stereo.plots.PlotCollection.umap

PlotCollection.umap(gene_names=None, res_key='umap', cluster_key=None, title=None, x_label='umap1', y_label='umap2', dot_size=None, colors='stereo', width=None, height=None, palette=None, vmin=None, vmax=None, **kwargs)[source]

Scatter plot of UMAP after reducing dimensionalities.

Parameters:

  • gene_names (Union[list, ndarray, str, None]) – the list of gene names.

  • cluster_key (Optional[str]) – the result key of clustering.

  • res_key (str) – the result key of UMAP.

  • title (Union[str, list, None]) – the plot title.

  • x_label (Union[str, list, None]) – the x label.

  • y_label (Union[str, list, None]) – the y label.

  • dot_size (Optional[int]) – the dot size.

  • colors (Union[str, list, None]) – the color list.

  • width (Optional[int]) – the figure width in pixels.

  • height (Optional[int]) – the figure height in pixels.

  • palette (Optional[int]) – color theme.

  • out_path – the path to save the figure.

  • out_dpi – the dpi when the figure is saved.

  • vmin (Optional[float]) – The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin.

  • vmax (Optional[float]) – The value representing the higher limit of the color scale. Values greater than vmax are plotted with the same color as vmax.