commot.pl.plot_cell_communication

commot.pl.plot_cell_communication(adata, database_name=None, pathway_name=None, lr_pair=None, keys=None, plot_method='cell', background='summary', background_legend=False, clustering=None, summary='sender', cmap='coolwarm', cluster_cmap=None, pos_idx=array([0, 1]), ndsize=1, scale=1.0, normalize_v=False, normalize_v_quantile=0.95, arrow_color='#333333', grid_density=1.0, grid_knn=None, grid_scale=1.0, grid_thresh=1.0, grid_width=0.005, stream_density=1.0, stream_linewidth=1, stream_cutoff_perc=5, filename=None, ax=None)

Plot spatial directions of cell-cell communication.

../_images/cell_communication.png

The cell-cell communication should have been computed by the function commot.tl.spatial_communication(). The cell-cell communication direction should have been computed by the function commot.tl.communication_direction().

Parameters

  • adata (AnnData) – The data matrix of shape n_obs × n_var. Rows correspond to cells or positions and columns to genes.

  • database_name (Optional[str]) – Name of the ligand-receptor interaction database.

  • pathway_name (Optional[str]) – Name of the signaling pathway to be plotted. Will be used only when lr_pair and keys are None. If none of pathway_name, lr_pair, and keys are given, the total signaling through all pairs will be plotted.

  • lr_pair – A tuple of ligand name and receptor name. If given, pathway_name will be ignored. Will be ignored if keys is given.

  • keys – A list of keys for example ‘ligA-recA’ for a LR pair or ‘pathwayX’ for a signaling pathway ‘pathwayX’. If given, pathway_name and lr_pair will be ignored. If more than one is given, the average will be plotted.

  • plot_method (str) – ‘cell’ plot vectors on individual cells. ‘grid’ plot interpolated vectors on regular grids. ‘stream’ streamline plot.

  • background (str) – ‘summary’: scatter plot with color representing total sent or received signal. ‘image’: the image in Visium data. ‘cluster’: scatter plot with color representing cell clusters.

  • background_legend (bool) – Whether to include the background legend when background is set to summary or cluster.

  • clustering (Optional[str]) – The key for clustering result. Needed if background is set to cluster. For example, if clustering=='leiden', the clustering result should be available in .obs['leiden'].

  • summary (str) – If background is set to ‘summary’, the numerical value to plot for background. ‘sender’: node color represents sender weight. ‘receiver’: node color represents receiver weight.

  • cmap (str) – matplotlib colormap name for node summary if numerical (background set to ‘summary’), e.g., ‘coolwarm’. plotly colormap name for node color if summary is (background set to ‘cluster’). e.g., ‘Alphabet’.

  • cluster_cmap (Optional[dict]) – A dictionary that maps cluster names to colors when setting background to ‘cluster’. If given, cmap will be ignored.

  • pos_idx (ndarray) – The coordinates to use for plotting (2D plot).

  • ndsize (float) – The node size of the spots.

  • scale (float) – The scale parameter passed to the matplotlib quiver function matplotlib.pyplot.quiver() for vector field plots. The smaller the value, the longer the arrows.

  • normalize_v (bool) – Whether the normalize the vector field to uniform lengths to highlight the directions without showing magnitudes.

  • normalize_v_quantile (float) – The vector length quantile to use to normalize the vector field.

  • arrow_color (str) – The color of the arrows.

  • grid_density (float) – The density of grid if plot_method=='grid'.

  • grid_knn (Optional[int]) – If plot_method=='grid', the number of nearest neighbors to interpolate the signaling directions from spots to grid points.

  • grid_scale (float) – The scale parameter (relative to grid size) for the kernel function of mapping directions of spots to grid points.

  • grid_thresh (float) – The threshold of interpolation weights determining whether to include a grid point. A smaller value gives a tighter cover of the tissue by the grid points.

  • grid_width (float) – The value passed to the width parameter of the function matplotlib.pyplot.quiver() when plot_method=='grid'.

  • stream_density (float) – The density of stream lines passed to the density parameter of the function matplotlib.pyplot.streamplot() when plot_method=='stream'.

  • stream_linewidth (float) – The width of stream lines passed to the linewidth parameter of the function matplotlib.pyplot.streamplot() when plot_method=='stream'.

  • stream_cutoff_perc (float) – The quantile cutoff to ignore the weak vectors. Default to 5 that the vectors shorter than the 5% quantile will not be plotted.

  • filename (Optional[str]) – If given, save to the filename. For example ‘ccc_direction.pdf’.

  • ax (Optional[Axes]) – An existing matplotlib ax (matplotlib.axis.Axis).

Returns

ax – The matplotlib ax object of the plot.

Return type

matplotlib.axis.Axis