def create_edge_schemas(type: str = "confounder"):
edge_schemas = [
NetworkEdgeSchema(
from_col="exposure.id",
to_col="outcome.id",
from_meta_node="GwasExposure",
hover_title_formatter=mr_eve_title_formatter(
exposure_id="exposure.id",
outcome_id="outcome.id",
estimate="r2.b",
se="r2.se",
p="r2.pval",
selection="r2.selection",
method="r2.method",
),
),
edge_confounder_exposure[type],
edge_confounder_outcome[type],
]
return edge_schemas
node_schemas = [
NetworkNodeSchema(
meta_node="Gwas",
id_col="trait.id",
label_formatter=gwas_label_formatter(node_name=None,
id_col="trait.id",
trait_col="trait.trait"),
),
NetworkNodeSchema(
meta_node="Gwas",
id_col="assoc_trait.id",
label_formatter=gwas_label_formatter(
node_name=None,
id_col="assoc_trait.id",
trait_col="assoc_trait.trait",
),
),
]
edge_schemas = [
NetworkEdgeSchema(
from_col="trait.id",
to_col="assoc_trait.id",
from_meta_node="Gwas",
arrows=False,
meta_rel="GENETIC_COR",
hover_title_formatter=lambda row: None,
)
]
meta_node="Pathway",
id_col="pathway.name",
label_col="pathway.name",
match_node_by="name",
),
],
edges=[
NetworkEdgeSchema(
from_col="gwas.id",
to_col="variant.name",
from_meta_node="Gwas",
hover_title_formatter=lambda row: """
<b>gwas.id</b>: {gwas_id},
<b>variant.name</b>: {variant_name}</br>
<b>beta</b>: {beta:.2E},
<b>se</b>: {se:.2E},
<b>p</b>: {p:.2E}
""".format(
gwas_id=row["gwas.id"],
variant_name=row["variant.name"],
beta=row["gwas_to_variant.beta"],
se=row["gwas_to_variant.se"],
p=row["gwas_to_variant.pval"],
),
),
NetworkEdgeSchema(
from_col="variant.name",
to_col="gene.name",
from_meta_node="Variant",
),
NetworkEdgeSchema(
from_col="gene.name",
),
NetworkNodeSchema(meta_node="Variant", id_col="variant.name"),
NetworkNodeSchema(
meta_node="Gene", id_col="gene.name", match_node_by="name"
),
NetworkNodeSchema(meta_node="Drug", id_col="drug.label"),
]
edge_schemas = [
NetworkEdgeSchema(
from_col="assoc_trait.id",
to_col="trait.id",
from_meta_node="Gwas",
hover_title_formatter=mr_eve_title_formatter(
exposure_id="assoc_trait.id",
outcome_id="trait.id",
estimate="mr.b",
se="mr.se",
p="mr.pval",
selection="mr.selection",
method="mr.method",
),
),
NetworkEdgeSchema(
from_col="variant.name", to_col="assoc_trait.id", from_meta_node="Gwas"
),
NetworkEdgeSchema(
from_col="variant.name", to_col="gene.name", from_meta_node="Variant"
),
NetworkEdgeSchema(
from_col="drug.label", to_col="gene.name", from_meta_node="Drug"
),
),
),
NetworkNodeSchema(meta_node="Variant", id_col="variant.name"),
NetworkNodeSchema(
meta_node="Gene", id_col="gene.name", match_node_by="name"
),
NetworkNodeSchema(meta_node="Drug", id_col="drug.label"),
],
edges=[
NetworkEdgeSchema(
from_col="risk_factor_gwas.id",
to_col="disease_gwas.id",
from_meta_node="Gwas",
hover_title_formatter=mr_eve_title_formatter(
exposure_id="risk_factor_gwas.id",
outcome_id="disease_gwas.id",
estimate="mr.b",
se="mr.se",
p="mr.pval",
selection="mr.selection",
method="mr.method",
),
),
# NetworkEdgeSchema(
# from_col="risk_factor_gwas.id",
# to_col="disease_gwas.id",
# cols=["obs_cor.cor"],
# from_meta_node="Gwas",
# dashes=True,
# arrows=False,
# ),
NetworkEdgeSchema(
from app.funcs.network_graph import NetworkEdgeSchema, NetworkNodeSchema
from app.utils.meta_graph import gwas_label_formatter
node_schemas = [
NetworkNodeSchema(
id_col="gwas.id",
label_formatter=gwas_label_formatter(node_name="gwas"),
meta_node="Gwas",
),
NetworkNodeSchema(id_col="triple.id", meta_node="LiteratureTriple"),
NetworkNodeSchema(id_col="lit.id", meta_node="Literature"),
]
edge_schemas = [
NetworkEdgeSchema(from_col="gwas.id",
to_col="triple.id",
from_meta_node="Gwas"),
NetworkEdgeSchema(
from_col="gwas.id",
to_col="lit.id",
from_meta_node="Gwas",
arrows=False,
dashes=True,
),
NetworkEdgeSchema(
from_col="triple.id",
to_col="lit.id",
from_meta_node="LiteratureTriple",
),
]
NetworkNodeSchema(
meta_node="GwasSecondary",
id_col="assoc_gwas.id",
label_col="assoc_gwas.trait",
),
NetworkNodeSchema(
meta_node="Gwas",
id_col="assoc_gwas2.id",
label_col="assoc_gwas2.trait",
),
],
edges=[
NetworkEdgeSchema(
from_col="gwas.id",
to_col="assoc_gwas.id",
from_meta_node="Gwas",
meta_rel="MR_EVE_MR",
