spatialcells.plotting

Module for plotting spatial cells regions.

Access via either spatialcells.plotting or spatialcells.plt.

plotBoundary

spatialcells.plt.plotBoundary(boundary, ax=None, **kwargs)

Plot the boundary.

Parameters:

  • boundary – the MultiPolygon boundary of the region

  • ax – the matplotlib ax object. If None (default), use plt.

  • kwargs – kwargs for matplotlib.pyplot.plot

plotCommunities

spatialcells.plt.plotCommunities(adata, ret, communitycolumn, plot_first_n_clusters=10, **kwargs)

Plot largest communities on a scatter plot. Each community is labelled as: (rank in descending number of cells : index of community)

Parameters:

  • adata – AnnData object

  • ret – return value of spc.spa.getCommunities

  • communitycolumn – column name of the community column in adata.obs

  • plot_first_n_clusters – plot and number the largest n communities

  • kwargs – keyword arguments for matplotlib.pyplot.plot

plotRegions

spatialcells.plt.plotRegions(regions_list, ax=None, add_label=True, label_prefix='', x_offset=0, y_offset=0, fontsize=12, label_bounds=None, colors_list=['k', 'r', 'b', 'g'], fontcolor='black', foreground_linewidth=5, **kwargs)

Plot the regions in the regions_list and label them with their index in the list. labels are placed at the lower left corner of each region. Their position can be adjusted by x_offset and y_offset, and the overall label_bounds.

Parameters:

  • regions_list – a list of MultiPolygon regions

  • add_label – whether to label the regions

  • ax – the matplotlib ax object.

  • label_prefix – a prefix to the label of each region

  • x_offset – the x offset of each label

  • y_offset – the y offset of the label

  • fontsize – the fontsize of the label

  • label_bounds – the bounds of all the label (minx, miny, maxx, maxy). If None, the bounds of the regions_list will be used.

  • colors_list – a list of colors that will be cycled through for each region.

  • fontcolor – the fontcolor of the label

  • foreground_linewidth – the foreground linewidth of the label. Adjusts the thickness of the white border around each label.

  • kwargs – kwargs for matplotlib.pyplot.plot