schist.tools._draw_graph
Module Contents
Functions
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Extends scanpy.tools.draw_graph function using some layouts available in |
Attributes
- schist.tools._draw_graph._LAYOUTS = ('fr', 'sfdp', 'arf')
- schist.tools._draw_graph._Layout
- schist.tools._draw_graph.draw_graph(adata: anndata.AnnData, layout: _Layout = 'sfdp', use_tree: bool = False, random_seed: int | None = None, adjacency: scipy.sparse.spmatrix | None = None, key_added_ext: str | None = None, key: str | None = 'schist', copy: bool = False, **kwds)
Extends scanpy.tools.draw_graph function using some layouts available in graph-tool library. Three layouts are available here:
SFDP spring-block layout.
ARF spring-block layout.
Fruchterman-Reingold spring-block layout.
Fruchterman-Reingold is already available in scanpy, but here can be used to render the nested model tree.
In order to use these plotting function, the NestedBlockState needs to be saved when building the model, so save_state=True needs to be set.
Parameters
- adata
Annotated data matrix. A NestedBlockState object needs to be saved
- layout
A layout among ‘sfdp’, ‘fr’ or ‘arf’. Other graph-tool layouts haven’t been implemented.
- use_tree
When this is set, the tree of the nested model is used to generate layout, otherwise the layout only accounts for the neighborhood graph.
- random_seed
Random number to be used as seed for graph-tool
- adjacency
Sparse adjacency matrix of the graph, defaults to adata.uns[‘neighbors’][‘connectivities’].
- key_added_ext
By default, append layout.
- key
The slot in AnnData.uns containing the state. Default is ‘nsbm’
- copy
Return a copy instead of writing to adata.
- **kwds
Parameters of chosen igraph layout. See e.g. fruchterman-reingold [Fruchterman91]. One of the most important ones is maxiter.
Returns
Depending on copy, returns or updates adata with the following field.
- X_draw_graph_layoutadata.obsm
Coordinates of graph layout. E.g. for layout=’fa’ (the default), the field is called ‘X_draw_graph_fa’