path_integral_B {fitlandr} | R Documentation |
Bhattacharya method for path integration
Description
A method to construct potential landscapes using path integration. See references for details.
Usage
path_integral_B(
f,
lims,
n_path_int = 20,
stepsize = 0.01,
tol = 0.01,
numTimeSteps = 1400,
...
)
Arguments
f |
The vector field function. It should return |
lims |
The limits of the range for the estimation as |
n_path_int |
The number of equally spaced points in each axis, at which the path integrals is to be calculated. |
stepsize |
The time step used in each iteration. |
tol |
The tolerance to test convergence. |
numTimeSteps |
Number of time steps for integrating along each path (to ensure uniform arrays). Choose high-enough number for convergence with given stepsize. |
... |
Not in use. |
Value
A list with the following elements:
-
numPaths
Integer. Total Number of paths for defined grid spacing. -
pot_path
Matrix. Potential along the paths. -
path_tag
Vector. Tag for given paths. -
attractors_pot
Vector. Potential value of each identified attractor by the path integral approach. -
x_path
Vector. x-coord. along path. -
y_path
Vector. y-coord. along path.
References
Bhattacharya, S., Zhang, Q., & Andersen, M. E. (2011). A deterministic map of Waddington’s epigenetic landscape for cell fate specification. BMC Systems Biology, 5(1), 85. https://doi.org/10.1186/1752-0509-5-85. The functions in this file were translated from the Matlab code provided with the reference above, and its Python translation at https://dynamo-release.readthedocs.io/en/v0.95.2/_modules/dynamo/vectorfield/Bhattacharya.html