from .constants import GRAPH_BUILDER_DEFAULT_PARAMS
from .mappings import GRAPH_BUILDERS
import networkx as nx
from pandas import DataFrame
[docs]def build_graph(so, spl: str, builder_type = 'knn', mask_key = 'cellmasks', key_added=None, config = None, inplace=True):
"""Build graph representation for a sample
Args:
so:
spl:
builder_type: graph type to construct {knn, radius, contact}
mask_key: key in so.masks[spl] to use as segmentation masks
key_added:
config: dict containing a dict 'builder_params' that specifies the graph construction parameters
inplace: whether to return a new SpatialOmics instance
Returns:
None or SpatialOmics if inplace = False
"""
if builder_type not in GRAPH_BUILDERS:
raise ValueError(f'invalid type {builder_type}. Available types are {GRAPH_BUILDERS.keys()}')
if config is None:
config = GRAPH_BUILDER_DEFAULT_PARAMS[builder_type].copy()
if key_added is None:
key_added = builder_type
if mask_key is None:
ndat = so.obs[spl][['x','y']]
builder = GRAPH_BUILDERS[builder_type](config)
g = builder(ndata=ndat)
else:
mask = so.get_mask(spl,mask_key)
g = GRAPH_BUILDERS[builder_type].from_mask(config, mask)
if 'include_self' in config['builder_params'] and config['builder_params']['include_self'] and builder_type == 'contact':
edge_list = [(i,i) for i in g.nodes]
g.add_edges_from(edge_list)
so = so if inplace else so.copy()
if spl in so.G:
so.G[spl].update({key_added: g})
else:
so.G[spl] = {key_added:g}