tangram.plot_utils.quick_plot_gene

tangram.plot_utils.quick_plot_gene(gene, adata, x='x', y='y', s=50, log=False, cmap='viridis', robust=False, perc=0)

Utility function to quickly plot a gene in a AnnData structure ordered by intensity of the gene signal.

Parameters

• gene (str) – Gene name.

• adata (AnnData) – spot-by-gene spatial data.

• x (str) – Optional. Column name for spots x-coordinates (must be in adata.var). Default is ‘x’.

• y (str) – Optional. Column name for spots y-coordinates (must be in adata.var). Default is ‘y’.

• s (float) – Optional. Marker size. Default is 5.

• log – Optional. Whether to apply the log before plotting. Default is False.

• cmap (str) – Optional. Name of colormap. Default is ‘viridis’.

• robust (bool) – Optional. If True, the colormap range is computed with given percentiles instead of extreme values.

• perc (float) – Optional. percentile used to calculate colormap range, only used when robust is True. Default is zero.

Returns

None