pegasus.embedding

pegasus.embedding(adata, basis, keys=None, cmap=None, palette=None, alpha=1, size=None, width=400, height=400, sort=True, cols=None, use_raw=None, nbins=-1, reduce_function=<function amax>, brush_categorical=False, legend='right', tooltips=None, legend_font_size=None, opacity_min=0, opacity_max=1, **kwds)[source]

Generate an embedding plot.

Parameters

  • adata (AnnData) – Annotated data matrix.

  • keys (Union[None, str, List[str], Tuple[str]]) – Key for accessing variables of adata.var_names or a field of adata.obs used to color the plot. Can also use count to plot cell count when binning.

  • basis (Union[str, List[str], Tuple[str]]) – String in adata.obsm containing coordinates.

  • alpha (float) – Points alpha value.

  • size (Optional[float]) – Point pixel size.

  • sort (bool) – Plot higher values on top of lower values. Disable for linked brushing.

  • brush_categorical (bool) – Enable linked brushing on categorical variables (disables categorical legend).

  • cmap (Union[str, List[str], Tuple[str], None]) – Color map for continous variables.

  • palette (Union[str, List[str], Tuple[str], None]) – Color map for categorical variables.

  • nbins (int) – Number of bins used to summarize plot on a grid. Useful for large datasets. Negative one means automatically bin the plot.

  • reduce_function (Callable[[array], float]) – Function used to summarize overlapping cells if nbins is specified.

  • cols (Optional[int]) – Number of columns for laying out multiple plots

  • width (int) – Plot width.

  • height (int) – Plot height.

  • tooltips (Union[str, List[str], Tuple[str], None]) – List of additional fields to show on hover.

  • legend (str) – `top’, ‘bottom’, ‘left’, ‘right’, or ‘data’ to draw labels for categorical features on the plot.

  • legend_font_size (Union[int, str, None]) – Font size for labels_on_data

  • use_raw (Optional[bool]) – Use raw attribute of adata if present.

  • opacity_min (float) – Minimum value for encoding categorical data purity when binning using opacity.

  • opacity_max (float) – Maximum value for encoding categorical data purity when binning using opacity.

Return type

Element