c6 package

Subpackages

• c6.data package
  • Module contents
• c6.utils package
  • Submodules
  • c6.utils.encoding module
  • c6.utils.math module
  • c6.utils.nameing module
  • c6.utils.serialize module
  • Module contents

Submodules

c6.cell module

class c6.cell.Cell(space=None, loc=[0, 0], radius=2, **kwargs)

Bases: object

A circular cell that meanders about

Create our circular cell. Values given in µm/sec

Parameters

• space (c6.space) – a parent space, default is None

• loc (2 tuple) – starting xy location of this cell, (default 0,0)

• radius (float) – cell size

• dir (2 tuple) – initial direction of movement

• speed (float) – initial migratory speed

• age (int) – how many timesteps old this cell is

• sensing (float) – distance across which we sense other cells

• influence_max (float) – level of influence max value

• influence_decay (float) – level of influence `exponential decay`_ constant

• adhesion (float) – well depth for LJP

• direction_dispersion (float) – how strong our directional memory is

• repel_limit (float) – how far a cell can move to avoid overlap, tuned along with adhesion to avoid oscillation

• rad_mult (float) – cell-to-nuclear radius ratio, used for repulsion

• id (int or str) – unique name of this cell, defaults to 6 random alphanumerics

• parent (int or str or None) – id of parent of this cell, if any

• .. _exponential decay (http://mathworld.wolfram.com/ExponentialDecay.html)

remove()

Remove self from simulation

step()

c6.plot module

Manage plotting of circles in a box

c6.plot.animate(fig, ax, space, frames, callback=None)

c6.plot.plot_cells(cells, ax=None)

c6.plot.pop_patch_dec(cell, patches)

Decorate remove method so it kills that cell’s patches

c6.space module

class c6.space.Space

Bases: object

Space tracks the locations of cells within a space

add_cell(cell)

Add cell and regenerate distance tree

nearest(cell, n=1)

The n nearest cells to a given cell Must call step first to generate search tree.

plot(ax=None)

Quick plot cells onto a provided matplotlib axis

remove_cell(cell)

Remove cell and regenerate distance tree

step()

Tell every cell to go through one time step

within(cell, rad)

Find all cells within a radius of a given cell. Must call step first to generate search tree.

Module contents

Top-level package for Circular Center-based Cell Colony Creation and Clustering.

c6.get_module_version()