sccloud.scatter

sccloud.scatter(adata, x, y, color=None, size=None, dot_min=2, dot_max=14, use_raw=None, sort=True, width=400, height=400, nbins=-1, reduce_function=<function mean>, cmap='viridis', **kwds)[source]

Generate a scatter plot.

Parameters

  • adata (AnnData) – Annotated data matrix.

  • x (str) – Key for accessing variables of adata.var_names, field of adata.var, or field of adata.obs

  • y (str) – Key for accessing variables of adata.var_names, field of adata.var, or field of adata.obs

  • 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.

  • color – Field in .var_names, adata.var, or adata.obs to color the points by.

  • sort (bool) – Plot higher color by values on top of lower values.

  • size (Union[int, str, None]) – Field in .var_names, adata.var, or adata.obs to size the points by or a pixel size.

  • dot_min – Minimum dot size when sizing points by a field.

  • dot_max – Maximum dot size when sizing points by a field.

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

  • 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[[<built-in function array>], float]) – Function used to summarize overlapping cells if nbins is specified

Return type

Element