spateo.plotting.static.networks#

Module Contents#

Classes#

PlotNetwork

Functions#

plot_network(→ plotly.graph_objects.FigureWidget)

Network graph using plotly, used to plot intercellular GRN as inferred by Spateo.
class spateo.plotting.static.networks.PlotNetwork(G: networkx.Graph | networkx.DiGraph, layout: str)[source]#
generate_node_traces(colorscale: str, colorbar_title: str, color_method: str | List[str], node_label: str, node_text: List[str], node_label_size: int, node_label_position: str, node_opacity: float, size_method: str | List[str], show_colorbar: bool = True) → plotly.graph_objects.Scatter[source]#

Formatting for nodes.

Parameters:
colorscale

Colormap to use for nodes

colorbar_title

Title for the colorbar

color_method

Either label of node property or list containing the color of each node

node_label

Node property to be used as label

node_text

List containing properties to be displayed when hovering over nodes

node_label_size

Font size of node text

node_label_position

Position of node labels. Options: ‘top left’, ‘top center’, ‘top right’, ‘middle left’, ‘middle center’, ‘middle right’, ‘bottom left’, ‘bottom center’, ‘bottom right’

node_opacity

Transparency of nodes

size_method

Either label of node property or list containing the size of each node

show_colorbar

Set True to include colorbar, False to remove from plotting window

Returns:

Plotly graph objects scatter plot

Return type:

node_trace

generate_edge_traces(edge_label: str, edge_label_size: int, edge_label_position: str, edge_text: List[str], edge_attribute_for_linestyle: str | None = None, edge_attribute_for_thickness: str | None = None, add_text: bool = False) → Tuple[List[plotly.graph_objects.Scatter], plotly.graph_objects.Scatter][source]#

Formatting for edges

Parameters:
edge_label

Edge property to be used as label

edge_label_size

Font size of edge text

edge_label_position

Position of edge labels. Options: ‘top left’, ‘top center’, ‘top right’, ‘middle left’, ‘middle center’, ‘middle right’, ‘bottom left’, ‘bottom center’, ‘bottom right’

edge_text

List containing properties to be displayed when hovering over edges

edge_attribute_for_linestyle

Optional edge property to use for linestyle. If not given, will default to property given to ‘edge_label’.

edge_attribute_for_thickness

Optional edge property to use for thickness. If not given, all edges will have thickness 1.

add_text

If True, will add text corresponding to edge_label onto the edges rather than only adding different line styles.

Returns:

Plotly graph objects scatter plots middle_node_trace: Labels are created by adding invisible nodes to the middle of each edge. This

trace contains information for these invisible nodes.

Return type:

edge_traces

generate_figure(node_trace: plotly.graph_objects.Scatter, edge_traces: List[plotly.graph_objects.Scatter], middle_node_trace: plotly.graph_objects.Scatter, title: str, title_font_size: int, arrow_size: float, transparent_background: bool, highlight_neighbors_on_hover: bool, upper_margin: float = 40, lower_margin: float = 20, left_margin: float = 50, right_margin: float = 50) → plotly.graph_objects.FigureWidget[source]#

Generate figure for graph

_apply_layout(G, layout)[source]#

Applies a layout to a Graph.

on_hover(trace: plotly.graph_objects.Scatter, points: plotly.callbacks.Points, state: plotly.callbacks.InputDeviceState)[source]#

Callback function for when a node is hovered over

Parameters:
trace

Figure trace for the node

points

Points that are hovered over

on_unhover(trace: plotly.graph_objects.Scatter, points: plotly.callbacks.Points, state: plotly.callbacks.InputDeviceState)[source]#

Callback function for when a node is unhovered over.

Parameters:
trace

go.Scatter Figure trace for the node

points

callbacks.Points Points that are hovered over

spateo.plotting.static.networks.plot_network(G: networkx.Graph | networkx.DiGraph, title: str, size_method: str | List[float], color_method: str | List[str], layout: str | None = None, node_label: str | None = None, node_label_position: str = 'top center', node_text: List[str] = None, nodefont_size: int = 8, edge_label: str | None = None, edge_thickness_attr: str | None = None, edge_label_position: str = 'middle center', edge_text: List[str] = None, edgefont_size: int = 8, titlefont_size: int = 16, show_colorbar: bool = True, colorscale: str = 'YlGnBu', colorbar_title: str | None = None, node_opacity: float = 0.8, arrow_size: float = 2, transparent_background: bool = True, highlight_neighbors_on_hover: bool = True, upper_margin: float = 40, lower_margin: float = 20, left_margin: float = 50, right_margin: float = 50) → plotly.graph_objects.FigureWidget[source]#

Network graph using plotly, used to plot intercellular GRN as inferred by Spateo.

Parameters:
G

Networkx graph object

title

Title of the plot

size_method

Either label of node property or list containing the size of each node

color_method

Either label of node property or list containing the color of each node

layout

Controls shape of the plot. Options: - random (default): Position nodes uniformly at random in the unit square.

For every node, a position is generated by choosing each of dim coordinates uniformly at random on the interval [0.0, 1.0).

  • circular: Position nodes on a circle

  • kamada: Position nodes using Kamada-Kawai path-length cost-function

  • planar: Position nodes without edges intersecting (only if possible)

  • spring: Position nodes using Fruchterman-Reingold force-directed algorithm

  • spectral: Position nodes using eigenvectors of the graph Laplacian

  • spiral: Position nodes in a spiral layout

node_label

Node property to be used as label

node_label_position

Position of node labels. Options: ‘top left’, ‘top center’, ‘top right’, ‘middle left’, ‘middle center’, ‘middle right’, ‘bottom left’, ‘bottom center’, ‘bottom right’

node_text

List containing properties to be displayed when hovering over nodes

nodefont_size

Size of ‘node_label’

edge_label

Edge property to be used as label

edge_label_position

Position of edge labels. Options: ‘top left’, ‘top center’, ‘top right’, ‘middle left’, ‘middle center’, ‘middle right’, ‘bottom left’, ‘bottom center’, ‘bottom right’

edge_thickness_attr

Edge property to be used for determining edge thickness

edge_text

List containing properties to be displayed when hovering over edges

edgefont_size

Size of ‘edge_label’

titlefont_size

Size of title

show_colorbar

Set True to display colorbar

colorscale

Colormap used for the colorbar. Options: ‘Greys’, ‘YlGnBu’, ‘Greens’, ‘YlOrRd’, ‘Bluered’, ‘RdBu’, ‘Reds’, ‘Blues’, ‘Picnic’, ‘Rainbow’, ‘Portland’, ‘Jet’, ‘Hot’, ‘Blackbody’, ‘Earth’, ‘Electric’, ‘Viridis’

colorbar_title

Colorbar title

node_opacity

Node transparency, from 0 to 1, where 0 is completely transparent

arrow_size

Size of the arrow for directed graphs, by default 2

transparent_background

Set True for transparent background

highlight_neighbours_on_hover

Set True to highlight neighbors of a node (by name) when hovering over it

upper_margin

Margin between top of the plot and top of the figure

lower_margin

Margin between bottom of the plot and bottom of the figure

left_margin

Margin between left of the plot and left of the figure

right_margin

Margin between right of the plot and right of the figure

Returns:

Plotly figure widget object

Return type:

fig