sc_toolbox.plot.annotated_cell_type_umap#

sc_toolbox.plot.annotated_cell_type_umap(adata, primary_color, cell_type_color, legend_loc='on data', legend_fontsize=8, title='Plot title', palette=None, cmap=None, figsize=(8, 6), save=None)[source]#

Plots a UMAP which is colored by the primary_color, but also draws all labels on top of all clusters.

Parameters:

  • adata – AnnData object

  • primary_color (Union[str, Sequence[str]]) – Primary color to color all cells by, e.g. ‘genotype’

  • cell_type_color (str) – Key containing all cell types, e.g. ‘cell_type’

  • legend_loc (str) – Location of the legend (default: ‘on data’)

  • legend_fontsize (int) – Font size of the legend (default: 8)

  • title (str) – Title of the plot

  • palette – Color

  • cmap – Color map of the UMAP

  • figsize – Size of the figure

  • save – Path to save the plot to

Returns:

fig and axs Matplotlib objects

Example

../../_images/annotated_cell_type_umap.png