seqme.utils.plot_embeddings

seqme.utils.plot_embeddings#

seqme.utils.plot_embeddings(embeddings, *, values=None, colors=None, cmap=None, title=None, xlabel='dim1', ylabel='dim2', outline_width=0, point_size=20, show_legend=True, legend_point_size=20, alpha=0.6, show_ticks=False, legend_loc='right margin', figsize=(4, 3), ax=None)[source]#

Plot projections for one or more groups.

Parameters:

  • embeddings (ndarray | list[ndarray]) – Groups of arrays, each containing 2d embeddings.

  • values (Union[str, ndarray, list[str], list[ndarray], None]) – Either group names or values for each individual embedding.

  • colors (Union[list[str], str, None]) – Colors for each group of points.

  • cmap (Optional[str]) – Colors used for values.

  • title (Optional[str]) – Optional plot title.

  • xlabel (str) – x-axis label.

  • ylabel (str) – y-axis label.

  • outline_width (float) – Width of the outline around points.

  • point_size (float) – Size of scatter points.

  • show_legend (bool) – Whether to show legend (only for categorical data).

  • legend_point_size (float | None) – Size of scatter points in the legend.

  • alpha (float) – Transparency of points.

  • show_ticks (bool) – Whether to show axis ticks.

  • legend_loc (Union[Literal['right margin'], str, None]) – Legend location.

  • figsize (tuple[int, int]) – Size of the figure (if no Axes provided).

  • ax (Optional[Axes]) – Optional matplotlib Axes to plot on.

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