adhesion_class module

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

class adhesion_class.Adhesion(cells: List[Cell], s_coords: List[int], average_lifespan: int, adhesion_type: str = '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(cell_id)[source]

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

Parameters: cell_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.