def cypher_diagram(trait: str, pval_threshold: float):
diagram_nodes = [
DiagramNode(id=1, meta_node="GwasExposure", label=f"Trait\n{trait}"),
DiagramNode(id=2, meta_node="Gwas", label="Assoc_trait"),
DiagramNode(id=3, meta_node="Variant"),
DiagramNode(id=4, meta_node="Gene"),
DiagramNode(id=5, meta_node="Drug"),
]
diagram_edges = [
DiagramEdge(
from_id=2,
to_id=1,
meta_rel="MR_EVE_MR",
sub_label=f"\npval < {pval_threshold}"
if pval_threshold is not None else "",
),
DiagramEdge(
from_id=2,
to_id=3,
meta_rel="GWAS_TO_VARIANT",
sub_label="pval < 1e-8",
),
DiagramEdge(from_id=4, to_id=3, meta_rel="VARIANT_TO_GENE"),
DiagramEdge(from_id=5, to_id=4),
]
diagram = CypherDiagram(nodes=diagram_nodes, edges=diagram_edges)
diagram_data = diagram.generate_diagram()
return diagram_data
def cypher_diagram(
exposure_trait: Optional[str],
outcome_trait: Optional[str],
pval_threshold: float = 1e-5,
):
"""A diagram of cypher queries."""
exposure_label = (f"exposure GWAS\n{exposure_trait}"
if exposure_trait is not None else "exposure GWAS")
outcome_label = (f"outcome GWAS\n{outcome_trait}"
if outcome_trait is not None else "outcome GWAS")
diagram_nodes = [
DiagramNode(id=1, meta_node="Gwas", sub_label=exposure_label),
DiagramNode(id=2, meta_node="Gwas", sub_label=outcome_label),
]
diagram_edges = [
DiagramEdge(
from_id=1,
to_id=2,
meta_rel="MR_EVE_MR",
sub_label=f"p < {pval_threshold}",
)
]
diagram = CypherDiagram(nodes=diagram_nodes, edges=diagram_edges)
diagram_data = diagram.generate_diagram()
return diagram_data
def cypher_diagram(
trait: Optional[str],
efo_term: Optional[str],
disease_label: Optional[str],
score_threshold: float,
):
id = {"gwas": 1, "efo": 2, "disease": 3}
diagram_nodes = [
DiagramNode(id=id["gwas"], meta_node="Gwas", sub_label=trait),
DiagramNode(id=id["efo"], meta_node="Efo", sub_label=efo_term),
DiagramNode(
id=id["disease"], meta_node="Disease", sub_label=disease_label
),
]
edge_label = (
f"score > {score_threshold}" if score_threshold is not None else ""
)
diagram_edges = [
DiagramEdge(
from_id=id["gwas"],
to_id=id["efo"],
meta_rel="GWAS_NLP_EFO",
arrows=False,
sub_label=edge_label,
),
DiagramEdge(
from_id=id["efo"],
to_id=id["disease"],
meta_rel="MONDO_MAP_EFO",
arrows=False,
),
]
diagram = CypherDiagram(nodes=diagram_nodes, edges=diagram_edges)
diagram_data = diagram.generate_diagram()
return diagram_data
def cypher_diagram(trait: str, cor_coef_threshold: float = 0.8) -> str:
"""A diagram of cypher queries."""
