sccloud.dotplot

sccloud.dotplot(adata, keys, by, reduce_function=<function mean>, fraction_min=0, fraction_max=None, dot_min=0, dot_max=14, use_raw=None, cmap='Reds', sort_function=None, **kwds)[source]

Generate a dot plot.

Parameters

  • adata (AnnData) – Annotated data matrix.

  • keys (Union[str, List[str], Tuple[str]]) – Keys for accessing variables of adata.var_names

  • by (str) – Group plot by specified observation.

  • cmap (Union[str, List[str], Tuple[str]]) – Color map name (hv.plotting.list_cmaps()) or a list of hex colors. See http://holoviews.org/user_guide/Styling_Plots.html for more information.

  • reduce_function (Callable[[ndarray], float]) – Function to summarize an element in the heatmap

  • fraction_min (float) – Minimum fraction expressed value.

  • fraction_max (Optional[float]) – Maximum fraction expressed value.

  • dot_min (int) – Minimum pixel dot size.

  • dot_max (int) – Maximum pixel dot size.

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

  • sort_function (Optional[Callable[[DataFrame], List[str]]]) – Optional function that accepts summarized data frame and returns a list of row indices in the order to render in the heatmap.

Return type

Element