ehrapy.plot.paga

ehrapy.plot.paga(adata, threshold=None, color=None, layout=None, layout_kwds=mappingproxy({}), init_pos=None, root=0, labels=None, single_component=False, solid_edges='connectivities', dashed_edges=None, transitions=None, fontsize=None, fontweight='bold', fontoutline=None, text_kwds=mappingproxy({}), node_size_scale=1.0, node_size_power=0.5, edge_width_scale=1.0, min_edge_width=None, max_edge_width=None, arrowsize=30, title=None, left_margin=0.01, random_state=0, pos=None, normalize_to_color=False, cmap=None, cax=None, cb_kwds=mappingproxy({}), frameon=None, add_pos=True, export_to_gexf=False, use_raw=True, plot=True, show=None, save=None, ax=None)[source]

Plot the PAGA graph through thresholding low-connectivity edges.

Compute a coarse-grained layout of the data. Reuse this by passing init_pos=’paga’ to umap() or draw_graph() and obtain embeddings with more meaningful global topology [Wolf19]. This uses ForceAtlas2 or igraph’s layout algorithms for most layouts [Csardi06].

Parameters:

  • adata (AnnData) – AnnData object object containing all observations.

  • threshold (float | None) – Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph.

  • color (str | Mapping[str | int, Mapping[Any, float]] | None) – Feature name or obs annotation defining the node colors. Also plots the degree of the abstracted graph when passing {‘degree_dashed’, ‘degree_solid’}. Can be also used to visualize pie chart at each node in the following form: {<group name or index>: {<color>: <fraction>, …}, …}. If the fractions do not sum to 1, a new category called ‘rest’ colored grey will be created.

  • layout (Optional[Literal['fa', 'fr', 'rt', 'rt_circular', 'drl', 'eq_tree', Ellipsis]]) – The node labels. If None, this defaults to the group labels stored in the categorical for which paga() has been computed.

  • layout_kwds (Mapping[str, Any]) – Keywords for the layout.

  • init_pos (ndarray | None) – Two-column array storing the x and y coordinates for initializing the layout.

  • root (int | str | Sequence[int] | None) – If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is None or an empty list, the root vertices are automatically calculated based on topological sorting.

  • labels (str | Sequence[str] | Mapping[str, str] | None) – The node labels. If None, this defaults to the group labels stored in the categorical for which paga() has been computed.

  • single_component (bool) – Restrict to largest connected component.

  • solid_edges (str) – Key for .uns[‘paga’] that specifies the matrix that stores the edges to be drawn solid black.

  • dashed_edges (str | None) – Key for .uns[‘paga’] that specifies the matrix that stores the edges to be drawn dashed grey. If None, no dashed edges are drawn.

  • transitions (str | None) – Key for .uns[‘paga’] that specifies the matrix that stores the arrows, for instance ‘transitions_confidence’.

  • fontsize (int | None) – Font size for node labels.

  • fontweight (str) – Weight of the font.

  • fontoutline (int | None) – Width of the white outline around fonts.

  • text_kwds (Mapping[str, Any]) – Keywords for text().

  • node_size_scale (float) – Increase or decrease the size of the nodes.

  • node_size_power (float) – The power with which groups sizes influence the radius of the nodes.

  • edge_width_scale (float) – Edge with scale in units of rcParams[‘lines.linewidth’].

  • min_edge_width (float | None) – Min width of solid edges.

  • max_edge_width (float | None) – Max width of solid and dashed edges.

  • arrowsize (int) – For directed graphs, choose the size of the arrow head head’s length and width. See :py:class: matplotlib.patches.FancyArrowPatch for attribute mutation_scale for more info.

  • title (str | None) – Provide a title.

  • left_margin (float) – Margin to the left of the plot.

  • random_state (int | None) – For layouts with random initialization like ‘fr’, change this to use different intial states for the optimization. If None, the initial state is not reproducible.

  • pos (ndarray | str | Path | None) – Two-column array-like storing the x and y coordinates for drawing. Otherwise, path to a .gdf file that has been exported from Gephi or a similar graph visualization software.

  • normalize_to_color (bool) – Whether to normalize categorical plots to color or the underlying grouping.

  • cmap (str | Colormap) – The Matplotlib color map.

  • cax (Axes | None) – A matplotlib axes object for a potential colorbar.

  • cb_kwds (Mapping[str, Any]) – Keyword arguments for ColorbarBase, for instance, ticks.

  • frameon (bool | None) – Draw a frame around the PAGA graph.

  • add_pos (bool) – Add the positions to adata.uns[‘paga’].

  • export_to_gexf (bool) – Export to gexf format to be read by graph visualization programs such as Gephi.

  • use_raw (bool) – Whether to use raw attribute of adata. Defaults to True if .raw is present.

  • plot (bool) – If False, do not create the figure, simply compute the layout.

  • ax (Axes | None) – Matplotlib Axis object.

  • show (bool | None) – Whether to show the plot.

  • save (bool | str | None) – Whether or where to save the plot.

Return type:

Axes | list[Axes] | None

Returns:

A Axes object, if ax is None, else None. If return_data, return the timeseries data in addition to an axes.

Examples

>>> import ehrapy as ep
>>> adata = ep.dt.mimic_2(encoded=True)
>>> ep.pp.knn_impute(adata)
>>> ep.pp.log_norm(adata, offset=1)
>>> ep.pp.neighbors(adata)
>>> ep.tl.leiden(adata, resolution=0.5, key_added="leiden_0_5")
>>> ep.tl.paga(adata, groups="leiden_0_5")
>>> ep.pl.paga(
...     adata,
...     color=["leiden_0_5", "day_28_flg"],
...     cmap=ep.pl.Colormaps.grey_red.value,
...     title=["Leiden 0.5", "Died in less than 28 days"],
... )
Preview:
../../_images/paga.png