adhesion_class module

Implementation of a class to represent the cell-cell adhesions.

class adhesion_class.Adhesion(cells, s_coords, average_lifespan, adhesion_type='cadherin')[source]

Bases: object

A class to represent an adhesion agent in a tissue. This is a useful object to keep track of which cells the adhesion is attached to and the coordinates and locations in the deformed and undeformed cortex configurations.

cell_index_by_id(id)[source]

Get the local index on a cortex that the adhesion is attached to.

Parameters

id (string) – The identity of the cell to look on.

Returns

The local index that the adhesion is connected to for the given cell.

Return type

string

get_angle_relative_to_cortices()[source]

Get the angle the adhesion makes relative to the tangent along both cortices

Returns

The angle that the adhesion makes relative to the tangent along the connected cortices.

Return type

(float, float)

get_cell_id_at_other_end(this_cell_id)[source]

Returns the identity at the other side of the adhesion, given that we are in this_cell

Parameters

this_cell_id (string) – The identity of the cell that we know.

Returns

The identity of the cell on the other side.

Return type

string

get_force_magnitude(cell_id_for_new_xy='None', new_xy=(0, 0))[source]

Force acting on adhesion

Parameters
  • cell_id_for_new_xy (string) – (Default value = ‘None’) Optional identifier for cell that we want to change the position of.

  • new_xy (tuple) – (Default value = (0, 0) The new (x,y) position of the given cell.

Returns

The magnitude of (spring) force in the adhesion.

Return type

float

get_length(cell_id_for_new_xy='None', new_xy=(0, 0))[source]

Get the length of the adhesion. Can change the xy location of one of the cells.

Parameters
  • cell_id_for_new_xy (string) – (Default value = ‘None’) Optional identifier for cell that we want to change the position of.

  • new_xy (tuple) – (Default value = (0, 0) The new (x,y) position of the given cell.

Returns

The length of the adhesion.

Return type

float

get_spacing_at_other_end(this_cell_id)[source]

Returns the spacing at the other side of the adhesion, given that we are in cell with this_cell_id

Parameters

this_cell_id (string) – The identity of the cell that we know/are in.

Returns

The discretised spacing on the other cortex.

Return type

float

get_unit_direction(cell_id_for_new_xy='None', new_xy=(0, 0))[source]

Get a vector describing the direction of the adhesion

Parameters
  • cell_id_for_new_xy (string) – (Default value = ‘None’) Optional identifier for cell that we want to change the position of.

  • new_xy (tuple) – (Default value = (0, 0) The new (x,y) position of the given cell.

Returns

The direction of the adhesion, from cell1 to cell2

Return type

list

get_vector_force(from_cell_id, new_xy_for_from_cell=(0, 0))[source]

Get a vector for the adhesion force, acting on from_cell_id

Parameters
  • cell_id_for_new_xy (string) – (Default value = ‘None’) Optional identifier for cell that we want to change the position of.

  • new_xy (tuple) – (Default value = (0, 0) The new (x,y) position of the given cell.

Returns

The vector force exerted by the adhesion on cell 1.

Return type

list

get_xy()[source]

Get the [(x_1, y_1), (x_2, y_2)] coords of the cell connections

Returns

The coords of the adhesion connections.

Return type

list

get_xy_at_other_end(this_cell_id)[source]

Returns the spacing at the other side of the adhesion, given that we are in this_cell

Parameters

this_cell_id (string) – The identifier of the cell we know.

Returns

The (x,y) coords that the adhesion is connected to on the other end.

Return type

list

get_xy_at_this_end(this_cell_id)[source]

Returns the discrete cortex spacing where the adhesion is attached to a given cell

Parameters

this_cell_id (string) – The identity of the cell to get the spacing.

Returns

The (x,y) coords that the adhesion is connected to on the given cell.

Return type

list

plot(ax=None, **plot_params)[source]
Parameters
  • ax (mpl axis) – (Default value = None) Axis object to plot on.

  • plot_params (dict) – Optional plotting arguments.

update_local_cell_indices_with_s()[source]

Updates the local cortex indices by the s values for the cells.

update_s_by_local_cell_indices()[source]

Updates the local cortex indices by the s values for the cells.