funcs

Granger Causality as functions.

Shift Trajectories

shift_trajectories

 shift_trajectories (df:pandas.core.frame.DataFrame,
                     shift:Optional[int]=10, copy:Optional[bool]=True)

	Type	Default	Details
df	DataFrame		Pandas DataFrame where rows are the response variable (genes), and columns are predictors (expression).
shift	Optional	10	number to shift `df`’s values by
copy	Optional	True	Whether or not to copy input `df`
Returns	DataFrame		Pandas DataFrame of `df - df_shift`

source

get_pval_from_granger_causality_tests

 get_pval_from_granger_causality_tests (df:pandas.core.frame.DataFrame,
                                        test:Optional[str]='ssr_chi2test',
                                        lag_order:Optional[int]=1,
                                        max_lag:Optional[tuple]=(1,))

	Type	Default	Details
df	DataFrame		Pandas DataFrame where rows are the response variable (genes), and columns are predictors (expression).
test	Optional	ssr_chi2test	the kind of statistical test to use
lag_order	Optional	1	how long to lag
max_lag	Optional	(1,)	if `None` coerced to `(1, )`
Returns	float		minimum p-value of Granger Causality Tests

Granger Causation

source

grangers_causation_matrix

 grangers_causation_matrix (df:pandas.core.frame.DataFrame, x_vars:Union[l
                            ist,pandas.core.series.Series,numpy.ndarray,It
                            erable[numbers.Number],Any,List[int],List[Unio
                            n[bool,numpy.bool_,Literal[0],Literal[1]]],pan
                            das.core.indexes.base.Index,NoneType]=None, y_
                            vars:Union[list,pandas.core.series.Series,nump
                            y.ndarray,Iterable[numbers.Number],Any,List[in
                            t],List[Union[bool,numpy.bool_,Literal[0],Lite
                            ral[1]]],pandas.core.indexes.base.Index,NoneTy
                            pe]=None, test:Optional[str]='ssr_chi2test',
                            lag_order:Optional[int]=1,
                            max_lag:Optional[tuple]=(1,),
                            n_jobs:Optional[int]=-1)

Computes Granger Causality

	Type	Default	Details
df	DataFrame		Pandas DataFrame where rows are the response variable (genes), and columns are predictors (expression).
x_vars	Union	None	A subset of response variable (genes) to compute granger’s causality test with. If not provided, defaults to `df.index.values` i.e. all rows in `df`.
y_vars	Union	None	A subset of response variable (genes) to compute granger’s causality test with. If not provided, defaults to `df.index.values` i.e. all rows in `df`.
test	Optional	ssr_chi2test	the kind of statistical test to use
lag_order	Optional	1	how long to lag
max_lag	Optional	(1,)	if `None` coerced to `(1, )`
n_jobs	Optional	-1	number of cpu threads to use during calculation
Returns	DataFrame		Pandas DataFrame with shape `(len(x_vars), len(y_vars))` containing the minimum p-value from Granger’s Causation Tests

source

calculate_granger_causation

 calculate_granger_causation (df:pandas.core.frame.DataFrame, x_vars:Union
                              [list,pandas.core.series.Series,numpy.ndarra
                              y,Iterable[numbers.Number],Any,List[int],Lis
                              t[Union[bool,numpy.bool_,Literal[0],Literal[
                              1]]],pandas.core.indexes.base.Index,NoneType
                              ]=None, y_vars:Union[list,pandas.core.series
                              .Series,numpy.ndarray,Iterable[numbers.Numbe
                              r],Any,List[int],List[Union[bool,numpy.bool_
                              ,Literal[0],Literal[1]]],pandas.core.indexes
                              .base.Index,NoneType]=None,
                              shift:Optional[int]=10,
                              test:Optional[str]='ssr_chi2test',
                              lag_order:Optional[int]=1,
                              max_lag:Optional[tuple]=(1,),
                              n_jobs:Optional[int]=-1)

Computes Granger Causality

	Type	Default	Details
df	DataFrame		Pandas DataFrame where rows are the response variable (genes), and columns are predictors (expression).
x_vars	Union	None	A subset of response variable (genes) to compute granger’s causality test with. If not provided, defaults to `df.index.values` i.e. all rows in `df`.
y_vars	Union	None	A subset of response variable (genes) to compute granger’s causality test with. If not provided, defaults to `df.index.values` i.e. all rows in `df`.
shift	Optional	10	number to shift `df`’s values by
test	Optional	ssr_chi2test	the kind of statistical test to use
lag_order	Optional	1	how long to lag
max_lag	Optional	(1,)	if `None` coerced to `(1, )`
n_jobs	Optional	-1	number of cpu threads to use during calculation
Returns	DataFrame		Pandas DataFrame with shape `(len(x_vars), len(y_vars))` containing the minimum p-value from Granger’s Causation Tests