ageas.Plot

class ageas.Plot(depth: int = 1, hide_bridge: bool = True, plot_class: str = 'all', network=None, root_gene: Optional[str] = None, weight_thread: float = 0.0)

Visualize GRN or Regulon extracted with AGEAS.

__init__(depth: int = 1, hide_bridge: bool = True, plot_class: str = 'all', network=None, root_gene: Optional[str] = None, weight_thread: float = 0.0)

Initialize a new plot object.

Parameters

• depth – <int Default = 1> If ‘root_gene’ is specified, borrowing concept of tree graph, this means how far the tree graph shall reach.

• hide_bridge – <bool Default = True> Whether hide non-AGEAS-extracted GRPs which can link key genes or not.

• plot_class –

  <str Default = ‘all’> What kind of information to show for GRPs on plot.

  Supporting:

  ’all’: In which sample class a GRP has higher correlation.

  ’class1’: GRP’s correlation value calculated with samples in class1

  ’class2’: GRP’s correlation value calculated with samples in class2

• network – <ageas.tool.grn.GRN Default = None> Which network to plot out.

• root_gene – <str Default = None> Specific gene of interest. Only GRPs being capable to link with this gene directly or indirectly will be visualized. Borrowing concept of tree graph, this will be the root to expand a tree.

• weight_thread – <float Default = 0.0> Minimun weight for a GRP to be kept on plot.

Methods

__init__([depth, hide_bridge, plot_class, ...])	Initialize a new plot object.
draw([colorbar_shrink, edge_width_scale, ...])	Draw the plot for selected GRN.
save([path, format])	Save the plot.