squidpy.pl.ligrec
- squidpy.pl.ligrec(adata, cluster_key=None, source_groups=None, target_groups=None, means_range=(-inf, inf), pvalue_threshold=1.0, remove_empty_interactions=True, remove_nonsig_interactions=False, dendrogram=None, alpha=0.001, swap_axes=False, title=None, figsize=None, dpi=None, save=None, **kwargs)[source]
Plot the result of a receptor-ligand permutation test.
The result was computed by
squidpy.gr.ligrec()
.\(molecule_1\) belongs to the source clusters displayed on the top (or on the right, if
swap_axes = True
, whereas \(molecule_2\) belongs to the target clusters.- Parameters:
adata (
AnnData
|Mapping
[str
,DataFrame
]) – Annotated data object. It can also be adict
, as returned bysquidpy.gr.ligrec()
.cluster_key (
Optional
[str
]) – Key inanndata.AnnData.obs
where clustering is stored. Only used whenadata
is of typeAnnData
.source_groups (
Union
[str
,Sequence
[str
],None
]) – Source interaction clusters. If None, select all clusters.target_groups (
Union
[str
,Sequence
[str
],None
]) – Target interaction clusters. If None, select all clusters.means_range (
tuple
[float
,float
]) – Only show interactions whose means are within this closed interval.pvalue_threshold (
float
) – Only show interactions with p-value <=pvalue_threshold
.remove_empty_interactions (
bool
) – Remove rows and columns that only contain interactions with NaN values.remove_nonsig_interactions (
bool
) – Remove rows and columns that only contain interactions that are larger thanalpha
.How to cluster based on the p-values. Valid options are:
None - do not perform clustering.
’interacting_molecules’ - cluster the interacting molecules.
’interacting_clusters’ - cluster the interacting clusters.
’both’ - cluster both rows and columns. Note that in this case, the dendrogram is not shown.
alpha (
float
|None
) – Significance threshold. All elements with p-values <=alpha
will be marked by tori instead of dots.swap_axes (
bool
) – Whether to show the cluster combinations as rows and the interacting pairs as columns.figsize (
Optional
[tuple
[float
,float
]]) – Size of the figure in inches.scalebar_kwargs – Keyword arguments for
matplotlib_scalebar.ScaleBar()
.edges_kwargs – Keyword arguments for
networkx.draw_networkx_edges()
.kwargs (
Any
) – Keyword arguments formatplotlib.pyplot.scatter()
ormatplotlib.pyplot.imshow()
.kwargs – Keyword arguments for
scanpy.pl.DotPlot.style()
orscanpy.pl.DotPlot.legend()
.
- Return type:
- Returns:
: Nothing, just plots the figure and optionally saves the plot.