cellrank.pl.graph
- cellrank.pl.graph(data, graph_key=None, ixs=None, layout='umap', keys='incoming', keylocs='uns', node_size=400, labels=None, top_n_edges=None, self_loops=True, self_loop_radius_frac=None, filter_edges=None, edge_reductions=<function sum>, edge_reductions_restrict_to_ixs=None, edge_weight_scale=10, edge_width_limit=None, edge_alpha=1.0, edge_normalize=False, edge_use_curved=True, arrows=True, font_size=12, font_color='black', color_nodes=True, cat_cmap=<matplotlib.colors.ListedColormap object>, cont_cmap=<matplotlib.colors.ListedColormap object>, legend_loc='best', title=None, figsize=None, dpi=None, save=None, layout_kwargs=mappingproxy({}))[source]
Plot a graph, visualizing incoming and outgoing edges or self-transitions.
This is a utility function to look in more detail at the transition matrix in areas of interest, e.g. around an endpoint of development. This function is meant to visualise a small subset of nodes (~100-500) and the most likely transitions between them. Note that limiting edges visualized using
top_n_edges
will speed things up, as well as reduce the visual clutter.- Parameters
data (
Union
[AnnData
,ndarray
,spmatrix
]) – The graph data to be plotted.graph_key (
Optional
[str
]) – Key inanndata.AnnData.obsp
where the graph is stored. Only used whendata
isanndata.Anndata
object.ixs (
Union
[range
,array
,None
]) – Subset of indices of the graph to visualize.layout (
Union
[str
,Dict
[str
,Any
],Callable
[...
,ndarray
]]) –Layout to use for graph drawing.
If
str
, search for embedding inanndata.AnnData.obsm
['X_{layout}']
. Uselayout_kwargs={'components': [0, 1]}
to select components.If
dict
, keys should be values in interval [0, len(ixs)) and values (x, y) pairs corresponding to node positions.
keys (
Sequence
[Union
[str
,Literal
[‘incoming’, ‘outgoing’, ‘self_loops’]]]) –Keys in
anndata.AnnData.obs
,anndata.AnnData.obsm
oranndata.AnnData.obsm
used to color the nodes.If ‘incoming’, ‘outgoing’ or ‘self_loops’, visualize reduction (see
edge_reductions
) for each node based on incoming or outgoing edges, respectively.keylocs (
Union
[str
,Sequence
[str
]]) – Locations ofkeys
. Can be any attribute ofdata
if it’sanndata.AnnData
object.node_size (
float
) – Size of the nodes.labels (
Union
[Sequence
[str
],Sequence
[Sequence
[str
]],None
]) – Labels of the nodes.top_n_edges (
Union
[int
,Tuple
[int
,bool
,str
],None
]) – Either top N outgoing edges in descending order or a tuple(top_n_edges, in_ascending_order, {'incoming', 'outgoing'})
. If None, show all edges.self_loops (
bool
) – Whether visualize self transitions and also to consider them intop_n_edges
.self_loop_radius_frac (
Optional
[float
]) – Fraction of a unit circle to visualize self transitions. If None, usenode_size / 1000
.filter_edges (
Optional
[Tuple
[float
,float
]]) – Whether to remove all edges not in [min, max] interval.edge_reductions (
Union
[Callable
,Sequence
[Callable
]]) – Aggregation function to use when coloring nodes by edge weights.edge_reductions_restrict_to_ixs (
Union
[range
,ndarray
,None
]) – Whether to use the full graph when calculating theedge_reductions
or just use the nodes marked by theixs
and this parameter. If None, it’s the same asixs
.edge_weight_scale (
float
) – Number by which to scale the width of the edges. Useful when the weights are small.edge_width_limit (
Optional
[float
]) – Upper bound for the width of the edges. Useful when weights are unevenly distributed.edge_alpha (
float
) – Alpha channel value for edges and arrows.edge_normalize (
bool
) – If True, normalize edges to [0, 1] interval prior to applying any scaling or truncation.edge_use_curved (
bool
) – If True, use curved edges. This can improve visualization at a small performance cost.arrows (
bool
) – Whether to show the arrows. Setting this to False may dramatically speed things up.font_size (
int
) – Font size for node labels.font_color (
str
) – Label color of the nodes.color_nodes (
bool
) – Whether to color the nodescat_cmap (
ListedColormap
) – Categorical colormap used whenkeys
contain categorical variables.cont_cmap (
ListedColormap
) – Continuous colormap used whenkeys
contain continuous variables.title (
Union
[str
,Sequence
[Optional
[str
]],None
]) – Title of the figure(s), one for eachkey
.figsize (
Optional
[Tuple
[float
,float
]]) – Size of the figure.save (
Union
[str
,Path
,None
]) – Filename where to save the plot.layout_kwargs (
Dict
[str
,Any
]) – Keyword arguments forlayout
.
- Return type
- Returns
Nothing, just plots the figure. Optionally saves it based on
save
.