#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 22 13:53:34 2019
@author: mwu
"""
import _pickle as pk
import copy
import pandas as pd
import scipy
[docs]class Gnetdata:
"""
Gnetdata class includes dataset specifically
------------------------------------------------
for building GRNs. It consists four sub-classes:
1) Exp: A dict of sparse matrix, var_names and obj_names
2) CellAttrs: A dict gives information about cells. eg. cluster_nr, annotation
3) GeneAttrs: A dict gives information about genes. eg. module_nr, marker_annotation
4) NetAttrs: A dict includes Networks attributes. eg. node centralities.
"""
def __init__(self, Exp, CellAttrs=None, GeneAttrs=None):
self.Exp = Exp
self.CellAttrs = CellAttrs or {}
self.GeneAttrs = GeneAttrs or {}
self.NetAttrs = {'parameters': {}}
def _add_cellattr(self, attr_name, attr):
self.CellAttrs[attr_name] = attr
def _add_geneattr(self, attr_name, attr):
self.GeneAttrs[attr_name] = attr
def _add_netattr(self, attr_name, attr):
self.NetAttrs[attr_name] = attr
def _add_netattr_para(self, attr_name, attr):
self.NetAttrs['parameters'][attr_name] = attr
@property
def shape(self):
"""return the shape of Exp"""
return self.Exp['matrix'].shape
@property
def deepcopy(self):
"""make a deepcopy of gnetData """
return copy.deepcopy(self)
@property
def info(self):
""" return the shape of Exp and the keys of CellAttrs, GeneAttrs, NetAttrs"""
text = 'Gnetdata object with \nExp: {} x {}'.format(self.shape[0], self.shape[1])
attr = ['CellAttrs', 'GeneAttrs', 'NetAttrs']
for at in attr:
keys = getattr(self, at).keys() if getattr(self, at) is not None else None
text += '\n' + at + ':' + str(keys)
print(text)
[docs] def save_as(self, outpath):
"""save as pickle object """
if outpath is not None:
with open(outpath, 'wb') as outfile:
pk.dump(self, outfile)
else:
raise Exception('filepath cannot be null!')
[docs]def load_Gnetdata_object(filepath):
"""
load Gnetdata (pickle) from local
----------------------------------
:param filepath: str, default None.
:return: Gnetdata
"""
with open(filepath, 'rb') as input:
gnetdata = pk.load(input)
return gnetdata
[docs]def load_from_anndata(anndata_obj=None):
"""
Load adata object
--------------------------------------------
:param anndata_obj: adata object, default None
:return: Gnetdata
"""
if anndata_obj is None:
return None
matrix = scipy.sparse.csr_matrix(anndata_obj.X) if scipy.sparse.issparse(anndata_obj.X) else anndata_obj.X
gnetdata = Gnetdata(
Exp={
'matrix': matrix,
'feature': anndata_obj.var_names,
'cell': anndata_obj.obs_names
},
CellAttrs={
'CellInfo': anndata_obj.obs
},
GeneAttrs={
'GeneInfo': anndata_obj.var
}
)
return gnetdata