bento.pl.lp_genes

bento.pl.lp_genes(sdata, groupby='feature_name', points_key='transcripts', instance_key='cell_boundaries', annotate=None, sizes=(2, 100), size_norm=(0, 100), ax=None, fname=None, **kwargs)

Plot the pattern distribution of each group in a RadViz plot. RadViz projects an N-dimensional data set into a 2D space where the influence of each dimension can be interpreted as a balance between the influence of all dimensions.

Parameters:

  • sdata (SpatialData) – Spatial formatted SpatialData

  • groupby (str) – Grouping variable, default “gene”

  • annotate (int, list of str, optional) – Annotate the top n genes or a list of genes, by default None

  • sizes (tuple) – Minimum and maximum point size to scale points, default (2, 100)

  • size_norm (tuple) – Minimum and maximum data values to scale point size, default (0, 100)

  • ax (matplotlib.Axes, optional) – Axis to plot on, by default None

  • fname (str, optional) – Save the figure to specified filename, by default None

  • **kwargs – Options to pass to matplotlib plotting method.