(Pairwise) Graph

For graph layoout related functions

to_net

 to_net (col_node_id:str, col_source:str, col_target:str,
         col_subset_id:str, nodes:pandas.core.frame.DataFrame=None,
         edges:pandas.core.frame.DataFrame=None, nodes_path:str=None,
         edges_path:str=None, col_node_name:str=None,
         col_subset_name:str=None, cmap_subsets=None,
         remove_orphans:bool=True, show_node_names:bool=True,
         off_subset_name:int=15, config_base_path:str=None,
         defaults:dict=None, use_urls:bool=False, out:str=None,
         plot:bool=True, testn:int=None, verbose:bool=False)

*Plots the interactive pairwise graph.

Args: nodes (pd.DataFrame): node data edges (pd.DataFrame): edge data col_node_id (str): node id col_node_name (str): node name col_source (str): source column col_target (str): target column col_subset_id (str): subset id col_subset_name (str): subset name nodes_path (str, optional): path to nodes file. Defaults to None. edges_path (str, optional): path to edges file. Defaults to None. cmap_subsets (type, optional): colormap. Defaults to None. show_node_names (bool, optional): show node names. Defaults to True. off_subset_name (int, optional): offset of the subset names from the node names. Defaults to 15. config_base_path (str, optional): vega config path. Defaults to None. defaults (dict, optional): default vega settings. Defaults to None. use_urls (bool, optional): use urls in the vega config. Defaults to False. out (str, optional): output format. Defaults to None. plot (bool, optional): plot or not. Defaults to True. testn (int, optional): test n nodes. Defaults to None. verbose (bool, optional): verbose. Defaults to False.

Returns: tuple: vega config, nodes*

	Type	Default	Details
col_node_id	str
col_source	str
col_target	str
col_subset_id	str
nodes	DataFrame	None	data
edges	DataFrame	None
nodes_path	str	None
edges_path	str	None
col_node_name	str	None	labels
col_subset_name	str	None	‘gene set name’,
cmap_subsets	NoneType	None	‘nipy_spectral’
remove_orphans	bool	True	# switches
show_node_names	bool	True
off_subset_name	int	15	# knobs
config_base_path	str	None	‘inputs/edge_bundle.json’,
defaults	dict	None
use_urls	bool	False
out	str	None
plot	bool	True
testn	int	None	# etc
verbose	bool	False
Returns	tuple

source

get_preprocessed

 get_preprocessed (nodes:pandas.core.frame.DataFrame,
                   edges:pandas.core.frame.DataFrame, col_node_id:str,
                   col_node_name:str, col_subset_id:str,
                   col_subset_name:str, _col_node_id:str,
                   _col_node_name:str, _col_node_parent:str,
                   _col_source:str, _col_target:str, _col_subset_name:str,
                   col_source:str, col_target:str, remove_orphans:bool,
                   testn:int=None, verbose:bool=False)

*Get preprocessed nodes and edges

Returns: tuple: nodes, edges*

source

center_subset_label

 center_subset_label (ds1:pandas.core.series.Series)

Removes the subset label except at the middle.

Demo data

## demo data
from parag.core import get_net_data
import scanpy as sc
nodes,edges=get_net_data(sc.datasets.pbmc68k_reduced())

nodes.head(1)

edges.head(1)

cfg_base,nodes_=to_net(
    nodes=nodes,
    edges=edges,
    col_node_id='cell id',
    col_source='cell id1',
    col_target='cell id2',
    col_subset_id='bulk_labels',
    defaults=dict(
        radius=165,
        textSize=8,
        textOffset=7,
    ),
    # show_node_names=False,
)

nodes_.head()