cols=["gwas.id", "assoc_gwas.id", "mr.pval"],
),
# prs
NetworkEdgeSchema(
from_col="gwas.id",
to_col="assoc_gwas2.id",
from_meta_node="Gwas",
meta_rel="PRS",
cols=["gwas.id", "assoc_gwas2.id", "prs1.p"],
),
NetworkEdgeSchema(
from_col="assoc_gwas2.id",
to_col="assoc_gwas.id",
from_meta_node="Gwas",
from app.funcs.network_graph import NetworkEdgeSchema, NetworkNodeSchema
from app.utils.meta_graph import gwas_label_formatter
node_schemas = [
NetworkNodeSchema(
id_col="gwas.id",
label_formatter=gwas_label_formatter(node_name="gwas"),
meta_node="Gwas",
),
NetworkNodeSchema(id_col="efo.id", label_col="efo.value", meta_node="Efo"),
NetworkNodeSchema(id_col="disease.id",
label_col="disease.label",
meta_node="Disease"),
]
edge_schemas = [
NetworkEdgeSchema(
from_col="gwas.id",
to_col="efo.id",
from_meta_node="Gwas",
arrows=False,
),
NetworkEdgeSchema(
from_col="efo.id",
to_col="disease.id",
from_meta_node="Disease",
arrows=False,
),
]
""",
query_type=GalleryQueryType.cypher,
schema=GallerySchema(
nodes=[
NetworkNodeSchema(
meta_node="Gwas", id_col="g1.id", label_col="g1.trait"
),
NetworkNodeSchema(
meta_node="Gwas", id_col="g2.id", label_col="g2.trait"
),
NetworkNodeSchema(
meta_node="EfoPrimary", id_col="e.id", label_col="e.value"
),
NetworkNodeSchema(
meta_node="Efo", id_col="eChild.id", label_col="eChild.value"
),
],
edges=[
NetworkEdgeSchema(
from_col="e.id", to_col="eChild.id", from_meta_node="Efo"
),
NetworkEdgeSchema(
from_col="eChild.id", to_col="g1.id", from_meta_node="Efo"
),
NetworkEdgeSchema(
from_col="e.id", to_col="g2.id", from_meta_node="Efo"
),
],
),
)
meta_node="Gwas",
id_col="cf.id",
label_formatter=gwas_label_formatter(node_name="cf"),
),
]
edge_confounder_exposure = {
"confounder":
NetworkEdgeSchema(
from_col="cf.id",
to_col="exposure.id",
from_meta_node="Gwas",
dashes=True,
hover_title_formatter=mr_eve_title_formatter(
exposure_id="cf.id",
outcome_id="exposure.id",
estimate="r1.b",
se="r1.se",
p="r1.pval",
selection="r1.selection",
method="r1.method",
),
),
"intermediate":
NetworkEdgeSchema(
from_col="exposure.id",
to_col="cf.id",
from_meta_node="GwasExposure",
dashes=True,
hover_title_formatter=mr_eve_title_formatter(
exposure_id="exposure.id",
id_col="cf.id",
label_col="cf.trait"),
NetworkNodeSchema(
meta_node="GwasExposure",
id_col="exposure.id",
label_col="exposure.trait",
),
NetworkNodeSchema(
meta_node="GwasOutcome",
id_col="outcome.id",
label_col="outcome.trait",
),
],
edges=[
NetworkEdgeSchema(from_col="cf.id",
to_col="exposure.id",
from_meta_node="Gwas"),
NetworkEdgeSchema(
from_col="exposure.id",
to_col="outcome.id",
from_meta_node="GwasExposure",
),
NetworkEdgeSchema(
from_col="cf.id",
to_col="outcome.id",
from_meta_node="GwasOutcome",
),
],
),
)
# NOTE: it is impossible to specify a study to be exposure or outcome
# in the current api spec, as a study can be both exposure or outcome
# each time.
node_schemas = [
NetworkNodeSchema(
meta_node="Gwas",
id_col="exposure.id",
label_formatter=gwas_label_formatter(
node_name=None, id_col="exposure.id", trait_col="exposure.trait"
),
),
NetworkNodeSchema(
meta_node="Gwas",
id_col="outcome.id",
label_formatter=gwas_label_formatter(
node_name=None, id_col="outcome.id", trait_col="outcome.trait"
),
),
]
edge_schemas = [
NetworkEdgeSchema(
from_col="exposure.id",
to_col="outcome.id",
from_meta_node="Gwas",
hover_title_formatter=mr_eve_title_formatter(
exposure_id="exposure.id", outcome_id="outcome.id"
),
)
]
node_schemas_multi_snp = [
NetworkNodeSchema(meta_node="Gene",
id_col="gene.ensembl_id",
label_col="gene.name"),
NetworkNodeSchema(
meta_node="Gwas",
id_col="gwas.id",
label_formatter=lambda row: "{id}: {name}".format(
id=row["gwas.id"], name=row["gwas.trait"]),
),
]
edge_schemas_single_snp = [
NetworkEdgeSchema(
from_col="gene.ensembl_id",
to_col="gwas.id",
from_meta_node="Gene",
hover_title_formatter=single_snp_mr_title_formatter,
),
NetworkEdgeSchema(from_col="r.rsid",
to_col="gene.ensembl_id",
from_meta_node="Variant"),
]
edge_schemas_multi_snp = [
NetworkEdgeSchema(
from_col="gene.ensembl_id",
to_col="gwas.id",
from_meta_node="Gene",
hover_title_formatter=multi_snp_mr_title_formatter,
)
]