diagram_nodes = [
DiagramNode(id=1, meta_node="Gwas", sub_label=trait),
DiagramNode(id=2, meta_node="Gwas", sub_label="Associated trait"),
]
diagram_edges = [
DiagramEdge(
from_id=1,
to_id=2,
meta_rel="OBS_COR",
sub_label=f"abs(cor_coef) > {cor_coef_threshold}",
arrows=False,
)
]
diagram = CypherDiagram(nodes=diagram_nodes, edges=diagram_edges)
diagram_data = diagram.generate_diagram()
return diagram_data
def cypher_diagram(
xqtl_mode: str,
exposure_gene: Optional[str],
outcome_trait: Optional[str],
variant: Optional[str],
mr_method: Optional[str],
qtl_type: Optional[str],
pval_threshold: float,
):
if xqtl_mode == "multi_snp_mr":
diagram_nodes = [
DiagramNode(id=1, meta_node="Gene", sub_label=exposure_gene),
DiagramNode(id=2, meta_node="Gwas", sub_label=outcome_trait),
]
diagram_edges = [
DiagramEdge(
from_id=1,
to_id=2,
meta_rel="XQTL_MULTI_SNP_MR",
sub_label=f"p < {pval_threshold}\n{mr_method}\n{qtl_type}",
)
]
else:
diagram_nodes = [
DiagramNode(id=1, meta_node="Gene", sub_label=exposure_gene),
DiagramNode(id=2, meta_node="Gwas", sub_label=outcome_trait),
DiagramNode(id=3, meta_node="Variant", sub_label=variant),
]
diagram_edges = [
DiagramEdge(
from_id=1,
to_id=2,
meta_rel="XQTL_SINGLE_SNP_MR_GENE_GWAS",
sub_label=f"p < {pval_threshold}\n{qtl_type}",
),
DiagramEdge(from_id=3,
to_id=1,
meta_rel="XQTL_SINGLE_SNP_MR_SNP_GENE"),
]
diagram = CypherDiagram(nodes=diagram_nodes, edges=diagram_edges)
diagram_data = diagram.generate_diagram()
return diagram_data
def cypher_diagram(
exposure_trait: Optional[str],
outcome_trait: Optional[str],
type: str,
pval_threshold: Optional[float],
):
edge_label = (
f"pval < {pval_threshold}" if pval_threshold is not None else ""
)
diagram_nodes = [
DiagramNode(id=1, meta_node="GwasExposure", sub_label=exposure_trait),
DiagramNode(id=2, meta_node="GwasOutcome", sub_label=outcome_trait),
DiagramNode(id=3, meta_node="Gwas", sub_label=type.capitalize()),
]
diagram_edges = [
# r2
DiagramEdge(
from_id=1, to_id=2, meta_rel="MR_EVE_MR", sub_label=edge_label
),
# r1
DiagramEdge(
from_id=int(r1.at[type, "from_id"]),
to_id=int(r1.at[type, "to_id"]),
meta_rel="MR_EVE_MR",
sub_label=edge_label,
dashes=True,
),
# r3
DiagramEdge(
from_id=int(r3.at[type, "from_id"]),
to_id=int(r3.at[type, "to_id"]),
meta_rel="MR_EVE_MR",
sub_label=edge_label,
dashes=True,
),
]
diagram = CypherDiagram(nodes=diagram_nodes, edges=diagram_edges)
diagram_data = diagram.generate_diagram()
return diagram_data
def cypher_diagram(
trait: str,
semmed_predicates: Optional[List[str]],
pval_threshold: float,
limit: int,
):
id = {"gwas": 1, "triple": 2, "lit": 3}
diagram_nodes = [
DiagramNode(id=id["gwas"], meta_node="Gwas", sub_label=trait),
DiagramNode(id=id["lit"], meta_node="Literature"),
DiagramNode(
id=id["triple"],
meta_node="LiteratureTriple",
sub_label=semmed_predicates[0]
if semmed_predicates is not None
else None,
),
]
diagram_edges = [
DiagramEdge(
from_id=id["gwas"],
to_id=id["triple"],
meta_rel="GWAS_TO_LITERATURE_TRIPLE",
),
DiagramEdge(
from_id=id["gwas"],
to_id=id["lit"],
meta_rel="GWAS_TO_LIT",
arrows=False,
dashes=True,
),
DiagramEdge(
from_id=id["triple"], to_id=id["lit"], meta_rel="SEMMEDDB_TO_LIT"
),
]
diagram = CypherDiagram(nodes=diagram_nodes, edges=diagram_edges)
diagram_data = diagram.generate_diagram()
return diagram_data
def cypher_diagram(trait: str, pval_threshold: float):
diagram_nodes = [
DiagramNode(id=1, meta_node="Gwas", sub_label=f"{trait}"),
DiagramNode(id=2, meta_node="Variant"),
DiagramNode(id=3, meta_node="Gene"),
DiagramNode(id=4, meta_node="Protein"),
DiagramNode(id=5, meta_node="Pathway"),
]
diagram_edges = [
DiagramEdge(
from_id=1,
to_id=2,
meta_rel="GWAS_TO_VARIANT",
sub_label=f"pval < {pval_threshold}"
if pval_threshold is not None else "",
),
DiagramEdge(from_id=2, to_id=3, meta_rel="VARIANT_TO_GENE"),
DiagramEdge(from_id=4, to_id=3, meta_rel="PROTEIN_TO_GENE"),
DiagramEdge(from_id=4, to_id=5, meta_rel="PROTEIN_IN_PATHWAY"),
]
diagram = CypherDiagram(nodes=diagram_nodes, edges=diagram_edges)
diagram_data = diagram.generate_diagram()
return diagram_data