omicverse.pl.umap

omicverse.pl.umap(adata, convert=True, **kwargs)[source]

Plot UMAP embedding.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • color – Keys for annotations of observations/cells or variables/genes. (None)

  • gene_symbols – Key for field in .var that stores gene symbols. (None)

  • use_raw – Use .raw attribute of adata if present. (None)

  • sort_order – For continuous annotations used as color parameter, plot data points with higher values on top of others. (True)

  • edges – Show edges between cells. (False)

  • edges_width – Width of edges. (0.1)

  • edges_color – Color of edges. (‘grey’)

  • neighbors_key – Key to use for neighbors. (None)

  • arrows – Show arrows for velocity. (False)

  • arrows_kwds – Keyword arguments for arrow plots. (None)

  • groups – Groups to highlight. (None)

  • components – Components to plot. (None)

  • dimensions – Dimensions to plot. (None)

  • layer – Name of the layer to use for coloring. (None)

  • projection – Type of projection (‘2d’ or ‘3d’). (‘2d’)

  • scale_factor – Scaling factor for sizes. (None)

  • color_map – Colormap to use for continuous variables. (None)

  • cmap – Colormap to use for continuous variables. (None)

  • palette – Colors to use for categorical variables. (None)

  • na_color – Color to use for NaN values. (‘lightgray’)

  • na_in_legend – Include NaN values in legend. (True)

  • size – Size of the dots. (None)

  • frameon – Draw a frame around the plot. (‘small’)

  • legend_fontsize – Font size for legend. (None)

  • legend_fontweight – Font weight for legend. (‘bold’)

  • legend_loc – Location of legend. (‘right margin’)

  • legend_fontoutline – Outline width for legend text. (None)

  • colorbar_loc – Location of colorbar. (‘right’)

  • vmax – Maximum value for colorbar. (None)

  • vmin – Minimum value for colorbar. (None)

  • vcenter – Center value for colorbar. (None)

  • norm – Normalization for colorbar. (None)

  • add_outline – Add outline to points. (False)

  • outline_width – Width of outline. ((0.3, 0.05))

  • outline_color – Color of outline. ((‘black’, ‘white’))

  • ncols – Number of columns for subplots. (4)

  • hspace – Height spacing between subplots. (0.25)

  • wspace – Width spacing between subplots. (None)

  • title – Title for the plot. (None)

  • show – Show the plot. (None)

  • save – Save the plot. (None)

  • ax – Matplotlib axes object. (None)

  • return_fig – Return figure object. (None)

  • marker – Marker style. (‘.’)

  • **kwargs – Additional keyword arguments.

Returns:

figure and axis ax: axis

Return type:

fig