ID: GO:0007242 135 L04 D04 AB intracellular signal transduction
alt_goid_middle = 'GO:0007242' # Alt GO ID. Key GO (GO:0035556) NOT in go2color
alt_goid_color = '#f6cefc' # very light purple (Alt GO ID)
goid_key = gosubdag_all.go2obj[alt_goid_middle].id
# dcnt lev dep D1 Description
goids = [ # ---- --- --- ---- ----------------------------------------------
"GO:0007165", # 716 L03 D03 AB signal transduction (Header)
"GO:0007166", # 336 L04 D04 AB cell surface receptor signaling pathway
"GO:0007186", # 99 L04 D04 AB G-protein coupled receptor signaling pathway
"GO:0097527", # 0 L04 D04 AB necroptotic signaling pathway
"GO:0007167", # 120 L05 D05 AB enzyme linked receptor protein signaling pathway
"GO:0042770", # 11 L05 D05 ABCG signal transduction in response to DNA damage
"GO:0007229", # 0 L05 D05 AB integrin-mediated signaling pathway
"GO:0007205", # 0 L05 D05 AB protein kinase C-activating GPCR signaling pathway
"GO:0008630", # 1 L05 D06 ABCG intrinsic apoptotic signaling pw in rsp to DNA damage
"GO:0070059", # 1 L05 D06 ABCG intrinsic apoptotic signaling pw in rsp to ER stress
"GO:0035590", # 1 L06 D06 AB purinergic nucleotide receptor signaling pathway
"GO:0038063", # 0 L06 D07 AB collagen-activated tyrosine kinase receptor signaling pw
]
# If Alt ID is colored, then all equivalent GO IDs should be colored the same (unless overrode)
go2color = {go: '#d6fffa' for go in goids} # klash ice
go2color[alt_goid_middle] = alt_goid_color # very light purple (Alt GO ID)
# Check that middle parent was NOT colored by user, even tho alt GO ID's color was set
assert goid_key not in go2color
# Plot
godagplot = plt_goids(gosubdag_all,
"test_get_parents1.png",
goids,
go2color=go2color)
# Check that middle parent is colored properly, even if alt GO ID was used to set color
assert godagplot.pydotnodego.go2color[alt_goid_middle] == alt_goid_color
assert godagplot.pydotnodego.go2color[goid_key] == alt_goid_color
# Check that original user data is NOT modified (User not expecting their data modified)
assert goid_key not in go2color