sfa.analysis.perturb module

sfa.analysis.perturb.analyze_perturb(alg, data, targets, b=None, get_trj=False)[source]

Perform signal flow analysis under perturbations.

Parameters
algsfa.Algorithm

Algorithm object.

datasfa.Data

Data object which has perturbation data.

targetslist

List of node names, which are the keys of data.n2i.

bnumpy.ndarray

Basic vector for signaling sources or basal activities.

get_trjbool (optional)

Decide to get the trajectory of activity change.

Returns
actnumpy.ndarray

Change in the activities. It is usually calculated as x2 - x1, where x is the a vector of activities at steady-state.

Fnumpy.ndarray

A matrix of signal flows. It is usually calculated as W2*x1 - W1*x1, where W is weight matrix and x is a vector of activities at steady-state.

trjnumpy.ndarray (optional)

Trajectory of activity change, which is returned if get_trj is True.

sfa.analysis.perturb.resize_trj(trj_ctrl, trj_pert)[source]