liana.plotting.dotplot_by_sample¶
- liana.plotting.dotplot_by_sample(adata: AnnData | None = None, uns_key: str = 'liana_res', liana_res: DataFrame | None = None, sample_key: str = 'sample', colour: str | None = None, size: str | None = None, inverse_colour: bool = False, inverse_size: bool = False, source_labels: str | None = None, target_labels: str | None = None, ligand_complex: None | str | list = None, receptor_complex: None | str | list = None, size_range: tuple = (2, 9), cmap: str = 'viridis', figure_size: tuple = (8, 6), return_fig: bool = True)¶
A dotplot of interactions by sample
- Parameters:
- adata
- Annotated data object.
- uns_key
- Key in `adata.uns` that contains the LIANA results. Default is `’liana_res’`.
- liana_res
- `liana_res` a `DataFrame` in liana’s format.
- sample_key
sample_key used to group different samples/contexts from liana_res. Defaults to ‘sample’.
- colour
- `column` in `liana_res` to define the colours of the dots.
- size
- `column` in `liana_res` to define the size of the dots.
- inverse_colour
- Whether to -log10 the `colour` column for plotting. `False` by default.
- inverse_size
- Whether to -log10 the `size` column for plotting. `False` by default.
- source_labels
- List of labels to use as `source`, the rest are filtered out.
- target_labels
- List of labels to use as `target`, the rest are filtered out.
- ligand_complex
- `list` of ligand complexes to filter the interactions to be plotted. Defaults to None.
- receptor_complex
- `list` of receptor complexes to filter the interactions to be plotted. Defaults to None.
- size_range
- Define size range. Tuple of (min, max) integers.
- cmap
- Colour map to use for plotting.
- figure_size
- Figure x,y size
- Returns:
- Returns a ggplot for the specified interactions by sample.